Starting phenix.real_space_refine on Sun Aug 24 20:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l9u_62913/08_2025/9l9u_62913.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l9u_62913/08_2025/9l9u_62913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l9u_62913/08_2025/9l9u_62913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l9u_62913/08_2025/9l9u_62913.map" model { file = "/net/cci-nas-00/data/ceres_data/9l9u_62913/08_2025/9l9u_62913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l9u_62913/08_2025/9l9u_62913.cif" } resolution = 3.12 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 14159 2.51 5 N 3644 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21836 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5459 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 19, 'TRANS': 653} Chain: "B" Number of atoms: 5477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5477 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 655} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5453 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 19, 'TRANS': 652} Chain: "D" Number of atoms: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5447 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 19, 'TRANS': 651} Time building chain proxies: 5.06, per 1000 atoms: 0.23 Number of scatterers: 21836 At special positions: 0 Unit cell: (124.504, 123.716, 184.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3933 8.00 N 3644 7.00 C 14159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 969.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 11 sheets defined 70.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 115 removed outlier: 4.576A pdb=" N VAL A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.236A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.723A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.604A pdb=" N ARG A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 195 through 226 removed outlier: 4.134A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.720A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 312 Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 336 through 352 Processing helix chain 'A' and resid 353 through 356 removed outlier: 3.696A pdb=" N THR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 365 through 384 removed outlier: 4.157A pdb=" N LYS A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Proline residue: A 379 - end of helix removed outlier: 3.605A pdb=" N VAL A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 492 through 510 removed outlier: 3.799A pdb=" N GLU A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 542 removed outlier: 4.556A pdb=" N LEU A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.611A pdb=" N LEU A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 removed outlier: 4.097A pdb=" N LEU A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.601A pdb=" N GLU A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.981A pdb=" N PHE A 631 " --> pdb=" O ASP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 706 through 722 Processing helix chain 'B' and resid 62 through 89 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 115 removed outlier: 3.682A pdb=" N ASP B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 removed outlier: 4.037A pdb=" N PHE B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.514A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.507A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 226 removed outlier: 4.002A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 removed outlier: 4.841A pdb=" N GLY B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 313 Processing helix chain 'B' and resid 315 through 334 removed outlier: 4.226A pdb=" N PHE B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 365 through 383 removed outlier: 4.457A pdb=" N LEU B 378 " --> pdb=" O GLN B 374 " (cutoff:3.500A) Proline residue: B 379 - end of helix Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 455 through 462 Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 492 through 510 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 516 through 542 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 566 through 575 removed outlier: 4.034A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 640 through 651 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 673 through 684 Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 706 through 724 removed outlier: 3.855A pdb=" N SER B 722 " --> pdb=" O ASN B 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 89 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 117 removed outlier: 3.700A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.753A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 removed outlier: 3.527A pdb=" N ARG C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 195 through 226 removed outlier: 4.048A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 removed outlier: 4.735A pdb=" N GLY C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.595A pdb=" N ILE C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 Processing helix chain 'C' and resid 281 through 312 removed outlier: 3.647A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 334 Processing helix chain 'C' and resid 336 through 353 Processing helix chain 'C' and resid 356 through 364 removed outlier: 3.706A pdb=" N ASP C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 Processing helix chain 'C' and resid 376 through 384 removed outlier: 4.784A pdb=" N TYR C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 455 through 462 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 492 through 508 Processing helix chain 'C' and resid 510 through 542 removed outlier: 3.877A pdb=" N LEU C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY C 525 " --> pdb=" O VAL C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.926A pdb=" N ARG C 552 " --> pdb=" O LYS C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.989A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 587 Processing helix chain 'C' and resid 599 through 608 removed outlier: 3.980A pdb=" N GLU C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 619 Processing helix chain 'C' and resid 627 through 639 Processing helix chain 'C' and resid 640 through 650 Processing helix chain 'C' and resid 663 through 671 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 696 through 705 Processing helix chain 'C' and resid 706 through 721 Processing helix chain 'D' and resid 62 through 90 Proline residue: D 84 - end of helix removed outlier: 3.820A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 115 removed outlier: 3.742A pdb=" N GLN D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.075A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 164 through 169' Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 195 through 225 Processing helix chain 'D' and resid 230 through 234 Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 312 Processing helix chain 'D' and resid 314 through 333 Processing helix chain 'D' and resid 336 through 353 Processing helix chain 'D' and resid 355 through 362 removed outlier: 4.031A pdb=" N VAL D 359 " --> pdb=" O TYR D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 382 removed outlier: 4.151A pdb=" N LEU D 378 " --> pdb=" O GLN D 374 " (cutoff:3.500A) Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 383 through 388 removed outlier: 6.305A pdb=" N LEU D 386 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 401 Processing helix chain 'D' and resid 455 through 462 removed outlier: 3.536A pdb=" N ILE D 459 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 493 through 506 Processing helix chain 'D' and resid 511 through 542 Processing helix chain 'D' and resid 543 through 552 Processing helix chain 'D' and resid 566 through 575 Processing helix chain 'D' and resid 576 through 587 Processing helix chain 'D' and resid 599 through 607 removed outlier: 3.641A pdb=" N ALA D 607 " --> pdb=" O GLU D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 619 Processing helix chain 'D' and resid 627 through 639 Processing helix chain 'D' and resid 640 through 650 Processing helix chain 'D' and resid 663 through 671 Processing helix chain 'D' and resid 673 through 684 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 720 Processing sheet with id=AA1, first strand: chain 'A' and resid 402 through 407 Processing sheet with id=AA2, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.829A pdb=" N TYR B 120 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.731A pdb=" N PHE B 407 " --> pdb=" O CYS B 475 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS B 475 " --> pdb=" O PHE B 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 442 through 444 Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.336A pdb=" N HIS C 476 " --> pdb=" O CYS C 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.665A pdb=" N VAL C 469 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 433 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR C 446 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.526A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 403 through 407 removed outlier: 3.689A pdb=" N LEU D 478 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 452 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 447 through 448 1350 hydrogen bonds defined for protein. 