Starting phenix.real_space_refine on Sun Aug 24 20:28:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9la2_62917/08_2025/9la2_62917.cif Found real_map, /net/cci-nas-00/data/ceres_data/9la2_62917/08_2025/9la2_62917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9la2_62917/08_2025/9la2_62917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9la2_62917/08_2025/9la2_62917.map" model { file = "/net/cci-nas-00/data/ceres_data/9la2_62917/08_2025/9la2_62917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9la2_62917/08_2025/9la2_62917.cif" } resolution = 3.2 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= 0.016 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 14216 2.51 5 N 3653 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s 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: 21917 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "B" 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: "C" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "D" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Time building chain proxies: 5.45, per 1000 atoms: 0.25 Number of scatterers: 21917 At special positions: 0 Unit cell: (124.504, 122.928, 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 3948 8.00 N 3653 7.00 C 14216 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 10 sheets defined 69.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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 97 Processing helix chain 'A' and resid 98 through 116 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 144 through 152 removed outlier: 3.550A pdb=" N PHE A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.693A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 195 through 226 removed outlier: 3.854A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.819A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.535A pdb=" N ILE A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 313 Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 365 through 384 removed outlier: 4.217A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Proline residue: A 379 - end of helix removed outlier: 3.727A pdb=" N LYS A 383 " --> pdb=" O PRO A 379 " (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 482 through 492 Processing helix chain 'A' and resid 492 through 508 removed outlier: 4.059A pdb=" N GLU A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 542 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.414A 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 608 Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.940A pdb=" N LEU A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 706 through 723 Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.608A pdb=" N PHE B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) 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 116 removed outlier: 3.549A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.878A pdb=" N PHE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.685A 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 189 Processing helix chain 'B' and resid 198 through 226 removed outlier: 3.970A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 removed outlier: 4.650A pdb=" N GLY B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.661A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 Processing helix chain 'B' and resid 336 through 352 Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.917A pdb=" N VAL B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 removed outlier: 3.814A pdb=" N ARG B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 3.941A 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 385 through 388 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.553A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) 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 508 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 516 through 542 removed outlier: 3.827A pdb=" N ILE B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 566 through 575 removed outlier: 3.741A 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 620 Processing helix chain 'B' and resid 627 through 639 removed outlier: 3.949A pdb=" N PHE B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) 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 722 Processing helix chain 'C' and resid 62 through 90 Proline residue: C 84 - end of helix removed outlier: 3.687A pdb=" N PHE C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 118 removed outlier: 3.740A pdb=" N VAL C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 3.578A 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 177 removed outlier: 3.579A pdb=" N LEU C 170 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 195 through 226 removed outlier: 4.287A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 removed outlier: 3.805A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLY C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 Processing helix chain 'C' and resid 281 through 313 removed outlier: 3.936A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 removed outlier: 4.211A pdb=" N SER C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 354 Processing helix chain 'C' and resid 356 through 364 removed outlier: 3.786A pdb=" N ASP C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 364 " --> pdb=" O MET C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 384 removed outlier: 4.372A pdb=" N LEU C 378 " --> pdb=" O GLN C 374 " (cutoff:3.500A) Proline residue: C 379 - end of helix Processing helix chain 'C' and resid 393 through 401 Processing helix chain 'C' and resid 456 through 462 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 492 through 511 removed outlier: 3.951A pdb=" N SER C 509 " --> pdb=" O GLU C 505 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 519 through 542 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.833A 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 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 627 through 638 Processing helix chain 'C' and resid 640 through 652 removed outlier: 4.025A pdb=" N MET C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 672 Processing helix chain 'C' and resid 673 through 682 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: 3.562A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.024A pdb=" N ILE D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'D' and resid 153 through 161 Processing helix 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 226 removed outlier: 4.038A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 removed outlier: 4.559A pdb=" N GLY D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 313 removed outlier: 3.560A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 Processing helix chain 'D' and resid 336 through 354 removed outlier: 4.207A pdb=" N GLN D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 removed outlier: 3.825A pdb=" N VAL D 359 " --> pdb=" O TYR D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 removed outlier: 4.266A 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 391 through 402 Processing helix chain 'D' and resid 455 through 460 removed outlier: 3.529A 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 492 through 501 removed outlier: 4.391A pdb=" N THR D 498 " --> pdb=" O HIS D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.842A pdb=" N ALA D 529 " --> pdb=" O GLY D 525 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA D 532 " --> pdb=" O GLU D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 566 through 575 Processing helix chain 'D' and resid 576 through 586 Processing helix chain 'D' and resid 599 through 607 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 672 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.654A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 405 Processing sheet with id=AA3, first strand: chain 'A' and resid 443 through 447 removed outlier: 5.465A pdb=" N SER A 444 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL A 435 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.676A pdb=" N TYR B 120 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 403 through 404 removed outlier: 3.621A pdb=" N PHE B 425 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 402 through 407 removed outlier: 3.754A pdb=" N PHE C 425 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 452 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 411 through 414 removed outlier: 6.714A pdb=" N VAL C 469 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 432 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'D' and resid 403 through 407 removed outlier: 3.708A pdb=" N PHE D 407 " --> pdb=" O CYS D 475 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS D 475 " --> pdb=" O PHE D 407 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU D 428 " --> pdb=" O HIS D 476 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU D 478 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 426 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR D 424 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 454 " --> pdb=" O TYR D 424 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 442 through 444 1326 hydrogen bonds defined for protein. 