3882 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: 4.11 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5703 1.33 - 1.46: 4504 1.46 - 1.58: 11982 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 22345 Sorted by residual: bond pdb=" N ASP C 561 " pdb=" CA ASP C 561 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.09e-02 8.42e+03 1.01e+01 bond pdb=" N ASP B 561 " pdb=" CA ASP B 561 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" N PHE D 407 " pdb=" CA PHE D 407 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.46e+00 bond pdb=" N ASP B 594 " pdb=" CA ASP B 594 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.22e-02 6.72e+03 9.40e+00 bond pdb=" N ILE B 266 " pdb=" CA ILE B 266 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.30e+00 ... (remaining 22340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 29650 2.70 - 5.41: 503 5.41 - 8.11: 52 8.11 - 10.82: 17 10.82 - 13.52: 1 Bond angle restraints: 30223 Sorted by residual: angle pdb=" N PHE C 596 " pdb=" CA PHE C 596 " pdb=" C PHE C 596 " ideal model delta sigma weight residual 113.02 107.20 5.82 1.20e+00 6.94e-01 2.35e+01 angle pdb=" CA GLN C 527 " pdb=" CB GLN C 527 " pdb=" CG GLN C 527 " ideal model delta sigma weight residual 114.10 123.64 -9.54 2.00e+00 2.50e-01 2.27e+01 angle pdb=" N THR B 358 " pdb=" CA THR B 358 " pdb=" C THR B 358 " ideal model delta sigma weight residual 113.50 107.91 5.59 1.23e+00 6.61e-01 2.07e+01 angle pdb=" N GLN A 527 " pdb=" CA GLN A 527 " pdb=" C GLN A 527 " ideal model delta sigma weight residual 111.28 106.44 4.84 1.09e+00 8.42e-01 1.97e+01 angle pdb=" N LYS D 312 " pdb=" CA LYS D 312 " pdb=" C LYS D 312 " ideal model delta sigma weight residual 112.87 107.71 5.16 1.20e+00 6.94e-01 1.85e+01 ... (remaining 30218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 11471 17.83 - 35.67: 1323 35.67 - 53.50: 342 53.50 - 71.33: 88 71.33 - 89.17: 13 Dihedral angle restraints: 13237 sinusoidal: 5369 harmonic: 7868 Sorted by residual: dihedral pdb=" CA PHE D 467 " pdb=" C PHE D 467 " pdb=" N THR D 468 " pdb=" CA THR D 468 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA CYS D 390 " pdb=" C CYS D 390 " pdb=" N SER D 391 " pdb=" CA SER D 391 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE D 454 " pdb=" C PHE D 454 " pdb=" N GLY D 455 " pdb=" CA GLY D 455 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 13234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3094 0.093 - 0.185: 245 0.185 - 0.278: 17 0.278 - 0.371: 3 0.371 - 0.463: 1 Chirality restraints: 3360 Sorted by residual: chirality pdb=" CB ILE D 520 " pdb=" CA ILE D 520 " pdb=" CG1 ILE D 520 " pdb=" CG2 ILE D 520 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CB ILE B 499 " pdb=" CA ILE B 499 " pdb=" CG1 ILE B 499 " pdb=" CG2 ILE B 499 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU C 434 " pdb=" CB LEU C 434 " pdb=" CD1 LEU C 434 " pdb=" CD2 LEU C 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 3357 not shown) Planarity restraints: 3813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 631 " -0.021 2.00e-02 2.50e+03 2.60e-02 1.18e+01 pdb=" CG PHE D 631 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE D 631 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 631 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 631 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 631 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 631 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 350 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.48e+00 pdb=" C GLN A 350 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN A 350 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR A 351 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 320 " -0.238 9.50e-02 1.11e+02 1.07e-01 7.04e+00 pdb=" NE ARG A 320 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 320 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 320 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 320 " -0.008 2.00e-02 2.50e+03 ... (remaining 3810 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2064 2.74 - 3.28: 24826 3.28 - 3.82: 40071 3.82 - 4.36: 49455 4.36 - 4.90: 76865 Nonbonded interactions: 193281 Sorted by model distance: nonbonded pdb=" O PHE D 87 " pdb=" NH2 ARG D 168 " model vdw 2.200 3.120 nonbonded pdb=" OG SER B 458 " pdb=" O ILE B 463 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR B 659 " pdb=" OD1 ASN C 630 " model vdw 2.212 3.040 nonbonded pdb=" NH1 ARG D 348 " pdb=" OD2 ASP D 352 " model vdw 2.221 3.120 nonbonded pdb=" O PHE A 87 " pdb=" NH2 ARG A 168 " model vdw 2.231 3.120 ... (remaining 193276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 50 through 128 or (resid 129 through 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 720)) selection = (chain 'B' and resid 50 through 720) selection = (chain 'C' and (resid 50 through 128 or (resid 129 through 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 720)) selection = (chain 'D' and (resid 50 through 128 or (resid 129 through 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 720)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.850 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.005 0.059 22345 Z= 0.309 Angle : 0.859 13.522 30223 Z= 0.508 Chirality : 0.053 0.463 3360 Planarity : 0.006 0.107 3813 Dihedral : 16.563 89.166 8189 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.74 % Allowed : 23.93 % Favored : 73.34 % 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 aren not related in a simple way. whole: -0.34 (0.16), residues: 2684 helix: 0.19 (0.12), residues: 1709 sheet: -2.12 (0.46), residues: 104 loop : -0.56 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 646 TYR 0.035 0.002 TYR C 126 PHE 0.060 0.002 PHE D 631 TRP 0.018 0.002 TRP A 68 HIS 0.013 0.002 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00504 (22345) covalent geometry : angle 0.85854 (30223) hydrogen bonds : bond 0.14172 ( 1350) hydrogen bonds : angle 6.81246 ( 3882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 571 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3193 (OUTLIER) cc_final: 0.1862 (p90) REVERT: A 97 LEU cc_start: 0.8086 (mt) cc_final: 0.7856 (mp) REVERT: A 166 LEU cc_start: 0.8756 (mt) cc_final: 0.8071 (tp) REVERT: A 301 TYR cc_start: 0.8494 (t80) cc_final: 0.8079 (t80) REVERT: A 312 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7619 (mtpt) REVERT: A 325 ASP cc_start: 0.8841 (t0) cc_final: 0.8419 (p0) REVERT: A 337 ARG cc_start: 0.7754 (mmp-170) cc_final: 0.7453 (tpp-160) REVERT: A 338 ASP cc_start: 0.8815 (t70) cc_final: 0.8597 (p0) REVERT: A 369 ARG cc_start: 0.8290 (ttt-90) cc_final: 0.7559 (mtp180) REVERT: A 380 TYR cc_start: 0.7705 (m-80) cc_final: 0.7432 (m-80) REVERT: A 383 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7132 (ptpp) REVERT: A 540 PHE cc_start: 0.8443 (t80) cc_final: 0.8080 (t80) REVERT: A 570 LEU cc_start: 0.8070 (mt) cc_final: 0.7640 (mm) REVERT: A 592 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8136 (tt) REVERT: A 606 LYS cc_start: 0.9037 (tppt) cc_final: 0.8817 (tttm) REVERT: A 676 MET cc_start: 0.8002 (mpp) cc_final: 0.7753 (mtm) REVERT: B 64 TRP cc_start: 0.7920 (m100) cc_final: 0.7714 (m-90) REVERT: B 70 MET cc_start: 0.7225 (ttt) cc_final: 0.6799 (mmp) REVERT: B 156 LEU cc_start: 0.8428 (tp) cc_final: 0.8197 (mp) REVERT: B 193 ARG cc_start: 0.6320 (mtp180) cc_final: 0.5937 (mmm-85) REVERT: B 326 LEU cc_start: 0.8607 (tp) cc_final: 0.8326 (tp) REVERT: B 376 LEU cc_start: 0.8069 (mm) cc_final: 0.7639 (mt) REVERT: B 401 ARG cc_start: 0.6085 (mtt90) cc_final: 0.5647 (tpt90) REVERT: B 428 GLU cc_start: 0.6570 (tt0) cc_final: 0.5807 (pt0) REVERT: B 467 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: B 504 MET cc_start: 0.8465 (ptp) cc_final: 0.8097 (ptp) REVERT: B 559 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7824 (mtpt) REVERT: B 563 ASP cc_start: 0.6676 (m-30) cc_final: 0.5145 (m-30) REVERT: B 625 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6258 (tp) REVERT: C 66 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7829 (tttt) REVERT: C 147 ASP cc_start: 0.8141 (m-30) cc_final: 0.7438 (m-30) REVERT: C 250 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.6925 (mtm-85) REVERT: C 319 PHE cc_start: 0.7587 (t80) cc_final: 0.7343 (t80) REVERT: C 327 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8302 (mp) REVERT: C 363 ASP cc_start: 0.8706 (m-30) cc_final: 0.8435 (m-30) REVERT: C 365 PRO cc_start: 0.8210 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: C 396 ASN cc_start: 0.8642 (t0) cc_final: 0.8337 (t0) REVERT: C 398 ILE cc_start: 0.8592 (mm) cc_final: 0.8309 (mm) REVERT: C 401 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.7972 (mmt-90) REVERT: C 402 LEU cc_start: 0.9257 (mt) cc_final: 0.8896 (mt) REVERT: C 477 LEU cc_start: 0.8309 (mp) cc_final: 0.7857 (mm) REVERT: C 504 MET cc_start: 0.6384 (mmt) cc_final: 0.5833 (tpp) REVERT: C 568 LEU cc_start: 0.8991 (tp) cc_final: 0.8702 (mt) REVERT: C 615 LEU cc_start: 0.7465 (mt) cc_final: 0.7099 (tt) REVERT: C 662 ARG cc_start: 0.4413 (mmm160) cc_final: 0.4117 (ttt180) REVERT: C 679 MET cc_start: 0.8432 (mpp) cc_final: 0.7304 (ptt) REVERT: D 56 TYR cc_start: 0.4598 (p90) cc_final: 0.3813 (m-80) REVERT: D 64 TRP cc_start: 0.7249 (m100) cc_final: 0.5997 (t60) REVERT: D 120 TYR cc_start: 0.7514 (p90) cc_final: 0.7091 (p90) REVERT: D 321 ASP cc_start: 0.9212 (t70) cc_final: 0.9007 (t0) REVERT: D 334 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8000 (mtmt) REVERT: D 346 HIS cc_start: 0.8114 (t70) cc_final: 0.7342 (t70) REVERT: D 365 PRO cc_start: 0.6532 (Cg_exo) cc_final: 0.6198 (Cg_endo) REVERT: D 394 PHE cc_start: 0.8910 (t80) cc_final: 0.8383 (t80) REVERT: D 397 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8524 (mm110) REVERT: D 426 VAL cc_start: 0.5817 (t) cc_final: 0.5525 (t) REVERT: D 428 GLU cc_start: 0.7159 (pt0) cc_final: 0.6927 (pp20) REVERT: D 454 PHE cc_start: 0.8255 (p90) cc_final: 0.8005 (p90) REVERT: D 479 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7181 (ttp80) REVERT: D 493 PHE cc_start: 0.7482 (m-80) cc_final: 0.6534 (m-80) REVERT: D 504 MET cc_start: 0.5984 (mmm) cc_final: 0.5775 (mmm) REVERT: D 526 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8522 (tppt) REVERT: D 565 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7383 (tpp80) REVERT: D 592 LEU cc_start: 0.8150 (tp) cc_final: 0.7862 (tp) REVERT: D 602 PHE cc_start: 0.8160 (t80) cc_final: 0.7904 (t80) REVERT: D 664 PRO cc_start: 0.7368 (Cg_endo) cc_final: 0.7046 (Cg_exo) outliers start: 65 outliers final: 24 residues processed: 613 average time/residue: 0.1776 time to fit residues: 159.4769 Evaluate side-chains 392 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 659 TYR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 695 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 477 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 422 HIS A 465 GLN A 487 ASN A 598 HIS ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS B 695 ASN B 706 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN C 494 HIS C 661 HIS C 706 ASN D 59 HIS D 278 HIS D 346 HIS D 403 HIS D 527 GLN D 546 GLN D 598 HIS D 695 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.169908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.113013 restraints weight = 41527.101| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.46 r_work: 0.3327 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 22345 Z= 0.348 Angle : 0.789 12.068 30223 Z= 0.412 Chirality : 0.049 0.235 3360 Planarity : 0.006 0.082 3813 Dihedral : 6.759 56.710 3031 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.15 % Allowed : 21.06 % Favored : 72.79 % 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 aren not related in a simple way. whole: -0.07 (0.16), residues: 2684 helix: 0.40 (0.12), residues: 1733 sheet: -2.20 (0.45), residues: 108 loop : -0.41 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 497 TYR 0.026 0.002 TYR B 263 PHE 0.032 0.003 PHE A 287 TRP 0.017 0.002 TRP D 75 HIS 0.011 0.002 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00810 (22345) covalent geometry : angle 0.78905 (30223) hydrogen bonds : bond 0.06447 ( 1350) hydrogen bonds : angle 5.71080 ( 3882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 386 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3476 (OUTLIER) cc_final: 0.2176 (p90) REVERT: A 155 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8445 (t0) REVERT: A 166 LEU cc_start: 0.8800 (mt) cc_final: 0.8045 (tp) REVERT: A 246 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: A 301 TYR cc_start: 0.8646 (t80) cc_final: 0.8298 (t80) REVERT: A 325 ASP cc_start: 0.8745 (t0) cc_final: 0.8375 (p0) REVERT: A 362 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6845 (tp40) REVERT: A 380 TYR cc_start: 0.7897 (m-80) cc_final: 0.7596 (m-80) REVERT: A 383 LYS cc_start: 0.7771 (mmtm) cc_final: 0.7465 (ptpp) REVERT: A 531 LEU cc_start: 0.9248 (mt) cc_final: 0.8875 (tp) REVERT: A 570 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7710 (mm) REVERT: A 592 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8200 (tt) REVERT: B 70 MET cc_start: 0.6956 (ttt) cc_final: 0.6332 (mmt) REVERT: B 121 ARG cc_start: 0.8050 (ttt-90) cc_final: 0.7681 (ttt-90) REVERT: B 126 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: B 131 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7966 (mttt) REVERT: B 193 ARG cc_start: 0.6122 (mtp180) cc_final: 0.5635 (mmm-85) REVERT: B 301 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 312 LYS cc_start: 0.8931 (tmtt) cc_final: 0.8459 (tttp) REVERT: B 330 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8347 (mpp) REVERT: B 376 LEU cc_start: 0.8011 (mm) cc_final: 0.7712 (mt) REVERT: B 467 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6312 (m-80) REVERT: B 478 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7562 (tp) REVERT: B 499 ILE cc_start: 0.8894 (mm) cc_final: 0.8676 (mm) REVERT: B 559 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7839 (mtpt) REVERT: B 565 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7387 (mtp180) REVERT: B 652 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4559 (pmm) REVERT: C 66 LYS cc_start: 0.8362 (mmmt) cc_final: 0.7752 (tttt) REVERT: C 147 ASP cc_start: 0.7957 (m-30) cc_final: 0.7566 (m-30) REVERT: C 174 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8455 (mtt90) REVERT: C 250 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7285 (mtm-85) REVERT: C 320 ARG cc_start: 0.8408 (mmm160) cc_final: 0.7739 (tpt-90) REVERT: C 323 MET cc_start: 0.8421 (mmm) cc_final: 0.8099 (mmm) REVERT: C 327 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8204 (mp) REVERT: C 401 ARG cc_start: 0.8389 (mmt-90) cc_final: 0.7896 (mmt-90) REVERT: C 402 LEU cc_start: 0.9289 (mt) cc_final: 0.8734 (mt) REVERT: C 493 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7864 (p90) REVERT: C 504 MET cc_start: 0.6217 (mmt) cc_final: 0.6000 (ttt) REVERT: C 568 LEU cc_start: 0.8991 (tp) cc_final: 0.8664 (mt) REVERT: C 615 LEU cc_start: 0.7517 (mt) cc_final: 0.7298 (tt) REVERT: C 679 MET cc_start: 0.8441 (mpp) cc_final: 0.7344 (ptt) REVERT: C 695 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7978 (p0) REVERT: C 709 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6233 (mp) REVERT: D 56 TYR cc_start: 0.4680 (p90) cc_final: 0.3875 (m-80) REVERT: D 64 TRP cc_start: 0.7332 (m100) cc_final: 0.6032 (t60) REVERT: D 320 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8390 (mmm-85) REVERT: D 321 ASP cc_start: 0.9216 (t70) cc_final: 0.8959 (t0) REVERT: D 334 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8056 (mtmt) REVERT: D 348 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8302 (tpt90) REVERT: D 412 VAL cc_start: 0.7982 (OUTLIER) cc_final: 0.7654 (m) REVERT: D 426 VAL cc_start: 0.6318 (t) cc_final: 0.5841 (t) REVERT: D 428 GLU cc_start: 0.7505 (pt0) cc_final: 0.7151 (pp20) REVERT: D 452 THR cc_start: 0.5882 (OUTLIER) cc_final: 0.5609 (p) REVERT: D 457 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7147 (tp) REVERT: D 467 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.5550 (p90) REVERT: D 470 ARG cc_start: 0.7938 (tpt170) cc_final: 0.7730 (tpt170) REVERT: D 479 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7501 (ttp80) REVERT: D 504 MET cc_start: 0.6078 (mmm) cc_final: 0.5803 (mmm) REVERT: D 513 ILE cc_start: 0.6940 (mt) cc_final: 0.6208 (mt) REVERT: D 516 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5969 (tt) REVERT: D 526 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8417 (tppt) REVERT: D 540 PHE cc_start: 0.8047 (t80) cc_final: 0.7424 (t80) REVERT: D 565 ARG cc_start: 0.8032 (tpp80) cc_final: 0.7474 (tpp80) REVERT: D 577 GLU cc_start: 0.7525 (mp0) cc_final: 0.7047 (tt0) REVERT: D 652 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7145 (tpt) outliers start: 146 outliers final: 68 residues processed: 498 average time/residue: 0.1710 time to fit residues: 129.5129 Evaluate side-chains 411 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 319 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 659 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 695 ASN Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 510 ASN Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 652 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 232 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN B 487 ASN ** B 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS C 695 ASN D 59 HIS ** D 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 624 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.172257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116379 restraints weight = 41836.433| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.73 r_work: 0.3401 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22345 Z= 0.169 Angle : 0.667 14.942 30223 Z= 