3807 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: 4.26 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6951 1.34 - 1.46: 4851 1.46 - 1.58: 10473 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 22431 Sorted by residual: bond pdb=" N VAL B 588 " pdb=" CA VAL B 588 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N VAL B 435 " pdb=" CA VAL B 435 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.30e-02 5.92e+03 9.51e+00 bond pdb=" N VAL B 267 " pdb=" CA VAL B 267 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.34e+00 bond pdb=" N VAL C 267 " pdb=" CA VAL C 267 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.12e+00 bond pdb=" N ILE D 266 " pdb=" CA ILE D 266 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.09e+00 ... (remaining 22426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 29314 2.22 - 4.43: 908 4.43 - 6.65: 86 6.65 - 8.87: 28 8.87 - 11.08: 7 Bond angle restraints: 30343 Sorted by residual: angle pdb=" N ARG A 177 " pdb=" CA ARG A 177 " pdb=" C ARG A 177 " ideal model delta sigma weight residual 113.20 107.73 5.47 1.21e+00 6.83e-01 2.05e+01 angle pdb=" N PHE B 82 " pdb=" CA PHE B 82 " pdb=" C PHE B 82 " ideal model delta sigma weight residual 114.04 108.43 5.61 1.24e+00 6.50e-01 2.05e+01 angle pdb=" N PRO B 557 " pdb=" CA PRO B 557 " pdb=" C PRO B 557 " ideal model delta sigma weight residual 113.86 108.41 5.45 1.25e+00 6.40e-01 1.90e+01 angle pdb=" N LEU B 81 " pdb=" CA LEU B 81 " pdb=" C LEU B 81 " ideal model delta sigma weight residual 112.92 107.63 5.29 1.23e+00 6.61e-01 1.85e+01 angle pdb=" N PHE A 82 " pdb=" CA PHE A 82 " pdb=" C PHE A 82 " ideal model delta sigma weight residual 113.12 107.83 5.29 1.25e+00 6.40e-01 1.79e+01 ... (remaining 30338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11457 17.95 - 35.90: 1373 35.90 - 53.85: 347 53.85 - 71.80: 93 71.80 - 89.75: 17 Dihedral angle restraints: 13287 sinusoidal: 5389 harmonic: 7898 Sorted by residual: dihedral pdb=" CA LEU B 197 " pdb=" C LEU B 197 " pdb=" N PHE B 198 " pdb=" CA PHE B 198 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CG ARG B 318 " pdb=" CD ARG B 318 " pdb=" NE ARG B 318 " pdb=" CZ ARG B 318 " ideal model delta sinusoidal sigma weight residual -90.00 -38.60 -51.40 2 1.50e+01 4.44e-03 1.30e+01 dihedral pdb=" CA TRP B 64 " pdb=" C TRP B 64 " pdb=" N TYR B 65 " pdb=" CA TYR B 65 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 13284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2409 0.049 - 0.098: 739 0.098 - 0.147: 161 0.147 - 0.196: 46 0.196 - 0.245: 17 Chirality restraints: 3372 Sorted by residual: chirality pdb=" CB ILE D 106 " pdb=" CA ILE D 106 " pdb=" CG1 ILE D 106 " pdb=" CG2 ILE D 106 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE D 277 " pdb=" N ILE D 277 " pdb=" C ILE D 277 " pdb=" CB ILE D 277 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE B 513 " pdb=" N ILE B 513 " pdb=" C ILE B 513 " pdb=" CB ILE B 513 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3369 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 693 " -0.016 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP B 693 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 693 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 693 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 693 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 693 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 693 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 693 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 693 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 693 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " -0.287 9.50e-02 1.11e+02 1.28e-01 1.01e+01 pdb=" NE ARG A 177 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 512 " 0.279 9.50e-02 1.11e+02 1.25e-01 9.57e+00 pdb=" NE ARG B 512 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 512 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 512 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 512 " 0.010 2.00e-02 2.50e+03 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2319 2.74 - 3.28: 25006 3.28 - 3.82: 40218 3.82 - 4.36: 49445 4.36 - 4.90: 77119 Nonbonded interactions: 194107 Sorted by model distance: nonbonded pdb=" O LEU A 386 " pdb=" ND2 ASN A 502 " model vdw 2.205 3.120 nonbonded pdb=" N GLY C 410 " pdb=" O VAL C 471 " model vdw 2.205 3.120 nonbonded pdb=" O PHE C 90 " pdb=" NH2 ARG C 168 " model vdw 2.224 3.120 nonbonded pdb=" O PHE D 631 " pdb=" OG1 THR D 635 " model vdw 2.232 3.040 nonbonded pdb=" O PHE C 631 " pdb=" OG1 THR C 635 " model vdw 2.232 3.040 ... (remaining 194102 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 722) selection = chain 'B' selection = (chain 'C' and resid 50 through 722) selection = (chain 'D' and resid 50 through 722) } 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: 4.450 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.960 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.006 0.107 22431 Z= 0.334 Angle : 0.860 11.081 30343 Z= 0.530 Chirality : 0.053 0.245 3372 Planarity : 0.007 0.128 3827 Dihedral : 16.857 89.750 8221 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.98 % Allowed : 23.77 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 2693 helix: 0.13 (0.12), residues: 1728 sheet: -2.48 (0.79), residues: 39 loop : -1.05 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 401 TYR 0.028 0.002 TYR D 351 PHE 0.043 0.002 PHE C 319 TRP 0.056 0.002 TRP B 693 HIS 0.018 0.002 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00552 (22431) covalent geometry : angle 0.86018 (30343) hydrogen bonds : bond 0.14218 ( 1326) hydrogen bonds : angle 6.75341 ( 3807) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 483 time to evaluate : 0.889 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: A 69 GLU cc_start: 0.8474 (tp30) cc_final: 0.8255 (mm-30) REVERT: A 70 MET cc_start: 0.7697 (mmp) cc_final: 0.6674 (mtt) REVERT: A 96 ARG cc_start: 0.7790 (ptm160) cc_final: 0.6089 (ptt90) REVERT: A 155 ASP cc_start: 0.8129 (t0) cc_final: 0.7851 (t0) REVERT: A 193 ARG cc_start: 0.7553 (ttt-90) cc_final: 0.7015 (ttp80) REVERT: A 205 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 386 LEU cc_start: 0.8826 (tp) cc_final: 0.8576 (tt) REVERT: A 477 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6464 (mt) REVERT: A 482 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7834 (ttmt) REVERT: A 492 TYR cc_start: 0.7153 (m-80) cc_final: 0.6946 (m-10) REVERT: A 499 ILE cc_start: 0.7699 (mm) cc_final: 0.7364 (mm) REVERT: A 504 MET cc_start: 0.8227 (mmp) cc_final: 0.7892 (mmp) REVERT: A 508 GLU cc_start: 0.8460 (tp30) cc_final: 0.7740 (pm20) REVERT: A 519 ASP cc_start: 0.8365 (t70) cc_final: 0.7792 (m-30) REVERT: A 581 LEU cc_start: 0.8864 (tp) cc_final: 0.8617 (mt) REVERT: A 652 MET cc_start: 0.6466 (tpt) cc_final: 0.5760 (mmt) REVERT: A 724 TYR cc_start: 0.5058 (OUTLIER) cc_final: 0.4819 (m-80) REVERT: B 54 TYR cc_start: 0.5491 (OUTLIER) cc_final: 0.5000 (p90) REVERT: B 64 TRP cc_start: 0.7080 (m100) cc_final: 0.6632 (m100) REVERT: B 243 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8166 (p0) REVERT: B 329 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 383 LYS cc_start: 0.8635 (mptt) cc_final: 0.8239 (mptt) REVERT: B 406 TYR cc_start: 0.7293 (m-80) cc_final: 0.7087 (m-80) REVERT: B 424 TYR cc_start: 0.8139 (m-80) cc_final: 0.7818 (m-80) REVERT: B 430 LEU cc_start: 0.7461 (tp) cc_final: 0.7071 (tp) REVERT: B 451 HIS cc_start: 0.8448 (m-70) cc_final: 0.8248 (m-70) REVERT: B 467 PHE cc_start: 0.7669 (p90) cc_final: 0.6621 (p90) REVERT: B 556 ASP cc_start: 0.8760 (t0) cc_final: 0.8536 (t0) REVERT: B 679 MET cc_start: 0.7882 (mmp) cc_final: 0.7347 (mtp) REVERT: B 680 LEU cc_start: 0.8665 (mt) cc_final: 0.8432 (tp) REVERT: C 66 LYS cc_start: 0.8073 (mttt) cc_final: 0.6832 (tmtt) REVERT: C 116 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: C 120 TYR cc_start: 0.7717 (p90) cc_final: 0.7078 (p90) REVERT: C 135 ILE cc_start: 0.7374 (mt) cc_final: 0.7140 (pt) REVERT: C 319 PHE cc_start: 0.8494 (t80) cc_final: 0.7730 (t80) REVERT: C 341 SER cc_start: 0.8422 (m) cc_final: 0.8079 (p) REVERT: C 364 ILE cc_start: 0.8607 (mm) cc_final: 0.8392 (tp) REVERT: C 369 ARG cc_start: 0.7900 (ptp-110) cc_final: 0.7696 (ptp90) REVERT: C 414 THR cc_start: 0.6651 (OUTLIER) cc_final: 0.6414 (t) REVERT: C 475 CYS cc_start: 0.5841 (OUTLIER) cc_final: 0.5378 (p) REVERT: C 506 GLU cc_start: 0.6601 (tt0) cc_final: 0.6132 (tt0) REVERT: C 603 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8852 (mt-10) REVERT: C 652 