0.337 Chirality : 0.044 0.292 3360 Planarity : 0.004 0.055 3813 Dihedral : 6.301 58.195 3018 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.01 % Allowed : 21.65 % Favored : 73.34 % 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 aren not related in a simple way. whole: 0.35 (0.16), residues: 2684 helix: 0.73 (0.12), residues: 1743 sheet: -2.16 (0.43), residues: 108 loop : -0.25 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 497 TYR 0.022 0.002 TYR C 351 PHE 0.042 0.002 PHE C 319 TRP 0.029 0.001 TRP B 693 HIS 0.010 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00369 (22345) covalent geometry : angle 0.66653 (30223) hydrogen bonds : bond 0.05511 ( 1350) hydrogen bonds : angle 5.30532 ( 3882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 356 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3222 (OUTLIER) cc_final: 0.1993 (p90) REVERT: A 116 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.8001 (t80) REVERT: A 143 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7386 (p90) REVERT: A 155 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8308 (t0) REVERT: A 166 LEU cc_start: 0.8689 (mt) cc_final: 0.7894 (tp) REVERT: A 301 TYR cc_start: 0.8529 (t80) cc_final: 0.8175 (t80) REVERT: A 329 PHE cc_start: 0.7937 (t80) cc_final: 0.7611 (t80) REVERT: A 362 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6827 (tp40) REVERT: A 380 TYR cc_start: 0.7838 (m-80) cc_final: 0.7480 (m-80) REVERT: A 383 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7690 (ptpt) REVERT: A 531 LEU cc_start: 0.9255 (mt) cc_final: 0.8956 (tp) REVERT: A 540 PHE cc_start: 0.8534 (t80) cc_final: 0.8222 (t80) REVERT: A 570 LEU cc_start: 0.8164 (mt) cc_final: 0.7860 (mm) REVERT: A 592 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8075 (tt) REVERT: A 606 LYS cc_start: 0.8485 (tttm) cc_final: 0.8131 (pttm) REVERT: B 70 MET cc_start: 0.6766 (ttt) cc_final: 0.6203 (mmt) REVERT: B 72 ILE cc_start: 0.8387 (tp) cc_final: 0.8142 (tp) REVERT: B 121 ARG cc_start: 0.7898 (ttt-90) cc_final: 0.7440 (ttt-90) REVERT: B 126 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: B 131 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7778 (mttt) REVERT: B 156 LEU cc_start: 0.8536 (tp) cc_final: 0.8185 (mp) REVERT: B 193 ARG cc_start: 0.5920 (mtp180) cc_final: 0.5361 (mmm-85) REVERT: B 301 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7487 (t80) REVERT: B 312 LYS cc_start: 0.8896 (tmtt) cc_final: 0.8441 (tttp) REVERT: B 330 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8103 (mpp) REVERT: B 376 LEU cc_start: 0.7865 (mm) cc_final: 0.7636 (mt) REVERT: B 430 LEU cc_start: 0.8892 (mm) cc_final: 0.8564 (tp) REVERT: B 467 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6335 (m-80) REVERT: B 478 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7484 (tp) REVERT: B 559 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7915 (mtpt) REVERT: B 652 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.4815 (pmm) REVERT: C 147 ASP cc_start: 0.7843 (m-30) cc_final: 0.7379 (m-30) REVERT: C 174 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8804 (mtt180) REVERT: C 250 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7087 (mtm-85) REVERT: C 323 MET cc_start: 0.8330 (mmm) cc_final: 0.8122 (mmm) REVERT: C 327 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8313 (mp) REVERT: C 398 ILE cc_start: 0.8560 (mm) cc_final: 0.8188 (pt) REVERT: C 401 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.7939 (mmt-90) REVERT: C 402 LEU cc_start: 0.9289 (mt) cc_final: 0.8842 (mt) REVERT: C 477 LEU cc_start: 0.8616 (mt) cc_final: 0.8359 (mm) REVERT: C 493 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7802 (p90) REVERT: C 504 MET cc_start: 0.6197 (mmt) cc_final: 0.5960 (ttt) REVERT: C 546 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6619 (mt0) REVERT: C 568 LEU cc_start: 0.8986 (tp) cc_final: 0.8678 (mt) REVERT: C 615 LEU cc_start: 0.7524 (mt) cc_final: 0.7284 (tt) REVERT: C 619 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6633 (mm-30) REVERT: C 695 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8146 (p0) REVERT: D 56 TYR cc_start: 0.4648 (p90) cc_final: 0.3844 (m-80) REVERT: D 64 TRP cc_start: 0.7203 (m100) cc_final: 0.5999 (t60) REVERT: D 254 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8303 (tp) REVERT: D 321 ASP cc_start: 0.9189 (t70) cc_final: 0.8945 (t0) REVERT: D 334 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8057 (mtmt) REVERT: D 348 ARG cc_start: 0.8618 (mmm160) cc_final: 0.8053 (tpt90) REVERT: D 412 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7740 (m) REVERT: D 426 VAL cc_start: 0.6147 (t) cc_final: 0.5605 (t) REVERT: D 428 GLU cc_start: 0.7679 (pt0) cc_final: 0.7265 (pp20) REVERT: D 452 THR cc_start: 0.5734 (OUTLIER) cc_final: 0.5496 (p) REVERT: D 479 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7316 (ttp80) REVERT: D 526 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8427 (tppt) REVERT: D 540 PHE cc_start: 0.8091 (t80) cc_final: 0.7448 (t80) REVERT: D 547 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7949 (mt) REVERT: D 577 GLU cc_start: 0.7567 (mp0) cc_final: 0.7259 (tp30) REVERT: D 652 MET cc_start: 0.7609 (tpt) cc_final: 0.7258 (tpt) outliers start: 119 outliers final: 56 residues processed: 444 average time/residue: 0.1524 time to fit residues: 103.7829 Evaluate side-chains 387 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 310 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 553 SER Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 695 ASN Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 217 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 258 optimal weight: 8.9990 chunk 127 optimal weight: 50.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 487 ASN B 62 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 510 ASN C 186 GLN C 324 ASN C 494 HIS D 346 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.168634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106804 restraints weight = 41883.540| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.60 r_work: 0.3344 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 22345 Z= 0.300 Angle : 0.736 14.771 30223 Z= 0.372 Chirality : 0.047 0.284 3360 Planarity : 0.005 0.054 3813 Dihedral : 6.136 59.969 3011 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.40 % Allowed : 21.69 % Favored : 71.90 % 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 aren not related in a simple way. whole: 0.19 (0.16), residues: 2684 helix: 0.58 (0.12), residues: 1761 sheet: -1.90 (0.45), residues: 104 loop : -0.35 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 332 TYR 0.020 0.002 TYR C 258 PHE 0.033 0.003 PHE B 144 TRP 0.016 0.002 TRP D 75 HIS 0.010 0.001 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00697 (22345) covalent geometry : angle 0.73554 (30223) hydrogen bonds : bond 0.05494 ( 1350) hydrogen bonds : angle 5.29726 ( 3882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 335 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3313 (OUTLIER) cc_final: 0.2105 (p90) REVERT: A 70 MET cc_start: 0.7328 (tpt) cc_final: 0.6473 (tmm) REVERT: A 143 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7530 (p90) REVERT: A 155 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8412 (t0) REVERT: A 166 LEU cc_start: 0.8750 (mt) cc_final: 0.7930 (tp) REVERT: A 301 TYR cc_start: 0.8577 (t80) cc_final: 0.8233 (t80) REVERT: A 362 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6889 (tp40) REVERT: A 380 TYR cc_start: 0.8001 (m-80) cc_final: 0.7547 (m-80) REVERT: A 383 LYS cc_start: 0.7945 (mmtm) cc_final: 0.7646 (ptpp) REVERT: A 516 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8804 (tt) REVERT: A 531 LEU cc_start: 0.9292 (mt) cc_final: 0.8962 (tp) REVERT: A 540 PHE cc_start: 0.8574 (t80) cc_final: 0.8201 (t80) REVERT: A 570 LEU cc_start: 0.8233 (mt) cc_final: 0.7931 (mt) REVERT: A 606 LYS cc_start: 0.8514 (tttm) cc_final: 0.8096 (mtpt) REVERT: A 676 MET cc_start: 0.7106 (mpp) cc_final: 0.6660 (mmt) REVERT: B 70 MET cc_start: 0.6996 (ttt) cc_final: 0.6400 (mmp) REVERT: B 72 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8348 (tp) REVERT: B 193 ARG cc_start: 0.5877 (mtp180) cc_final: 0.5310 (mmm-85) REVERT: B 301 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 312 LYS cc_start: 0.8876 (tmtt) cc_final: 0.8477 (tttp) REVERT: B 319 PHE cc_start: 0.8845 (t80) cc_final: 0.8634 (t80) REVERT: B 376 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 430 LEU cc_start: 0.8846 (mm) cc_final: 0.8385 (tp) REVERT: B 467 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: B 478 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7464 (tp) REVERT: B 520 ILE cc_start: 0.8238 (tt) cc_final: 0.8019 (pt) REVERT: B 559 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7999 (mtpt) REVERT: C 147 ASP cc_start: 0.7750 (m-30) cc_final: 0.7345 (m-30) REVERT: C 174 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8395 (mtt90) REVERT: C 191 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: C 250 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7326 (mtm-85) REVERT: C 323 MET cc_start: 0.8322 (mmm) cc_final: 0.8112 (mmm) REVERT: C 401 ARG cc_start: 0.8454 (mmt-90) cc_final: 0.8025 (mmt-90) REVERT: C 402 LEU cc_start: 0.9319 (mt) cc_final: 0.9106 (mt) REVERT: C 477 LEU cc_start: 0.8540 (mt) cc_final: 0.8268 (mm) REVERT: C 493 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7796 (p90) REVERT: C 504 MET cc_start: 0.6234 (mmt) cc_final: 0.5941 (ttt) REVERT: C 546 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6733 (mt0) REVERT: C 568 LEU cc_start: 0.8995 (tp) cc_final: 0.8689 (mt) REVERT: C 615 LEU cc_start: 0.7664 (mt) cc_final: 0.7413 (tt) REVERT: C 695 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8175 (p0) REVERT: D 56 TYR cc_start: 0.4850 (p90) cc_final: 0.4059 (m-80) REVERT: D 64 TRP cc_start: 0.7276 (m100) cc_final: 0.5980 (t60) REVERT: D 120 TYR cc_start: 0.7620 (p90) cc_final: 0.7215 (p90) REVERT: D 256 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8508 (tppt) REVERT: D 321 ASP cc_start: 0.9215 (t70) cc_final: 0.8959 (t0) REVERT: D 348 ARG cc_start: 0.8605 (mmm160) cc_final: 0.8266 (tpp-160) REVERT: D 426 VAL cc_start: 0.6280 (t) cc_final: 0.5762 (t) REVERT: D 428 GLU cc_start: 0.7727 (pt0) cc_final: 0.7324 (pp20) REVERT: D 452 THR cc_start: 0.6048 (OUTLIER) cc_final: 0.5778 (p) REVERT: D 479 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7255 (ttp80) REVERT: D 540 PHE cc_start: 0.8144 (t80) cc_final: 0.7509 (t80) REVERT: D 565 ARG cc_start: 0.8278 (tpp80) cc_final: 0.7783 (tpp80) REVERT: D 652 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7201 (tpt) outliers start: 152 outliers final: 92 residues processed: 447 average time/residue: 0.1628 time to fit residues: 112.2367 Evaluate side-chains 418 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 308 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 695 ASN Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 652 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 95 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 396 ASN B 397 GLN C 278 HIS C 494 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.171337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.112571 restraints weight = 41841.751| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.80 r_work: 0.3391 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22345 Z= 0.181 Angle : 0.645 14.453 30223 Z= 0.324 Chirality : 0.043 0.289 3360 Planarity : 0.004 0.041 3813 Dihedral : 5.919 57.513 3005 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.56 % Allowed : 22.87 % Favored : 71.57 % 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 aren not related in a simple way. whole: 0.49 (0.16), residues: 2684 helix: 0.80 (0.12), residues: 1758 sheet: -1.64 (0.46), residues: 104 loop : -0.22 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 497 TYR 0.022 0.002 TYR C 54 PHE 0.028 0.002 PHE D 582 TRP 0.011 0.001 TRP B 693 HIS 0.006 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00408 (22345) covalent geometry : angle 0.64505 (30223) hydrogen bonds : bond 0.05040 ( 1350) hydrogen bonds : angle 5.08318 ( 3882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 321 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3185 (OUTLIER) cc_final: 0.1933 (p90) REVERT: A 70 MET cc_start: 0.7381 (tpt) cc_final: 0.6557 (tmm) REVERT: A 116 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7821 (t80) REVERT: A 143 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7497 (p90) REVERT: A 155 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8324 (t0) REVERT: A 166 LEU cc_start: 0.8725 (mt) cc_final: 0.7962 (tp) REVERT: A 301 TYR cc_start: 0.8632 (t80) cc_final: 0.8306 (t80) REVERT: A 329 PHE cc_start: 0.8138 (t80) cc_final: 0.7610 (t80) REVERT: A 362 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6919 (tp40) REVERT: A 380 TYR cc_start: 0.7911 (m-80) cc_final: 0.7358 (m-80) REVERT: A 531 LEU cc_start: 0.9278 (mt) cc_final: 0.8955 (tp) REVERT: A 540 PHE cc_start: 0.8619 (t80) cc_final: 0.8270 (t80) REVERT: A 570 LEU cc_start: 0.8277 (mt) cc_final: 0.7953 (mt) REVERT: A 676 MET cc_start: 0.7094 (mpp) cc_final: 0.6678 (mmt) REVERT: B 70 MET cc_start: 0.7005 (ttt) cc_final: 0.6455 (mmp) REVERT: B 72 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8239 (tp) REVERT: B 179 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8439 (ttp80) REVERT: B 193 ARG cc_start: 0.5683 (mtp180) cc_final: 0.5129 (mmm-85) REVERT: B 204 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 301 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7633 (t80) REVERT: B 312 LYS cc_start: 0.8817 (tmtt) cc_final: 0.8435 (tttp) REVERT: B 330 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8357 (mpp) REVERT: B 428 GLU cc_start: 0.6535 (tt0) cc_final: 0.5890 (pt0) REVERT: B 430 LEU cc_start: 0.8812 (mm) cc_final: 0.8355 (tp) REVERT: B 467 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: B 478 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7579 (tp) REVERT: B 559 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7968 (mtmt) REVERT: B 652 MET cc_start: 0.4902 (OUTLIER) cc_final: 0.4663 (pmm) REVERT: C 100 LEU cc_start: 0.7840 (tp) cc_final: 0.7556 (tt) REVERT: C 147 ASP cc_start: 0.7745 (m-30) cc_final: 0.7419 (m-30) REVERT: C 250 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7308 (mtm-85) REVERT: C 477 LEU cc_start: 0.8560 (mt) cc_final: 0.8351 (mm) REVERT: C 492 TYR cc_start: 0.7684 (m-80) cc_final: 0.7116 (m-80) REVERT: C 504 MET cc_start: 0.6176 (mmt) cc_final: 0.5961 (ttt) REVERT: C 546 GLN cc_start: 0.7243 (tp-100) cc_final: 0.6803 (mt0) REVERT: C 568 LEU cc_start: 0.8986 (tp) cc_final: 0.8672 (mt) REVERT: C 615 LEU cc_start: 0.7763 (mt) cc_final: 0.7505 (tt) REVERT: C 679 MET cc_start: 0.8296 (mmm) cc_final: 0.7212 (ptt) REVERT: C 695 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8067 (p0) REVERT: D 56 TYR cc_start: 0.5010 (p90) cc_final: 0.4190 (m-80) REVERT: D 168 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8857 (mtm180) REVERT: D 254 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8252 (tp) REVERT: D 321 ASP cc_start: 0.9178 (t70) cc_final: 0.8922 (t0) REVERT: D 348 ARG cc_start: 0.8621 (mmm160) cc_final: 0.8224 (tpt90) REVERT: D 412 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7599 (m) REVERT: D 426 VAL cc_start: 0.6417 (t) cc_final: 0.5912 (t) REVERT: D 428 GLU cc_start: 0.7841 (pt0) cc_final: 0.7471 (pp20) REVERT: D 452 THR cc_start: 0.6102 (OUTLIER) cc_final: 0.5834 (p) REVERT: D 457 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7149 (tp) REVERT: D 467 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.5633 (p90) REVERT: D 479 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7684 (ttp80) REVERT: D 526 LYS cc_start: 0.8490 (tppt) cc_final: 0.8285 (ptmt) REVERT: D 540 PHE cc_start: 0.8164 (t80) cc_final: 0.7561 (t80) REVERT: D 652 MET cc_start: 0.7597 (tpt) cc_final: 0.7230 (tpt) outliers start: 132 outliers final: 74 residues processed: 420 average time/residue: 0.1525 time to fit residues: 99.9242 Evaluate side-chains 391 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 296 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 472 CYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 695 ASN Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 107 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 251 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 237 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN D 523 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.171992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115738 restraints weight = 41672.013| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.33 r_work: 0.3403 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22345 Z= 0.157 Angle : 0.646 17.310 30223 Z= 0.319 Chirality : 0.042 0.285 3360 Planarity : 0.004 0.043 3813 Dihedral : 5.829 56.549 3005 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.05 % Allowed : 23.63 % Favored : 71.31 % 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 aren not related in a simple way. whole: 0.63 (0.16), residues: 2684 helix: 0.92 (0.12), residues: 1762 sheet: -1.54 (0.47), residues: 104 loop : -0.21 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 497 TYR 0.022 0.001 TYR C 54 PHE 0.049 0.002 PHE C 493 TRP 0.010 0.001 TRP B 693 HIS 0.006 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00349 (22345) covalent geometry : angle 0.64605 (30223) hydrogen bonds : bond 0.04843 ( 1350) hydrogen bonds : angle 4.94523 ( 3882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 331 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3080 (OUTLIER) cc_final: 0.1949 (p90) REVERT: A 70 MET cc_start: 0.7232 (tpt) cc_final: 0.6411 (tmm) REVERT: A 116 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7827 (t80) REVERT: A 143 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.7499 (p90) REVERT: A 155 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8342 (t0) REVERT: A 166 LEU cc_start: 0.8683 (mt) cc_final: 0.7867 (tp) REVERT: A 301 TYR cc_start: 0.8563 (t80) cc_final: 0.8207 (t80) REVERT: A 329 PHE cc_start: 0.8074 (t80) cc_final: 0.7509 (t80) REVERT: A 361 LEU cc_start: 0.7793 (mt) cc_final: 0.7562 (mt) REVERT: A 362 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6991 (tp40) REVERT: A 415 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6694 (tt0) REVERT: A 443 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6185 (pm20) REVERT: A 456 ASP cc_start: 0.7588 (p0) cc_final: 0.7080 (t70) REVERT: A 516 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8796 (tt) REVERT: A 531 LEU cc_start: 0.9273 (mt) cc_final: 0.8958 (tp) REVERT: A 540 PHE cc_start: 0.8665 (t80) cc_final: 0.8331 (t80) REVERT: A 570 LEU cc_start: 0.8305 (mt) cc_final: 0.8008 (mt) REVERT: A 592 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8414 (pt) REVERT: A 676 MET cc_start: 0.7121 (mpp) cc_final: 0.6534 (mmt) REVERT: B 63 ARG cc_start: 0.7297 (ttt90) cc_final: 0.6747 (tmt170) REVERT: B 70 MET cc_start: 0.6874 (ttt) cc_final: 0.6281 (mmp) REVERT: B 72 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8150 (tp) REVERT: B 179 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8376 (ttp80) REVERT: B 193 ARG cc_start: 0.5666 (mtp180) cc_final: 0.5098 (mmm-85) REVERT: B 204 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8110 (mm) REVERT: B 301 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 312 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8424 (tttp) REVERT: B 330 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8194 (mpp) REVERT: B 428 GLU cc_start: 0.6463 (tt0) cc_final: 0.5944 (pt0) REVERT: B 430 LEU cc_start: 0.8804 (mm) cc_final: 0.8334 (tp) REVERT: B 467 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6431 (m-80) REVERT: B 478 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7503 (tp) REVERT: B 652 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.4543 (pmm) REVERT: C 100 LEU cc_start: 0.7848 (tp) cc_final: 0.7603 (tt) REVERT: C 147 ASP cc_start: 0.7652 (m-30) cc_final: 0.7296 (m-30) REVERT: C 174 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8849 (mtt180) REVERT: C 492 TYR cc_start: 0.7528 (m-80) cc_final: 0.7025 (m-80) REVERT: C 504 MET cc_start: 0.6278 (mmt) cc_final: 0.6000 (ttt) REVERT: C 546 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6750 (mt0) REVERT: C 568 LEU cc_start: 0.8987 (tp) cc_final: 0.8667 (mt) REVERT: C 615 LEU cc_start: 0.7832 (mt) cc_final: 0.7566 (tt) REVERT: D 56 TYR cc_start: 0.4893 (p90) cc_final: 0.4121 (m-80) REVERT: D 141 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6731 (tttt) REVERT: D 168 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8889 (mtm180) REVERT: D 289 MET cc_start: 0.9254 (mtm) cc_final: 0.9025 (mtp) REVERT: D 321 ASP cc_start: 0.9249 (t70) cc_final: 0.9014 (t0) REVERT: D 323 MET cc_start: 0.8760 (mtm) cc_final: 0.8497 (mtm) REVERT: D 348 ARG cc_start: 0.8596 (mmm160) cc_final: 0.8218 (tpt90) REVERT: D 412 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7532 (m) REVERT: D 426 VAL cc_start: 0.6139 (t) cc_final: 0.5552 (t) REVERT: D 428 GLU cc_start: 0.7861 (pt0) cc_final: 0.7468 (pp20) REVERT: D 452 THR cc_start: 0.5990 (OUTLIER) cc_final: 0.5725 (p) REVERT: D 457 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7132 (tp) REVERT: D 467 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5698 (p90) REVERT: D 522 ILE cc_start: 0.8223 (mm) cc_final: 0.7964 (mt) REVERT: D 540 PHE cc_start: 0.8160 (t80) cc_final: 0.7571 (t80) REVERT: D 652 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7242 (tpt) outliers start: 120 outliers final: 78 residues processed: 419 average time/residue: 0.1611 time to fit residues: 104.8802 Evaluate side-chains 402 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 300 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 168 ARG Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 523 HIS Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 652 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 103 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN C 374 GLN C 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.168776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.109023 restraints weight = 41777.730| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.98 r_work: 0.3342 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 22345 Z= 0.310 Angle : 0.724 15.509 30223 Z= 0.366 Chirality : 0.046 0.269 3360 Planarity : 0.005 0.041 3813 Dihedral : 5.773 56.883 2999 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.98 % Allowed : 22.91 % Favored : 71.10 % 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 aren not related in a simple way. whole: 0.42 (0.16), residues: 2684 helix: 0.75 (0.12), residues: 1763 sheet: -1.68 (0.48), residues: 109 loop : -0.24 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 348 TYR 0.024 0.002 TYR C 54 PHE 0.039 0.003 PHE C 493 TRP 0.017 0.002 TRP D 75 HIS 0.041 0.002 HIS D 523 Details of bonding type rmsd covalent geometry : bond 0.00721 (22345) covalent geometry : angle 0.72367 (30223) hydrogen bonds : bond 0.05131 ( 1350) hydrogen bonds : angle 5.08427 ( 3882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 314 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3147 (OUTLIER) cc_final: 0.1983 (p90) REVERT: A 70 MET cc_start: 0.7441 (tpt) cc_final: 0.6584 (tmm) REVERT: A 116 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.8103 (t80) REVERT: A 143 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7666 (p90) REVERT: A 155 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8435 (t0) REVERT: A 166 LEU cc_start: 0.8782 (mt) cc_final: 0.7966 (tp) REVERT: A 301 TYR cc_start: 0.8645 (t80) cc_final: 0.8311 (t80) REVERT: A 329 PHE cc_start: 0.8172 (t80) cc_final: 0.7631 (t80) REVERT: A 362 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6997 (tp40) REVERT: A 456 ASP cc_start: 0.7721 (p0) cc_final: 0.7215 (t70) REVERT: A 516 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8798 (tt) REVERT: A 531 LEU cc_start: 0.9280 (mt) cc_final: 0.9076 (mt) REVERT: A 540 PHE cc_start: 0.8646 (t80) cc_final: 0.8314 (t80) REVERT: A 570 LEU cc_start: 0.8381 (mt) cc_final: 0.8075 (mt) REVERT: A 592 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8307 (pt) REVERT: A 606 LYS cc_start: 0.8502 (tttm) cc_final: 0.8095 (mtpt) REVERT: A 676 MET cc_start: 0.7155 (mpp) cc_final: 0.6574 (mmt) REVERT: B 65 TYR cc_start: 0.8528 (t80) cc_final: 0.8109 (t80) REVERT: B 70 MET cc_start: 0.7120 (ttt) cc_final: 0.6514 (mmt) REVERT: B 72 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (tp) REVERT: B 96 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7373 (ttp-170) REVERT: B 193 ARG cc_start: 0.5580 (mtp180) cc_final: 0.4956 (mmm-85) REVERT: B 204 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8213 (mm) REVERT: B 301 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7762 (t80) REVERT: B 312 LYS cc_start: 0.8828 (tmtt) cc_final: 0.8479 (tttp) REVERT: B 330 MET cc_start: 0.8744 (mpp) cc_final: 0.8233 (mpp) REVERT: B 428 GLU cc_start: 0.6533 (tt0) cc_final: 0.6077 (pt0) REVERT: B 467 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: B 478 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7601 (tp) REVERT: B 513 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7520 (tt) REVERT: C 101 ASP cc_start: 0.7344 (t70) cc_final: 0.6912 (t0) REVERT: C 147 ASP cc_start: 0.7699 (m-30) cc_final: 0.7389 (m-30) REVERT: C 174 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8399 (mtt90) REVERT: C 191 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: C 401 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.7966 (mmt-90) REVERT: C 431 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8157 (mt) REVERT: C 451 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6710 (m-70) REVERT: C 504 MET cc_start: 0.6270 (mmt) cc_final: 0.5969 (ttt) REVERT: C 546 GLN cc_start: 0.7330 (tp-100) cc_final: 0.6886 (mt0) REVERT: C 568 LEU cc_start: 0.9002 (tp) cc_final: 0.8637 (mt) REVERT: C 615 LEU cc_start: 0.7786 (mt) cc_final: 0.7522 (tt) REVERT: C 679 MET cc_start: 0.7974 (mpp) cc_final: 0.6583 (ptt) REVERT: D 56 TYR cc_start: 0.4922 (p90) cc_final: 0.4196 (m-80) REVERT: D 141 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6716 (tttt) REVERT: D 256 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8557 (ttmm) REVERT: D 319 PHE cc_start: 0.8343 (t80) cc_final: 0.7964 (t80) REVERT: D 321 ASP cc_start: 0.9268 (t70) cc_final: 0.9050 (t0) REVERT: D 323 MET cc_start: 0.8839 (mtm) cc_final: 0.8385 (mtm) REVERT: D 348 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8316 (tpp-160) REVERT: D 412 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7626 (m) REVERT: D 426 VAL cc_start: 0.6491 (t) cc_final: 0.6009 (t) REVERT: D 428 GLU cc_start: 0.7936 (pt0) cc_final: 0.7539 (pp20) REVERT: D 452 THR cc_start: 0.6072 (OUTLIER) cc_final: 0.5742 (p) REVERT: D 457 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7165 (tp) REVERT: D 467 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.5861 (p90) REVERT: D 540 PHE cc_start: 0.8180 (t80) cc_final: 0.7579 (t80) REVERT: D 652 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7178 (tpt) outliers start: 142 outliers final: 95 residues