MET cc_start: 0.5851 (tpp) cc_final: 0.5448 (tpt) REVERT: C 659 TYR cc_start: 0.6084 (p90) cc_final: 0.5745 (p90) REVERT: C 679 MET cc_start: 0.8915 (ttt) cc_final: 0.8682 (ttm) REVERT: D 78 TYR cc_start: 0.7951 (t80) cc_final: 0.7713 (t80) REVERT: D 137 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7410 (t80) REVERT: D 154 TRP cc_start: 0.8592 (m100) cc_final: 0.8099 (m100) REVERT: D 325 ASP cc_start: 0.9010 (m-30) cc_final: 0.8741 (m-30) REVERT: D 376 LEU cc_start: 0.8994 (tt) cc_final: 0.8664 (mp) REVERT: D 377 TYR cc_start: 0.7197 (m-10) cc_final: 0.6948 (m-10) REVERT: D 401 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7328 (tpt170) REVERT: D 451 HIS cc_start: 0.8719 (m-70) cc_final: 0.8304 (m-70) REVERT: D 488 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8250 (tp) REVERT: D 497 ARG cc_start: 0.8952 (mtp-110) cc_final: 0.8544 (mtp85) REVERT: D 582 PHE cc_start: 0.7958 (t80) cc_final: 0.7601 (t80) REVERT: D 631 PHE cc_start: 0.8838 (m-80) cc_final: 0.8572 (m-80) REVERT: D 665 LEU cc_start: 0.8008 (tp) cc_final: 0.7674 (tp) outliers start: 71 outliers final: 27 residues processed: 537 average time/residue: 0.1741 time to fit residues: 140.9960 Evaluate side-chains 388 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 350 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 475 CYS Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 544 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 2.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 403 HIS A 418 ASN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 HIS ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN B 278 HIS B 354 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 510 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS C 354 HIS ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 HIS C 451 HIS ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN C 695 ASN D 59 HIS D 331 ASN D 346 HIS ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS D 451 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN D 541 GLN ** D 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 HIS D 718 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.161920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108747 restraints weight = 46459.961| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.73 r_work: 0.3384 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22431 Z= 0.222 Angle : 0.678 9.579 30343 Z= 0.358 Chirality : 0.044 0.163 3372 Planarity : 0.005 0.099 3827 Dihedral : 6.930 58.828 3050 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.95 % Allowed : 21.80 % Favored : 72.24 % 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: -0.16 (0.16), residues: 2693 helix: 0.44 (0.11), residues: 1740 sheet: -3.24 (0.62), residues: 57 loop : -0.80 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 318 TYR 0.051 0.002 TYR D 380 PHE 0.030 0.002 PHE D 117 TRP 0.017 0.002 TRP B 255 HIS 0.012 0.002 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00497 (22431) covalent geometry : angle 0.67763 (30343) hydrogen bonds : bond 0.05517 ( 1326) hydrogen bonds : angle 5.49918 ( 3807) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 370 time to evaluate : 0.883 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 56 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6866 (m-10) REVERT: A 69 GLU cc_start: 0.8568 (tp30) cc_final: 0.8316 (mm-30) REVERT: A 70 MET cc_start: 0.7953 (mmp) cc_final: 0.6916 (mtt) REVERT: A 96 ARG cc_start: 0.7944 (ptm160) cc_final: 0.6305 (ptt180) REVERT: A 111 ASP cc_start: 0.8387 (t0) cc_final: 0.7829 (t0) REVERT: A 131 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7907 (mttp) REVERT: A 139 TYR cc_start: 0.8369 (t80) cc_final: 0.8111 (t80) REVERT: A 159 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8047 (mttt) REVERT: A 329 PHE cc_start: 0.9196 (t80) cc_final: 0.8830 (t80) REVERT: A 330 MET cc_start: 0.7366 (mtm) cc_final: 0.6986 (mmm) REVERT: A 394 PHE cc_start: 0.8015 (t80) cc_final: 0.7704 (t80) REVERT: A 407 PHE cc_start: 0.7282 (m-10) cc_final: 0.6694 (m-10) REVERT: A 470 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.7983 (ttp-110) REVERT: A 477 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6506 (mt) REVERT: A 481 ASP cc_start: 0.8591 (t0) cc_final: 0.8250 (t70) REVERT: A 492 TYR cc_start: 0.7437 (m-80) cc_final: 0.7216 (m-10) REVERT: A 504 MET cc_start: 0.8315 (mmp) cc_final: 0.7920 (mmp) REVERT: A 508 GLU cc_start: 0.8479 (tp30) cc_final: 0.7757 (pm20) REVERT: A 652 MET cc_start: 0.6720 (tpt) cc_final: 0.6129 (mmt) REVERT: A 679 MET cc_start: 0.6403 (tpt) cc_final: 0.5673 (mmm) REVERT: A 724 TYR cc_start: 0.5155 (OUTLIER) cc_final: 0.4761 (t80) REVERT: B 54 TYR cc_start: 0.5569 (OUTLIER) cc_final: 0.4793 (p90) REVERT: B 64 TRP cc_start: 0.7091 (m100) cc_final: 0.6657 (m100) REVERT: B 127 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8028 (mmt90) REVERT: B 130 TYR cc_start: 0.7543 (m-80) cc_final: 0.6595 (m-80) REVERT: B 202 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8289 (tt) REVERT: B 243 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8323 (p0) REVERT: B 244 TYR cc_start: 0.8874 (t80) cc_final: 0.8617 (t80) REVERT: B 281 ASN cc_start: 0.8514 (m-40) cc_final: 0.8178 (m-40) REVERT: B 376 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 424 TYR cc_start: 0.8067 (m-80) cc_final: 0.7759 (m-80) REVERT: B 556 ASP cc_start: 0.8815 (t0) cc_final: 0.8596 (t0) REVERT: B 652 MET cc_start: 0.5401 (tpt) cc_final: 0.5057 (ttt) REVERT: B 679 MET cc_start: 0.7872 (mmp) cc_final: 0.7196 (mtp) REVERT: C 66 LYS cc_start: 0.7784 (mttt) cc_final: 0.6945 (tmtt) REVERT: C 116 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7223 (m-10) REVERT: C 120 TYR cc_start: 0.7848 (p90) cc_final: 0.7419 (p90) REVERT: C 135 ILE cc_start: 0.7525 (mt) cc_final: 0.7233 (pt) REVERT: C 210 TYR cc_start: 0.8268 (t80) cc_final: 0.8046 (t80) REVERT: C 282 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8901 (mp) REVERT: C 318 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8593 (mtt90) REVERT: C 319 PHE cc_start: 0.8551 (t80) cc_final: 0.7565 (t80) REVERT: C 323 MET cc_start: 0.8576 (mmm) cc_final: 0.7787 (mpp) REVERT: C 330 MET cc_start: 0.8096 (mmm) cc_final: 0.7798 (mmt) REVERT: C 341 SER cc_start: 0.8352 (m) cc_final: 0.8084 (p) REVERT: C 352 ASP cc_start: 0.9022 (m-30) cc_final: 0.8255 (t70) REVERT: C 473 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6861 (mm-30) REVERT: C 506 GLU cc_start: 0.6507 (tt0) cc_final: 0.6063 (tt0) REVERT: C 603 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8732 (mt-10) REVERT: C 652 MET cc_start: 0.5704 (tpp) cc_final: 0.5288 (tpp) REVERT: C 679 MET cc_start: 0.8882 (ttt) cc_final: 0.8564 (ttp) REVERT: D 137 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: D 325 ASP cc_start: 0.9082 (m-30) cc_final: 0.8768 (m-30) REVERT: D 376 LEU cc_start: 0.8903 (tt) cc_final: 0.8702 (mp) REVERT: D 377 TYR cc_start: 0.7582 (m-10) cc_final: 0.7336 (m-10) REVERT: D 401 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7654 (tpt170) REVERT: D 451 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8549 (m170) REVERT: D 482 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7905 (tttm) REVERT: D 488 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8327 (pt) REVERT: D 495 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7299 (p0) REVERT: D 497 ARG cc_start: 0.8825 (mtp-110) cc_final: 0.8393 (mtp85) REVERT: D 540 PHE cc_start: 0.9050 (t80) cc_final: 0.8818 (t80) REVERT: D 665 LEU cc_start: 0.7977 (tp) cc_final: 0.7684 (tp) outliers start: 142 outliers final: 67 residues processed: 482 average time/residue: 0.1463 time to fit residues: 110.1894 Evaluate side-chains 406 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 703 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 35 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 191 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 201 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 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 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 396 ASN C 451 HIS ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 ASN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.160083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105490 restraints weight = 46316.872| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.23 r_work: 0.3364 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22431 Z= 0.228 Angle : 0.655 8.977 30343 Z= 0.344 Chirality : 0.044 0.260 3372 Planarity : 0.005 0.066 3827 Dihedral : 6.410 59.742 3032 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.28 % Allowed : 22.35 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.16), residues: 2693 helix: 0.57 (0.12), residues: 1744 sheet: -3.30 (0.58), residues: 62 loop : -0.70 (0.22), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 512 TYR 0.026 0.002 TYR D 380 PHE 