processed: 423 average time/residue: 0.1634 time to fit residues: 108.4680 Evaluate side-chains 423 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 303 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 695 ASN Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 652 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 225 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 260 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 161 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.169911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.110251 restraints weight = 41641.652| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.81 r_work: 0.3381 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22345 Z= 0.226 Angle : 0.690 15.142 30223 Z= 0.344 Chirality : 0.045 0.275 3360 Planarity : 0.004 0.045 3813 Dihedral : 5.723 59.583 2995 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.48 % Allowed : 23.55 % Favored : 70.98 % 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 aren not related in a simple way. whole: 0.43 (0.16), residues: 2684 helix: 0.78 (0.12), residues: 1763 sheet: -1.62 (0.48), residues: 111 loop : -0.30 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 348 TYR 0.022 0.002 TYR C 54 PHE 0.036 0.002 PHE C 493 TRP 0.013 0.001 TRP D 75 HIS 0.007 0.001 HIS C 494 Details of bonding type rmsd covalent geometry : bond 0.00521 (22345) covalent geometry : angle 0.68986 (30223) hydrogen bonds : bond 0.04941 ( 1350) hydrogen bonds : angle 5.00769 ( 3882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 317 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3157 (OUTLIER) cc_final: 0.1989 (p90) REVERT: A 70 MET cc_start: 0.7406 (tpt) cc_final: 0.6555 (tmm) REVERT: A 116 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 155 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8353 (t0) REVERT: A 166 LEU cc_start: 0.8726 (mt) cc_final: 0.7953 (tp) REVERT: A 246 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: A 301 TYR cc_start: 0.8658 (t80) cc_final: 0.8328 (t80) REVERT: A 329 PHE cc_start: 0.8206 (t80) cc_final: 0.7671 (t80) REVERT: A 362 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7043 (tp40) REVERT: A 415 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6927 (tt0) REVERT: A 456 ASP cc_start: 0.7631 (p0) cc_final: 0.7227 (t70) REVERT: A 516 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8792 (tt) REVERT: A 531 LEU cc_start: 0.9275 (mt) cc_final: 0.9069 (mt) REVERT: A 540 PHE cc_start: 0.8662 (t80) cc_final: 0.8353 (t80) REVERT: A 570 LEU cc_start: 0.8380 (mt) cc_final: 0.8090 (mt) REVERT: A 606 LYS cc_start: 0.8492 (tttm) cc_final: 0.8091 (mtpt) REVERT: A 676 MET cc_start: 0.7197 (mpp) cc_final: 0.6877 (mmt) REVERT: B 63 ARG cc_start: 0.7438 (ttt90) cc_final: 0.6895 (tmt170) REVERT: B 65 TYR cc_start: 0.8551 (t80) cc_final: 0.8087 (t80) REVERT: B 70 MET cc_start: 0.7125 (ttt) cc_final: 0.6544 (mmt) REVERT: B 72 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8298 (tp) REVERT: B 96 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7360 (ttp-170) REVERT: B 168 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8323 (ttp80) REVERT: B 183 GLU cc_start: 0.8000 (tp30) cc_final: 0.7699 (tp30) REVERT: B 193 ARG cc_start: 0.5569 (mtp180) cc_final: 0.4939 (mmm-85) REVERT: B 204 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8205 (mm) REVERT: B 301 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7681 (t80) REVERT: B 312 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8437 (tttp) REVERT: B 330 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8201 (mpp) REVERT: B 428 GLU cc_start: 0.6516 (tt0) cc_final: 0.6037 (pt0) REVERT: B 467 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: B 478 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7551 (tp) REVERT: B 513 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7489 (tt) REVERT: C 101 ASP cc_start: 0.7264 (t70) cc_final: 0.6982 (t0) REVERT: C 147 ASP cc_start: 0.7650 (m-30) cc_final: 0.7367 (m-30) REVERT: C 174 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8756 (mtt180) REVERT: C 191 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: C 401 ARG cc_start: 0.8404 (mmt-90) cc_final: 0.8076 (mmt-90) REVERT: C 504 MET cc_start: 0.6270 (mmt) cc_final: 0.5972 (ttt) REVERT: C 546 GLN cc_start: 0.7351 (tp-100) cc_final: 0.6884 (mt0) REVERT: C 568 LEU cc_start: 0.9002 (tp) cc_final: 0.8643 (mt) REVERT: C 679 MET cc_start: 0.8084 (mpp) cc_final: 0.6690 (ptt) REVERT: D 56 TYR cc_start: 0.5016 (p90) cc_final: 0.4311 (m-80) REVERT: D 141 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6720 (tttt) REVERT: D 254 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8303 (tp) REVERT: D 256 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8564 (ttmm) REVERT: D 319 PHE cc_start: 0.8389 (t80) cc_final: 0.8180 (t80) REVERT: D 321 ASP cc_start: 0.9233 (t70) cc_final: 0.8984 (t0) REVERT: D 348 ARG cc_start: 0.8594 (mmm160) cc_final: 0.8226 (tpt90) REVERT: D 412 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7677 (m) REVERT: D 426 VAL cc_start: 0.6435 (t) cc_final: 0.5934 (t) REVERT: D 428 GLU cc_start: 0.7979 (pt0) cc_final: 0.7588 (pp20) REVERT: D 452 THR cc_start: 0.6072 (OUTLIER) cc_final: 0.5727 (p) REVERT: D 457 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7230 (tp) REVERT: D 467 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.5820 (p90) REVERT: D 540 PHE cc_start: 0.8170 (t80) cc_final: 0.7576 (t80) REVERT: D 652 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7219 (tpt) outliers start: 130 outliers final: 92 residues processed: 414 average time/residue: 0.1636 time to fit residues: 105.0905 Evaluate side-chains 424 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 307 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 652 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 167 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 164 optimal weight: 0.0470 chunk 209 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 211 optimal weight: 0.5980 chunk 229 optimal weight: 6.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.171113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114005 restraints weight = 41442.614| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.90 r_work: 0.3398 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22345 Z= 0.171 Angle : 0.679 14.999 30223 Z= 0.335 Chirality : 0.043 0.266 3360 Planarity : 0.004 0.040 3813 Dihedral : 5.600 58.056 2993 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.01 % Allowed : 24.14 % Favored : 70.85 % 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 aren not related in a simple way. whole: 0.58 (0.16), residues: 2684 helix: 0.90 (0.12), residues: 1750 sheet: -1.74 (0.46), residues: 115 loop : -0.20 (0.24), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 565 TYR 0.020 0.002 TYR C 54 PHE 0.037 0.002 PHE C 493 TRP 0.010 0.001 TRP A 172 HIS 0.015 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00386 (22345) covalent geometry : angle 0.67895 (30223) hydrogen bonds : bond 0.04801 ( 1350) hydrogen bonds : angle 4.92199 ( 3882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 316 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.3097 (OUTLIER) cc_final: 0.1930 (p90) REVERT: A 70 MET cc_start: 0.7388 (tpt) cc_final: 0.6568 (tmm) REVERT: A 116 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 155 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8365 (t0) REVERT: A 166 LEU cc_start: 0.8709 (mt) cc_final: 0.7939 (tp) REVERT: A 246 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 301 TYR cc_start: 0.8676 (t80) cc_final: 0.8332 (t80) REVERT: A 362 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7034 (tp40) REVERT: A 415 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6930 (tt0) REVERT: A 443 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.5977 (pm20) REVERT: A 456 ASP cc_start: 0.7682 (p0) cc_final: 0.7204 (t70) REVERT: A 516 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8798 (tt) REVERT: A 531 LEU cc_start: 0.9266 (mt) cc_final: 0.8953 (tp) REVERT: A 540 PHE cc_start: 0.8560 (t80) cc_final: 0.8285 (t80) REVERT: A 570 LEU cc_start: 0.8382 (mt) cc_final: 0.8110 (mt) REVERT: A 592 LEU cc_start: 0.7391 (pt) cc_final: 0.6948 (mt) REVERT: A 676 MET cc_start: 0.7117 (mpp) cc_final: 0.6597 (mmt) REVERT: B 63 ARG cc_start: 0.7450 (ttt90) cc_final: 0.6861 (tmt170) REVERT: B 65 TYR cc_start: 0.8530 (t80) cc_final: 0.8075 (t80) REVERT: B 70 MET cc_start: 0.7129 (ttt) cc_final: 0.6565 (mmp) REVERT: B 72 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8279 (tp) REVERT: B 96 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7328 (ttp-170) REVERT: B 168 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8369 (ttp80) REVERT: B 193 ARG cc_start: 0.5447 (mtp180) cc_final: 0.4838 (mmm-85) REVERT: B 204 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (mm) REVERT: B 301 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 312 LYS cc_start: 0.8812 (tmtt) cc_final: 0.8455 (tttp) REVERT: B 330 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8244 (mpp) REVERT: B 428 GLU cc_start: 0.6378 (tt0) cc_final: 0.5939 (pt0) REVERT: B 467 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: B 513 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7466 (tt) REVERT: C 101 ASP cc_start: 0.7345 (t70) cc_final: 0.7067 (t0) REVERT: C 147 ASP cc_start: 0.7633 (m-30) cc_final: 0.7367 (m-30) REVERT: C 174 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8797 (mtt180) REVERT: C 250 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7398 (mtm-85) REVERT: C 401 ARG cc_start: 0.8360 (mmt-90) cc_final: 0.7988 (mmt-90) REVERT: C 504 MET cc_start: 0.6274 (mmt) cc_final: 0.6023 (ttt) REVERT: C 546 GLN cc_start: 0.7350 (tp-100) cc_final: 0.6870 (mt0) REVERT: C 568 LEU cc_start: 0.9023 (tp) cc_final: 0.8672 (mt) REVERT: D 56 TYR cc_start: 0.5063 (p90) cc_final: 0.4351 (m-80) REVERT: D 114 LEU cc_start: 0.9175 (mt) cc_final: 0.8928 (tt) REVERT: D 254 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8261 (tp) REVERT: D 256 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8510 (tppt) REVERT: D 319 PHE cc_start: 0.8195 (t80) cc_final: 0.7921 (t80) REVERT: D 321 ASP cc_start: 0.9240 (t70) cc_final: 0.9025 (t0) REVERT: D 348 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8139 (tpt90) REVERT: D 426 VAL cc_start: 0.6246 (t) cc_final: 0.5673 (t) REVERT: D 428 GLU cc_start: 0.8010 (pt0) cc_final: 0.7566 (pp20) REVERT: D 452 THR cc_start: 0.6080 (OUTLIER) cc_final: 0.5736 (p) REVERT: D 457 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7267 (tp) REVERT: D 459 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8059 (tp) REVERT: D 467 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5784 (p90) REVERT: D 540 PHE cc_start: 0.8154 (t80) cc_final: 0.7560 (t80) REVERT: D 652 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7154 (tpt) outliers start: 119 outliers final: 82 residues processed: 406 average time/residue: 0.1526 time to fit residues: 96.8664 Evaluate side-chains 404 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 298 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 246 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 652 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 248 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 229 optimal weight: 0.0030 chunk 153 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 160 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.173389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117391 restraints weight = 41412.979| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.95 r_work: 0.3447 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22345 Z= 0.134 Angle : 0.679 15.581 30223 Z= 0.332 Chirality : 0.043 0.250 3360 Planarity : 0.004 0.040 3813 Dihedral : 5.533 56.806 2990 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.83 % Allowed : 25.40 % Favored : 70.77 % 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 aren not related in a simple way. whole: 0.79 (0.16), residues: 2684 helix: 1.07 (0.12), residues: 1743 sheet: -1.37 (0.47), residues: 117 loop : -0.18 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 470 TYR 0.019 0.001 TYR C 54 PHE 0.034 0.002 PHE C 493 TRP 0.010 0.001 TRP A 172 HIS 0.018 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00285 (22345) covalent geometry : angle 0.67876 (30223) hydrogen bonds : bond 0.04657 ( 1350) hydrogen bonds : angle 4.79997 ( 3882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 327 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.2965 (OUTLIER) cc_final: 0.1890 (p90) REVERT: A 70 MET cc_start: 0.7219 (tpt) cc_final: 0.6405 (tmm) REVERT: A 116 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7937 (t80) REVERT: A 155 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8302 (t0) REVERT: A 166 LEU cc_start: 0.8616 (mt) cc_final: 0.7867 (tp) REVERT: A 301 TYR cc_start: 0.8649 (t80) cc_final: 0.8286 (t80) REVERT: A 318 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.7816 (mtt90) REVERT: A 329 PHE cc_start: 0.8103 (t80) cc_final: 0.7538 (t80) REVERT: A 362 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6990 (tp40) REVERT: A 415 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6983 (tt0) REVERT: A 443 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6017 (pm20) REVERT: A 456 ASP cc_start: 0.7823 (p0) cc_final: 0.7264 (t70) REVERT: A 516 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8828 (tt) REVERT: A 528 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8733 (tp30) REVERT: A 531 LEU cc_start: 0.9253 (mt) cc_final: 0.8957 (tp) REVERT: A 540 PHE cc_start: 0.8541 (t80) cc_final: 0.8275 (t80) REVERT: A 570 LEU cc_start: 0.8337 (mt) cc_final: 0.8070 (mt) REVERT: A 592 LEU cc_start: 0.7415 (pt) cc_final: 0.6943 (mt) REVERT: A 606 LYS cc_start: 0.8484 (tttm) cc_final: 0.8088 (mtpt) REVERT: A 676 MET cc_start: 0.7061 (mpp) cc_final: 0.6639 (mmt) REVERT: B 63 ARG cc_start: 0.7310 (ttt90) cc_final: 0.6740 (tmt170) REVERT: B 65 TYR cc_start: 0.8456 (t80) cc_final: 0.8034 (t80) REVERT: B 70 MET cc_start: 0.6963 (ttt) cc_final: 0.6393 (mmp) REVERT: B 193 ARG cc_start: 0.5437 (mtp180) cc_final: 0.4814 (mmm-85) REVERT: B 204 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 301 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7397 (t80) REVERT: B 312 LYS cc_start: 0.8796 (tmtt) cc_final: 0.8454 (tttp) REVERT: B 330 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8227 (mpp) REVERT: B 428 GLU cc_start: 0.6224 (tt0) cc_final: 0.5804 (pt0) REVERT: B 467 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: B 470 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8075 (ptp-110) REVERT: B 603 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8294 (mp0) REVERT: C 146 MET cc_start: 0.8307 (mmm) cc_final: 0.7606 (mpp) REVERT: C 147 ASP cc_start: 0.7569 (m-30) cc_final: 0.7310 (m-30) REVERT: C 169 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7996 (t80) REVERT: C 191 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: C 250 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7346 (mtm-85) REVERT: C 401 ARG cc_start: 0.8403 (mmt-90) cc_final: 0.8090 (mmt-90) REVERT: C 473 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5975 (tt0) REVERT: C 546 GLN cc_start: 0.7311 (tp-100) cc_final: 0.6834 (mt0) REVERT: C 568 LEU cc_start: 0.9031 (tp) cc_final: 0.8696 (mt) REVERT: D 56 TYR cc_start: 0.4718 (p90) cc_final: 0.4087 (m-80) REVERT: D 114 LEU cc_start: 0.9125 (mt) cc_final: 0.8901 (tt) REVERT: D 256 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8280 (tppt) REVERT: D 319 PHE cc_start: 0.8235 (t80) cc_final: 0.7690 (t80) REVERT: D 348 ARG cc_start: 0.8561 (mmm160) cc_final: 0.7963 (tpt90) REVERT: D 426 VAL cc_start: 0.6054 (t) cc_final: 0.5430 (t) REVERT: D 428 GLU cc_start: 0.7998 (pt0) cc_final: 0.7525 (pp20) REVERT: D 452 THR cc_start: 0.5942 (OUTLIER) cc_final: 0.5654 (p) REVERT: D 457 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7224 (tp) REVERT: D 459 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7601 (tp) REVERT: D 540 PHE cc_start: 0.8125 (t80) cc_final: 0.7532 (t80) REVERT: D 652 MET cc_start: 0.7544 (tpt) cc_final: 0.7140 (tpt) outliers start: 91 outliers final: 63 residues processed: 395 average time/residue: 0.1551 time to fit residues: 94.1697 Evaluate side-chains 378 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 297 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TYR Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 652 MET Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 127 ARG Chi-restraints excluded: chain C residue 169 TYR Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 659 TYR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 406 TYR Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 588 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 97 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 146 optimal weight: 0.4980 chunk 192 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 630 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.169121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111122 restraints weight = 41620.344| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.25 r_work: 0.3356 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22345 Z= 0.285 Angle : 0.747 17.000 30223 Z= 0.377 Chirality : 0.046 0.261 3360 Planarity : 0.005 0.040 3813 Dihedral : 5.673 57.838 2990 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.96 % Allowed : 25.65 % Favored : 70.39 % 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 aren not related in a simple way. whole: 0.52 (0.16), residues: 2684 helix: 0.86 (0.12), residues: 1750 sheet: -1.39 (0.47), residues: 122 loop : -0.28 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 497 TYR 0.026 0.002 TYR D 258 PHE 0.032 0.003 PHE C 493 TRP 0.015 0.002 TRP D 75 HIS 0.014 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00660 (22345) covalent geometry : angle 0.74652 (30223) hydrogen bonds : bond 0.05012 ( 1350) hydrogen bonds : angle 4.97001 ( 3882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9932.89 seconds wall clock time: 169 minutes 38.45 seconds (10178.45 seconds total)