0.023 0.002 PHE A 319 TRP 0.016 0.002 TRP C 693 HIS 0.012 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00517 (22431) covalent geometry : angle 0.65538 (30343) hydrogen bonds : bond 0.05184 ( 1326) hydrogen bonds : angle 5.28188 ( 3807) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 355 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: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6931 (m-10) REVERT: A 69 GLU cc_start: 0.8634 (tp30) cc_final: 0.8365 (mm-30) REVERT: A 70 MET cc_start: 0.7955 (mmp) cc_final: 0.6911 (mtt) REVERT: A 96 ARG cc_start: 0.8008 (ptm160) cc_final: 0.7178 (tmt170) REVERT: A 131 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7865 (mttp) REVERT: A 319 PHE cc_start: 0.8148 (t80) cc_final: 0.7640 (t80) REVERT: A 335 LEU cc_start: 0.8661 (tp) cc_final: 0.8011 (mm) REVERT: A 481 ASP cc_start: 0.8598 (t0) cc_final: 0.8259 (t70) REVERT: A 504 MET cc_start: 0.8360 (mmp) cc_final: 0.8010 (mmp) REVERT: A 508 GLU cc_start: 0.8468 (tp30) cc_final: 0.7767 (mp0) REVERT: A 589 ASP cc_start: 0.5649 (t0) cc_final: 0.5433 (t0) REVERT: A 616 LEU cc_start: 0.8529 (mt) cc_final: 0.8164 (tp) REVERT: A 724 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.4884 (t80) REVERT: B 54 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.5207 (p90) REVERT: B 64 TRP cc_start: 0.7147 (m100) cc_final: 0.6743 (m100) REVERT: B 91 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: B 127 ARG cc_start: 0.8382 (mmm160) cc_final: 0.7978 (mmt90) REVERT: B 130 TYR cc_start: 0.7688 (m-80) cc_final: 0.6813 (m-80) REVERT: B 202 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8283 (tt) REVERT: B 243 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8334 (p0) REVERT: B 244 TYR cc_start: 0.8953 (t80) cc_final: 0.8713 (t80) REVERT: B 281 ASN cc_start: 0.8511 (m-40) cc_final: 0.8169 (m-40) REVERT: B 376 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8455 (tt) REVERT: B 377 TYR cc_start: 0.8543 (m-10) cc_final: 0.8005 (m-10) REVERT: B 430 LEU cc_start: 0.7428 (tp) cc_final: 0.7151 (tp) REVERT: B 556 ASP cc_start: 0.8819 (t0) cc_final: 0.8548 (t0) REVERT: B 609 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: B 679 MET cc_start: 0.7910 (mmp) cc_final: 0.7211 (mtp) REVERT: C 66 LYS cc_start: 0.7734 (mttt) cc_final: 0.7025 (tmtt) REVERT: C 116 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: C 120 TYR cc_start: 0.7837 (p90) cc_final: 0.7423 (p90) REVERT: C 135 ILE cc_start: 0.7511 (mt) cc_final: 0.7276 (pt) REVERT: C 210 TYR cc_start: 0.8315 (t80) cc_final: 0.8089 (t80) REVERT: C 282 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8867 (mp) REVERT: C 319 PHE cc_start: 0.8595 (t80) cc_final: 0.7887 (t80) REVERT: C 323 MET cc_start: 0.8546 (mmm) cc_final: 0.8043 (mtm) REVERT: C 341 SER cc_start: 0.8321 (m) cc_final: 0.8084 (p) REVERT: C 352 ASP cc_start: 0.9023 (m-30) cc_final: 0.8302 (t70) REVERT: C 374 GLN cc_start: 0.7955 (mt0) cc_final: 0.7593 (pp30) REVERT: C 473 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6897 (mm-30) REVERT: C 506 GLU cc_start: 0.6463 (tt0) cc_final: 0.6180 (tt0) REVERT: C 603 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8749 (mt-10) REVERT: C 652 MET cc_start: 0.5647 (tpp) cc_final: 0.5299 (tpp) REVERT: C 679 MET cc_start: 0.8898 (ttt) cc_final: 0.8668 (ttm) REVERT: D 66 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7631 (mtpt) REVERT: D 137 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: D 284 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: D 325 ASP cc_start: 0.9116 (m-30) cc_final: 0.8805 (m-30) REVERT: D 377 TYR cc_start: 0.7756 (m-10) cc_final: 0.7508 (m-10) REVERT: D 401 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7721 (tpt170) REVERT: D 428 GLU cc_start: 0.8599 (tp30) cc_final: 0.7814 (mp0) REVERT: D 451 HIS cc_start: 0.8654 (m-70) cc_final: 0.8444 (m170) REVERT: D 482 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7820 (tttm) REVERT: D 488 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8309 (pt) REVERT: D 497 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8423 (mtp85) REVERT: D 540 PHE cc_start: 0.9084 (t80) cc_final: 0.8856 (t80) REVERT: D 601 LEU cc_start: 0.8417 (tp) cc_final: 0.8062 (tp) REVERT: D 665 LEU cc_start: 0.8014 (tp) cc_final: 0.7717 (tp) outliers start: 126 outliers final: 78 residues processed: 446 average time/residue: 0.1553 time to fit residues: 107.8610 Evaluate side-chains 410 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 316 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 562 TYR Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 703 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 465 GLN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.160903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.106964 restraints weight = 46171.392| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.25 r_work: 0.3386 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22431 Z= 0.173 Angle : 0.610 10.882 30343 Z= 0.316 Chirality : 0.042 0.331 3372 Planarity : 0.004 0.050 3827 Dihedral : 6.070 59.799 3025 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.07 % Allowed : 22.22 % Favored : 72.70 % 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: 0.16 (0.16), residues: 2693 helix: 0.72 (0.12), residues: 1760 sheet: -3.32 (0.48), residues: 79 loop : -0.66 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 565 TYR 0.017 0.002 TYR A 126 PHE 0.022 0.002 PHE B 485 TRP 0.014 0.001 TRP B 75 HIS 0.010 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00386 (22431) covalent geometry : angle 0.61021 (30343) hydrogen bonds : bond 0.04817 ( 1326) hydrogen bonds : angle 5.02918 ( 3807) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 344 time to evaluate : 0.961 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 56 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6915 (m-10) REVERT: A 69 GLU cc_start: 0.8629 (tp30) cc_final: 0.8362 (mm-30) REVERT: A 70 MET cc_start: 0.7979 (mmp) cc_final: 0.6923 (mtt) REVERT: A 96 ARG cc_start: 0.8078 (ptm160) cc_final: 0.6323 (ptt180) REVERT: A 323 MET cc_start: 0.8317 (tpp) cc_final: 0.7987 (tpt) REVERT: A 335 LEU cc_start: 0.8590 (tp) cc_final: 0.8117 (tp) REVERT: A 346 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8232 (t70) REVERT: A 481 ASP cc_start: 0.8583 (t0) cc_final: 0.8234 (t70) REVERT: A 504 MET cc_start: 0.8353 (mmp) cc_final: 0.7956 (mmp) REVERT: A 508 GLU cc_start: 0.8469 (tp30) cc_final: 0.7714 (pm20) REVERT: A 512 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7242 (mmp-170) REVERT: A 671 GLU cc_start: 0.8562 (tp30) cc_final: 0.7904 (mt-10) REVERT: A 724 TYR cc_start: 0.5273 (OUTLIER) cc_final: 0.5030 (t80) REVERT: B 54 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.5163 (p90) REVERT: B 64 TRP cc_start: 0.7174 (m100) cc_final: 0.6762 (m100) REVERT: B 91 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7389 (ttm170) REVERT: B 127 ARG cc_start: 0.8387 (mmm160) cc_final: 0.7996 (mmt90) REVERT: B 130 TYR cc_start: 0.7802 (m-80) cc_final: 0.7040 (m-80) REVERT: B 202 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8261 (tt) REVERT: B 243 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8271 (p0) REVERT: B 281 ASN cc_start: 0.8504 (m-40) cc_final: 0.8124 (m110) REVERT: B 376 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8478 (tt) REVERT: B 430 LEU cc_start: 0.7520 (tp) cc_final: 0.7247 (tp) REVERT: B 556 ASP cc_start: 0.8784 (t0) cc_final: 0.8569 (t0) REVERT: B 609 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: B 679 MET cc_start: 0.7886 (mmp) cc_final: 0.7253 (ttp) REVERT: B 680 LEU cc_start: 0.8730 (mm) cc_final: 0.8380 (tp) REVERT: C 66 LYS cc_start: 0.7798 (mttt) cc_final: 0.6992 (tmtt) REVERT: C 116 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7625 (m-10) REVERT: C 135 ILE cc_start: 0.7504 (mt) cc_final: 0.7085 (pt) REVERT: C 210 TYR cc_start: 0.8211 (t80) cc_final: 0.7970 (t80) REVERT: C 282 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8769 (mp) REVERT: C 319 PHE cc_start: 0.8538 (t80) cc_final: 0.7847 (t80) REVERT: C 323 MET cc_start: 0.8592 (mmm) cc_final: 0.7999 (mtp) REVERT: C 330 MET cc_start: 0.8273 (mmm) cc_final: 0.7884 (mmt) REVERT: C 341 SER cc_start: 0.8286 (m) cc_final: 0.8044 (p) REVERT: C 374 GLN cc_start: 0.7931 (mt0) cc_final: 0.7699 (pp30) REVERT: C 405 GLU cc_start: 0.8239 (tt0) cc_final: 0.7864 (tt0) REVERT: C 407 PHE cc_start: 0.7673 (m-80) cc_final: 0.7098 (m-80) REVERT: C 448 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7637 (tp) REVERT: C 473 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6861 (mm-30) REVERT: C 506 GLU cc_start: 0.6425 (tt0) cc_final: 0.6171 (tt0) REVERT: C 552 ARG cc_start: 0.7814 (mpt180) cc_final: 0.7508 (mmt-90) REVERT: C 603 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8732 (mt-10) REVERT: C 652 MET cc_start: 0.5597 (tpp) cc_final: 0.5296 (tpp) REVERT: C 679 MET cc_start: 0.8884 (ttt) cc_final: 0.8663 (ttm) REVERT: D 66 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7566 (mtpp) REVERT: D 97 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5312 (mm) REVERT: D 137 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: D 317 GLU cc_start: 0.8913 (tt0) cc_final: 0.8496 (tp30) REVERT: D 325 ASP cc_start: 0.9071 (m-30) cc_final: 0.8664 (m-30) REVERT: D 401 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7762 (tpt170) REVERT: D 428 GLU cc_start: 0.8648 (tp30) cc_final: 0.7984 (mp0) REVERT: D 482 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7824 (tttm) REVERT: D 488 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8220 (pt) REVERT: D 497 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8392 (mtp85) REVERT: D 540 PHE cc_start: 0.9103 (t80) cc_final: 0.8784 (t80) REVERT: D 618 LYS cc_start: 0.9142 (tptp) cc_final: 0.8719 (ttpp) REVERT: D 631 PHE cc_start: 0.8825 (m-80) cc_final: 0.8574 (m-80) REVERT: D 665 LEU cc_start: 0.7980 (tp) cc_final: 0.7707 (tp) outliers start: 121 outliers final: 71 residues processed: 433 average time/residue: 0.1459 time to fit residues: 99.3659 Evaluate side-chains 401 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 312 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 562 TYR Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 703 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 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 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 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 = 0.4372 r_free = 0.4372 target = 0.159268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.105179 restraints weight = 46007.650| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.48 r_work: 0.3337 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22431 Z= 0.225 Angle : 0.643 14.069 30343 Z= 0.333 Chirality : 0.044 0.357 3372 Planarity : 0.004 0.041 3827 Dihedral : 6.085 58.192 3021 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.49 % Allowed : 22.64 % Favored : 71.87 % 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: 0.15 (0.16), residues: 2693 helix: 0.70 (0.12), residues: 1756 sheet: -3.31 (0.48), residues: 79 loop : -0.64 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 340 TYR 0.023 0.002 TYR C 65 PHE 0.027 0.002 PHE A 319 TRP 0.014 0.001 TRP B 255 HIS 0.010 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00514 (22431) covalent geometry : angle 0.64253 (30343) hydrogen bonds : bond 0.04847 ( 1326) hydrogen bonds : angle 4.99858 ( 3807) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 324 time to evaluate : 0.793 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: A 56 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.7020 (m-10) REVERT: A 69 GLU cc_start: 0.8678 (tp30) cc_final: 0.8413 (mm-30) REVERT: A 70 MET cc_start: 0.8054 (mmp) cc_final: 0.6982 (mtt) REVERT: A 96 ARG cc_start: 0.8213 (ptm160) cc_final: 0.6518 (ptt180) REVERT: A 137 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: A 330 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7146 (mmm) REVERT: A 335 LEU cc_start: 0.8437 (tp) cc_final: 0.7991 (tp) REVERT: A 381 ILE cc_start: 0.9118 (mm) cc_final: 0.8897 (tt) REVERT: A 407 PHE cc_start: 0.7863 (m-10) cc_final: 0.7572 (m-10) REVERT: A 504 MET cc_start: 0.8394 (mmp) cc_final: 0.7968 (mmp) REVERT: A 508 GLU cc_start: 0.8489 (tp30) cc_final: 0.7735 (pm20) REVERT: A 512 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7303 (mmp-170) REVERT: A 574 ARG cc_start: 0.8524 (mmp-170) cc_final: 0.8189 (tpt90) REVERT: A 616 LEU cc_start: 0.8508 (mt) cc_final: 0.8171 (tp) REVERT: A 671 GLU cc_start: 0.8531 (tp30) cc_final: 0.7878 (mt-10) REVERT: B 54 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.5127 (p90) REVERT: B 64 TRP cc_start: 0.7184 (m100) cc_final: 0.6781 (m100) REVERT: B 91 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7463 (ttm170) REVERT: B 127 ARG cc_start: 0.8363 (mmm160) cc_final: 0.8031 (mpt180) REVERT: B 130 TYR cc_start: 0.7801 (m-80) cc_final: 0.6441 (m-80) REVERT: B 243 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8329 (p0) REVERT: B 281 ASN cc_start: 0.8539 (m-40) cc_final: 0.8118 (m110) REVERT: B 317 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: B 424 TYR cc_start: 0.8186 (m-80) cc_final: 0.7982 (m-80) REVERT: B 430 LEU cc_start: 0.7662 (tp) cc_final: 0.7403 (tp) REVERT: B 556 ASP cc_start: 0.8769 (t0) cc_final: 0.8555 (t0) REVERT: B 679 MET cc_start: 0.7891 (mmp) cc_final: 0.7174 (ttp) REVERT: C 58 ILE cc_start: 0.8130 (mp) cc_final: 0.7837 (tp) REVERT: C 66 LYS cc_start: 0.7826 (mttt) cc_final: 0.7026 (tmtt) REVERT: C 116 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7399 (m-10) REVERT: C 135 ILE cc_start: 0.7543 (mt) cc_final: 0.7131 (pt) REVERT: C 282 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8850 (mp) REVERT: C 319 PHE cc_start: 0.8572 (t80) cc_final: 0.7840 (t80) REVERT: C 323 MET cc_start: 0.8584 (mmm) cc_final: 0.8088 (mtp) REVERT: C 341 SER cc_start: 0.8236 (m) cc_final: 0.8002 (p) REVERT: C 454 PHE cc_start: 0.8873 (p90) cc_final: 0.8592 (p90) REVERT: C 473 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6758 (mm-30) REVERT: C 506 GLU cc_start: 0.6489 (tt0) cc_final: 0.6272 (tt0) REVERT: C 544 PHE cc_start: 0.6753 (t80) cc_final: 0.6544 (t80) REVERT: C 552 ARG cc_start: 0.7796 (mpt180) cc_final: 0.7496 (mmt-90) REVERT: C 569 HIS cc_start: 0.8562 (m170) cc_final: 0.7892 (m90) REVERT: C 603 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8734 (mt-10) REVERT: C 652 MET cc_start: 0.5559 (tpp) cc_final: 0.5046 (tpp) REVERT: D 66 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7540 (mtpp) REVERT: D 97 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5269 (mm) REVERT: D 137 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: D 284 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: D 317 GLU cc_start: 0.8934 (tt0) cc_final: 0.8572 (tp30) REVERT: D 325 ASP cc_start: 0.9010 (m-30) cc_final: 0.8680 (m-30) REVERT: D 401 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7728 (tpt170) REVERT: D 477 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8093 (mm) REVERT: D 482 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7775 (tttm) REVERT: D 497 ARG cc_start: 0.8801 (mtp-110) cc_final: 0.8358 (mtp85) REVERT: D 540 PHE cc_start: 0.9132 (t80) cc_final: 0.8870 (t80) REVERT: D 544 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: D 618 LYS cc_start: 0.9154 (tptp) cc_final: 0.8766 (ttpp) REVERT: D 631 PHE cc_start: 0.8810 (m-80) cc_final: 0.8558 (m-80) REVERT: D 665 LEU cc_start: 0.8009 (tp) cc_final: 0.7719 (tt) outliers start: 131 outliers final: 83 residues processed: 428 average time/residue: 0.1631 time to fit residues: 108.5517 Evaluate side-chains 410 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 310 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 101 ASP 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 125 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 183 GLU 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 226 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 493 PHE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 703 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 205 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 152 optimal weight: 0.1980 chunk 164 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 ASN ** D 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.160828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.107568 restraints weight = 46157.263| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.55 r_work: 0.3381 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22431 Z= 0.160 Angle : 0.611 11.812 30343 Z= 0.313 Chirality : 0.042 0.262 3372 Planarity : 0.004 0.042 3827 Dihedral : 5.764 58.121 3013 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.53 % Allowed : 23.48 % Favored : 71.99 % 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: 2693 helix: 0.86 (0.12), residues: 1758 sheet: -3.21 (0.49), residues: 79 loop : -0.60 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 565 TYR 0.026 0.002 TYR C 65 PHE 0.027 0.002 PHE A 582 TRP 0.013 0.001 TRP B 75 HIS 0.009 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00361 (22431) covalent geometry : angle 0.61096 (30343) hydrogen bonds : bond 0.04554 ( 1326) hydrogen bonds : angle 4.84541 ( 3807) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 338 time to evaluate : 0.956 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 56 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: A 70 MET cc_start: 0.7980 (mmp) cc_final: 0.6951 (mtt) REVERT: A 137 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7313 (m-10) REVERT: A 335 LEU cc_start: 0.8375 (tp) cc_final: 0.7889 (tp) REVERT: A 407 PHE cc_start: 0.7817 (m-10) cc_final: 0.7438 (m-10) REVERT: A 504 MET cc_start: 0.8357 (mmp) cc_final: 0.7910 (mmp) REVERT: A 508 GLU cc_start: 0.8405 (tp30) cc_final: 0.7652 (pm20) REVERT: A 512 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7175 (mmp-170) REVERT: A 609 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7412 (tm-30) REVERT: A 671 GLU cc_start: 0.8508 (tp30) cc_final: 0.7854 (mt-10) REVERT: B 54 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.5310 (p90) REVERT: B 64 TRP cc_start: 0.7160 (m100) cc_final: 0.6766 (m100) REVERT: B 91 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7348 (ttm170) REVERT: B 127 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7979 (mmt90) REVERT: B 130 TYR cc_start: 0.7806 (m-80) cc_final: 0.7041 (m-80) REVERT: B 243 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8253 (p0) REVERT: B 281 ASN cc_start: 0.8501 (m-40) cc_final: 0.8146 (m110) REVERT: B 346 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7976 (t70) REVERT: B 424 TYR cc_start: 0.8243 (m-80) cc_final: 0.8014 (m-80) REVERT: B 430 LEU cc_start: 0.7712 (tp) cc_final: 0.7307 (tp) REVERT: B 492 TYR cc_start: 0.7922 (m-80) cc_final: 0.7610 (m-10) REVERT: B 556 ASP cc_start: 0.8737 (t0) cc_final: 0.8533 (t70) REVERT: B 582 PHE cc_start: 0.8564 (t80) cc_final: 0.8145 (t80) REVERT: B 679 MET cc_start: 0.7931 (mmp) cc_final: 0.6612 (ttp) REVERT: C 58 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7897 (tp) REVERT: C 66 LYS cc_start: 0.7791 (mttt) cc_final: 0.6980 (tmtt) REVERT: C 116 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: C 135 ILE cc_start: 0.7493 (mt) cc_final: 0.7093 (pt) REVERT: C 282 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8778 (mp) REVERT: C 319 PHE cc_start: 0.8563 (t80) cc_final: 0.7849 (t80) REVERT: C 323 MET cc_start: 0.8569 (mmm) cc_final: 0.8061 (mtp) REVERT: C 330 MET cc_start: 0.8378 (mmm) cc_final: 0.8129 (mmt) REVERT: C 341 SER cc_start: 0.8171 (m) cc_final: 0.7932 (p) REVERT: C 405 GLU cc_start: 0.8266 (tt0) cc_final: 0.7819 (tt0) REVERT: C 407 PHE cc_start: 0.7494 (m-80) cc_final: 0.7173 (m-80) REVERT: C 443 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: C 473 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6945 (mm-30) REVERT: C 506 GLU cc_start: 0.6476 (tt0) cc_final: 0.6199 (pt0) REVERT: C 552 ARG cc_start: 0.7781 (mpt180) cc_final: 0.7543 (mmt-90) REVERT: C 569 HIS cc_start: 0.8500 (m170) cc_final: 0.7609 (m90) REVERT: C 603 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8740 (mt-10) REVERT: C 640 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7315 (p0) REVERT: C 642 ASP cc_start: 0.8136 (m-30) cc_final: 0.7893 (m-30) REVERT: C 652 MET cc_start: 0.5566 (tpp) cc_final: 0.5077 (tpp) REVERT: C 679 MET cc_start: 0.8532 (ttm) cc_final: 0.8172 (ttp) REVERT: D 66 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7547 (mtpp) REVERT: D 97 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5168 (mm) REVERT: D 137 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: D 317 GLU cc_start: 0.8906 (tt0) cc_final: 0.8623 (tp30) REVERT: D 325 ASP cc_start: 0.9007 (m-30) cc_final: 0.8626 (m-30) REVERT: D 401 ARG cc_start: 0.8374 (ttm170) cc_final: 0.7817 (tpt170) REVERT: D 428 GLU cc_start: 0.8634 (tp30) cc_final: 0.7996 (mp0) REVERT: D 482 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7846 (tttm) REVERT: D 497 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.8451 (mtp85) REVERT: D 540 PHE cc_start: 0.9104 (t80) cc_final: 0.8829 (t80) REVERT: D 618 LYS cc_start: 0.9164 (tptp) cc_final: 0.8774 (ttpp) REVERT: D 631 PHE cc_start: 0.8829 (m-80) cc_final: 0.8566 (m-80) outliers start: 108 outliers final: 71 residues processed: 422 average time/residue: 0.1706 time to fit residues: 111.4652 Evaluate side-chains 393 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 306 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 493 PHE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 63 optimal weight: 40.0000 chunk 9 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 255 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN ** D 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.160528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106259 restraints weight = 46078.168| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.22 r_work: 0.3374 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22431 Z= 0.177 Angle : 0.626 11.534 30343 Z= 0.321 Chirality : 0.042 0.226 3372 Planarity : 0.004 0.043 3827 Dihedral : 5.633 58.066 3009 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.53 % Allowed : 24.07 % Favored : 71.40 % 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: 0.38 (0.16), residues: 2693 helix: 0.86 (0.12), residues: 1758 sheet: -3.04 (0.49), residues: 79 loop : -0.54 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 340 TYR 0.021 0.002 TYR C 196 PHE 0.029 0.002 PHE C 544 TRP 0.013 0.001 TRP B 255 HIS 0.010 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00403 (22431) covalent geometry : angle 0.62570 (30343) hydrogen bonds : bond 0.04547 ( 1326) hydrogen bonds : angle 4.82072 ( 3807) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 321 time to evaluate : 0.867 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: A 56 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.7060 (m-10) REVERT: A 70 MET cc_start: 0.7939 (mmp) cc_final: 0.6930 (mtt) REVERT: A 137 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: A 139 TYR cc_start: 0.8480 (t80) cc_final: 0.8202 (t80) REVERT: A 407 PHE cc_start: 0.7748 (m-10) cc_final: 0.7443 (m-10) REVERT: A 504 MET cc_start: 0.8351 (mmp) cc_final: 0.7930 (mmp) REVERT: A 508 GLU cc_start: 0.8360 (tp30) cc_final: 0.7595 (pm20) REVERT: A 512 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7119 (mmp-170) REVERT: A 574 ARG cc_start: 0.8529 (mmp-170) cc_final: 0.8238 (tpt90) REVERT: A 671 GLU cc_start: 0.8494 (tp30) cc_final: 0.7853 (mt-10) REVERT: B 54 TYR cc_start: 0.5624 (OUTLIER) cc_final: 0.5288 (p90) REVERT: B 64 TRP cc_start: 0.7161 (m100) cc_final: 0.6764 (m100) REVERT: B 91 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7378 (ttm170) REVERT: B 130 TYR cc_start: 0.7814 (m-80) cc_final: 0.7103 (m-80) REVERT: B 243 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8218 (p0) REVERT: B 281 ASN cc_start: 0.8484 (m-40) cc_final: 0.8115 (m110) REVERT: B 346 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7987 (t70) REVERT: B 424 TYR cc_start: 0.8179 (m-80) cc_final: 0.7951 (m-80) REVERT: B 430 LEU cc_start: 0.7766 (tp) cc_final: 0.7356 (tp) REVERT: B 492 TYR cc_start: 0.7932 (m-80) cc_final: 0.7609 (m-10) REVERT: B 556 ASP cc_start: 0.8724 (t0) cc_final: 0.8467 (t0) REVERT: B 582 PHE cc_start: 0.8541 (t80) cc_final: 0.8117 (t80) REVERT: B 680 LEU cc_start: 0.8722 (mm) cc_final: 0.8372 (tp) REVERT: C 58 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7931 (tp) REVERT: C 66 LYS cc_start: 0.7789 (mttt) cc_final: 0.7046 (tmtt) REVERT: C 116 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7518 (m-10) REVERT: C 135 ILE cc_start: 0.7480 (mt) cc_final: 0.7058 (pt) REVERT: C 282 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8757 (mp) REVERT: C 319 PHE cc_start: 0.8558 (t80) cc_final: 0.7826 (t80) REVERT: C 323 MET cc_start: 0.8611 (mmm) cc_final: 0.8080 (mtp) REVERT: C 330 MET cc_start: 0.8376 (mmm) cc_final: 0.8176 (mmt) REVERT: C 341 SER cc_start: 0.8199 (m) cc_final: 0.7978 (p) REVERT: C 405 GLU cc_start: 0.8239 (tt0) cc_final: 0.7853 (tt0) REVERT: C 443 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: C 448 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7642 (tp) REVERT: C 506 GLU cc_start: 0.6528 (tt0) cc_final: 0.6213 (pt0) REVERT: C 569 HIS cc_start: 0.8501 (m170) cc_final: 0.7603 (m90) REVERT: C 603 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8732 (mt-10) REVERT: C 640 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7320 (p0) REVERT: C 642 ASP cc_start: 0.8082 (m-30) cc_final: 0.7831 (m-30) REVERT: C 652 MET cc_start: 0.5642 (tpp) cc_final: 0.5130 (tpp) REVERT: C 679 MET cc_start: 0.8554 (ttm) cc_final: 0.8195 (ttp) REVERT: D 66 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7518 (mtpp) REVERT: D 97 LEU cc_start: 0.5611 (OUTLIER) cc_final: 0.5173 (mm) REVERT: D 137 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: D 284 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: D 323 MET cc_start: 0.8169 (tpt) cc_final: 0.7908 (tpt) REVERT: D 325 ASP cc_start: 0.9038 (m-30) cc_final: 0.8688 (m-30) REVERT: D 401 ARG cc_start: 0.8329 (ttm170) cc_final: 0.7764 (tpt170) REVERT: D 482 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7828 (tttm) REVERT: D 497 ARG cc_start: 0.8799 (mtp-110) cc_final: 0.8449 (mtp85) REVERT: D 540 PHE cc_start: 0.9087 (t80) cc_final: 0.8808 (t80) REVERT: D 618 LYS cc_start: 0.9176 (tptp) cc_final: 0.8793 (ttpp) REVERT: D 631 PHE cc_start: 0.8837 (m-80) cc_final: 0.8581 (m-80) outliers start: 108 outliers final: 65 residues processed: 400 average time/residue: 0.1670 time to fit residues: 103.8624 Evaluate side-chains 377 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 294 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 101 ASP 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 125 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 183 GLU 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 226 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 48 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 165 optimal weight: 0.3980 chunk 183 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 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 = 0.4402 r_free = 0.4402 target = 0.161791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.108886 restraints weight = 46215.479| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.74 r_work: 0.3399 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22431 Z= 0.141 Angle : 0.626 16.753 30343 Z= 0.315 Chirality : 0.042 0.199 3372 Planarity : 0.004 0.044 3827 Dihedral : 5.586 58.557 3007 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.98 % Allowed : 25.49 % Favored : 70.52 % 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: 0.54 (0.16), residues: 2693 helix: 0.96 (0.12), residues: 1757 sheet: -2.34 (0.53), residues: 83 loop : -0.47 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 497 TYR 0.026 0.001 TYR C 65 PHE 0.034 0.002 PHE C 544 TRP 0.012 0.001 TRP B 75 HIS 0.009 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00311 (22431) covalent geometry : angle 0.62645 (30343) hydrogen bonds : bond 0.04360 ( 1326) hydrogen bonds : angle 4.70907 ( 3807) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 323 time to evaluate : 0.840 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 56 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.7014 (m-10) REVERT: A 70 MET cc_start: 0.7992 (mmp) cc_final: 0.6978 (mtt) REVERT: A 109 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8622 (mm) REVERT: A 137 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: A 139 TYR cc_start: 0.8466 (t80) cc_final: 0.8220 (t80) REVERT: A 407 PHE cc_start: 0.7727 (m-10) cc_final: 0.7411 (m-10) REVERT: A 434 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7031 (mp) REVERT: A 504 MET cc_start: 0.8387 (mmp) cc_final: 0.7978 (mmp) REVERT: A 508 GLU cc_start: 0.8296 (tp30) cc_final: 0.7601 (mp0) REVERT: A 609 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7482 (tm-30) REVERT: A 671 GLU cc_start: 0.8447 (tp30) cc_final: 0.7818 (mt-10) REVERT: B 54 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5329 (p90) REVERT: B 64 TRP cc_start: 0.7113 (m100) cc_final: 0.6728 (m100) REVERT: B 91 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7311 (ttm170) REVERT: B 127 ARG cc_start: 0.8331 (mmm160) cc_final: 0.7983 (mmt90) REVERT: B 130 TYR cc_start: 0.7854 (m-80) cc_final: 0.7213 (m-80) REVERT: B 183 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7627 (pp20) REVERT: B 243 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8187 (p0) REVERT: B 281 ASN cc_start: 0.8451 (m-40) cc_final: 0.8052 (m110) REVERT: B 346 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7963 (t70) REVERT: B 430 LEU cc_start: 0.7730 (tp) cc_final: 0.7306 (tp) REVERT: B 556 ASP cc_start: 0.8696 (t0) cc_final: 0.8425 (t0) REVERT: B 679 MET cc_start: 0.7474 (mmp) cc_final: 0.6826 (ttp) REVERT: B 680 LEU cc_start: 0.8714 (mm) cc_final: 0.8375 (tp) REVERT: C 58 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7985 (tp) REVERT: C 66 LYS cc_start: 0.7775 (mttt) cc_final: 0.7008 (tmtt) REVERT: C 116 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7444 (m-10) REVERT: C 135 ILE cc_start: 0.7530 (mt) cc_final: 0.7109 (pt) REVERT: C 282 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8744 (mp) REVERT: C 319 PHE cc_start: 0.8558 (t80) cc_final: 0.7763 (t80) REVERT: C 323 MET cc_start: 0.8626 (mmm) cc_final: 0.7961 (mtp) REVERT: C 330 MET cc_start: 0.8436 (mmm) cc_final: 0.8230 (mmt) REVERT: C 341 SER cc_start: 0.8240 (m) cc_final: 0.8009 (p) REVERT: C 405 GLU cc_start: 0.8250 (tt0) cc_final: 0.7773 (tt0) REVERT: C 407 PHE cc_start: 0.7611 (m-80) cc_final: 0.7178 (m-80) REVERT: C 473 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 497 ARG cc_start: 0.8931 (tpt90) cc_final: 0.8678 (mmm-85) REVERT: C 506 GLU cc_start: 0.6579 (tt0) cc_final: 0.6337 (pt0) REVERT: C 569 HIS cc_start: 0.8486 (m170) cc_final: 0.7570 (m90) REVERT: C 603 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8723 (mt-10) REVERT: C 640 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7311 (p0) REVERT: C 642 ASP cc_start: 0.8023 (m-30) cc_final: 0.7746 (m-30) REVERT: C 652 MET cc_start: 0.5566 (tpp) cc_final: 0.5066 (tpp) REVERT: C 679 MET cc_start: 0.8561 (ttm) cc_final: 0.8236 (ttp) REVERT: D 66 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7504 (mtpp) REVERT: D 97 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5241 (mm) REVERT: D 137 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: D 284 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: D 325 ASP cc_start: 0.9032 (m-30) cc_final: 0.8670 (m-30) REVERT: D 401 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7826 (tpt170) REVERT: D 482 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7794 (tttm) REVERT: D 497 ARG cc_start: 0.8798 (mtp-110) cc_final: 0.8542 (mtm110) REVERT: D 570 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8878 (tt) REVERT: D 583 LEU cc_start: 0.7945 (mm) cc_final: 0.7689 (mt) REVERT: D 618 LYS cc_start: 0.9167 (tptp) cc_final: 0.8785 (ttpp) REVERT: D 715 ASP cc_start: 0.8426 (m-30) cc_final: 0.8099 (t70) outliers start: 95 outliers final: 56 residues processed: 396 average time/residue: 0.1604 time to fit residues: 98.7983 Evaluate side-chains 367 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 101 ASP 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 133 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 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 = 0.4392 r_free = 0.4392 target = 0.160894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.107195 restraints weight = 46167.037| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.21 r_work: 0.3384 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22431 Z= 0.171 Angle : 0.648 16.372 30343 Z= 0.326 Chirality : 0.042 0.203 3372 Planarity : 0.004 0.061 3827 Dihedral : 5.593 58.217 3006 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.65 % Allowed : 26.12 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2693 helix: 0.95 (0.12), residues: 1760 sheet: -2.41 (0.53), residues: 84 loop : -0.45 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 552 TYR 0.031 0.002 TYR A 576 PHE 0.030 0.002 PHE D 425 TRP 0.012 0.001 TRP B 255 HIS 0.023 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00390 (22431) covalent geometry : angle 0.64846 (30343) hydrogen bonds : bond 0.04382 ( 1326) hydrogen bonds : angle 4.73358 ( 3807) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 301 time to evaluate : 0.908 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 56 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.7054 (m-10) REVERT: A 70 MET cc_start: 0.7907 (mmp) cc_final: 0.6889 (mtt) REVERT: A 109 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8663 (mm) REVERT: A 137 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: A 139 TYR cc_start: 0.8494 (t80) cc_final: 0.8259 (t80) REVERT: A 504 MET cc_start: 0.8419 (mmp) cc_final: 0.7964 (mmp) REVERT: A 508 GLU cc_start: 0.8266 (tp30) cc_final: 0.7584 (mp0) REVERT: A 671 GLU cc_start: 0.8449 (tp30) cc_final: 0.7829 (mt-10) REVERT: B 54 TYR cc_start: 0.5610 (OUTLIER) cc_final: 0.5333 (p90) REVERT: B 64 TRP cc_start: 0.7113 (m100) cc_final: 0.6738 (m100) REVERT: B 91 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: B 127 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7913 (mpt180) REVERT: B 130 TYR cc_start: 0.7855 (m-80) cc_final: 0.7287 (m-80) REVERT: B 243 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8187 (p0) REVERT: B 281 ASN cc_start: 0.8536 (m-40) cc_final: 0.8160 (m110) REVERT: B 346 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.7953 (t70) REVERT: B 377 TYR cc_start: 0.8293 (m-10) cc_final: 0.7862 (m-10) REVERT: B 430 LEU cc_start: 0.7731 (tp) cc_final: 0.7292 (tp) REVERT: B 556 ASP cc_start: 0.8697 (t0) cc_final: 0.8429 (t0) REVERT: B 679 MET cc_start: 0.7515 (mmp) cc_final: 0.6817 (ttp) REVERT: C 58 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7980 (tp) REVERT: C 66 LYS cc_start: 0.7776 (mttt) cc_final: 0.6994 (tmtt) REVERT: C 116 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: C 135 ILE cc_start: 0.7507 (mt) cc_final: 0.7081 (pt) REVERT: C 282 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8744 (mp) REVERT: C 319 PHE cc_start: 0.8567 (t80) cc_final: 0.7784 (t80) REVERT: C 323 MET cc_start: 0.8602 (mmm) cc_final: 0.7943 (mtp) REVERT: C 330 MET cc_start: 0.8417 (mmm) cc_final: 0.8205 (mmt) REVERT: C 341 SER cc_start: 0.8217 (m) cc_final: 0.7994 (p) REVERT: C 443 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6939 (mm-30) REVERT: C 473 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6660 (mm-30) REVERT: C 552 ARG cc_start: 0.7286 (mmt-90) cc_final: 0.6918 (mmt-90) REVERT: C 569 HIS cc_start: 0.8463 (m170) cc_final: 0.7529 (m90) REVERT: C 603 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8718 (mt-10) REVERT: C 640 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7334 (p0) REVERT: C 642 ASP cc_start: 0.7999 (m-30) cc_final: 0.7729 (m-30) REVERT: C 652 MET cc_start: 0.5553 (tpp) cc_final: 0.5067 (tpp) REVERT: C 679 MET cc_start: 0.8574 (ttm) cc_final: 0.8248 (ttp) REVERT: C 707 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8410 (mppt) REVERT: D 66 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7491 (mtpp) REVERT: D 97 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5344 (mm) REVERT: D 137 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: D 284 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 323 MET cc_start: 0.8189 (tpt) cc_final: 0.7938 (tpt) REVERT: D 325 ASP cc_start: 0.9040 (m-30) cc_final: 0.8661 (m-30) REVERT: D 401 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7806 (tpt170) REVERT: D 482 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7830 (tttm) REVERT: D 497 ARG cc_start: 0.8791 (mtp-110) cc_final: 0.8464 (mtm110) REVERT: D 570 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8858 (tt) REVERT: D 583 LEU cc_start: 0.7949 (mm) cc_final: 0.7683 (mt) REVERT: D 618 LYS cc_start: 0.9166 (tptp) cc_final: 0.8783 (ttpp) REVERT: D 631 PHE cc_start: 0.8831 (m-80) cc_final: 0.8600 (m-80) REVERT: D 715 ASP cc_start: 0.8431 (m-30) cc_final: 0.8104 (t70) outliers start: 87 outliers final: 58 residues processed: 368 average time/residue: 0.1506 time to fit residues: 86.2736 Evaluate side-chains 369 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 ASP 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 125 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 577 GLU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 207 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 chunk 253 optimal weight: 40.0000 chunk 200 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.161559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106568 restraints weight = 46420.888| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.73 r_work: 0.3421 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22431 Z= 0.159 Angle : 0.650 16.436 30343 Z= 0.325 Chirality : 0.042 0.226 3372 Planarity : 0.004 0.046 3827 Dihedral : 5.579 58.020 3004 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.82 % Allowed : 25.83 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.16), residues: 2693 helix: 0.96 (0.12), residues: 1755 sheet: -2.38 (0.53), residues: 84 loop : -0.44 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 574 TYR 0.039 0.001 TYR A 576 PHE 0.038 0.002 PHE C 544 TRP 0.011 0.001 TRP B 75 HIS 0.020 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00361 (22431) covalent geometry : angle 0.64953 (30343) hydrogen bonds : bond 0.04367 ( 1326) hydrogen bonds : angle 4.71323 ( 3807) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 300 time to evaluate : 0.870 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 56 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: A 70 MET cc_start: 0.7852 (mmp) cc_final: 0.6948 (mtt) REVERT: A 109 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8566 (mm) REVERT: A 137 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: A 434 LEU cc_start: 0.7220 (mp) cc_final: 0.6808 (mp) REVERT: A 504 MET cc_start: 0.8370 (mmp) cc_final: 0.7908 (mmp) REVERT: A 508 GLU cc_start: 0.8221 (tp30) cc_final: 0.7548 (mp0) REVERT: A 671 GLU cc_start: 0.8479 (tp30) cc_final: 0.7879 (mt-10) REVERT: B 54 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.5468 (p90) REVERT: B 64 TRP cc_start: 0.7031 (m100) cc_final: 0.6732 (m100) REVERT: B 91 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: B 127 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7965 (mpt180) REVERT: B 130 TYR cc_start: 0.7843 (m-80) cc_final: 0.7323 (m-80) REVERT: B 183 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7541 (pp20) REVERT: B 243 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8154 (p0) REVERT: B 281 ASN cc_start: 0.8334 (m-40) cc_final: 0.8113 (m110) REVERT: B 346 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.7976 (t70) REVERT: B 377 TYR cc_start: 0.8308 (m-10) cc_final: 0.7842 (m-10) REVERT: B 430 LEU cc_start: 0.7792 (tp) cc_final: 0.7512 (tp) REVERT: B 556 ASP cc_start: 0.8684 (t0) cc_final: 0.8453 (t0) REVERT: B 679 MET cc_start: 0.7646 (mmp) cc_final: 0.6935 (ttp) REVERT: C 58 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8023 (tp) REVERT: C 66 LYS cc_start: 0.7896 (mttt) cc_final: 0.7114 (tmtt) REVERT: C 116 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: C 135 ILE cc_start: 0.7558 (mt) cc_final: 0.7133 (pt) REVERT: C 210 TYR cc_start: 0.8082 (t80) cc_final: 0.7855 (t80) REVERT: C 282 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8661 (mp) REVERT: C 319 PHE cc_start: 0.8555 (t80) cc_final: 0.7783 (t80) REVERT: C 323 MET cc_start: 0.8677 (mmm) cc_final: 0.8029 (mtp) REVERT: C 330 MET cc_start: 0.8455 (mmm) cc_final: 0.8180 (mmt) REVERT: C 341 SER cc_start: 0.8250 (m) cc_final: 0.8027 (p) REVERT: C 405 GLU cc_start: 0.8260 (tt0) cc_final: 0.7839 (tt0) REVERT: C 443 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6920 (mm-30) REVERT: C 473 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6667 (mm-30) REVERT: C 552 ARG cc_start: 0.7402 (mmt-90) cc_final: 0.7076 (mmt-90) REVERT: C 569 HIS cc_start: 0.8432 (m170) cc_final: 0.7510 (m90) REVERT: C 582 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7716 (t80) REVERT: C 603 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8724 (mt-10) REVERT: C 640 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7328 (p0) REVERT: C 642 ASP cc_start: 0.7948 (m-30) cc_final: 0.7653 (m-30) REVERT: C 652 MET cc_start: 0.5509 (tpp) cc_final: 0.5035 (tpp) REVERT: C 679 MET cc_start: 0.8590 (ttm) cc_final: 0.8252 (ttp) REVERT: C 707 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8395 (mppt) REVERT: D 66 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7567 (mtpp) REVERT: D 97 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5414 (mm) REVERT: D 137 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: D 284 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: D 323 MET cc_start: 0.8279 (tpt) cc_final: 0.8043 (tpt) REVERT: D 325 ASP cc_start: 0.9069 (m-30) cc_final: 0.8684 (m-30) REVERT: D 401 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7846 (tpt170) REVERT: D 482 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7858 (tttm) REVERT: D 497 ARG cc_start: 0.8776 (mtp-110) cc_final: 0.8447 (mtm110) REVERT: D 570 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8905 (tt) REVERT: D 583 LEU cc_start: 0.7927 (mm) cc_final: 0.7637 (mt) REVERT: D 618 LYS cc_start: 0.9160 (tptp) cc_final: 0.8798 (ttpp) REVERT: D 631 PHE cc_start: 0.8834 (m-80) cc_final: 0.8595 (m-80) REVERT: D 715 ASP cc_start: 0.8440 (m-30) cc_final: 0.8085 (t70) outliers start: 91 outliers final: 60 residues processed: 369 average time/residue: 0.1710 time to fit residues: 97.2172 Evaluate side-chains 374 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 293 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 101 ASP 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 125 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 650 SER Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 GLU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 476 HIS Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 137 PHE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 482 LYS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 544 PHE Chi-restraints excluded: chain D residue 570 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 86 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 237 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.162598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110954 restraints weight = 46395.550| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.55 r_work: 0.3437 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22431 Z= 0.136 Angle : 0.643 16.077 30343 Z= 0.321 Chirality : 0.041 0.203 3372 Planarity : 0.004 0.046 3827 Dihedral : 5.528 58.498 3004 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.61 % Allowed : 25.91 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.16), residues: 2693 helix: 1.01 (0.12), residues: 1759 sheet: -2.33 (0.54), residues: 83 loop : -0.33 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 497 TYR 0.034 0.001 TYR A 139 PHE 0.030 0.002 PHE A 582 TRP 0.012 0.001 TRP B 75 HIS 0.018 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00301 (22431) covalent geometry : angle 0.64342 (30343) hydrogen bonds : bond 0.04289 ( 1326) hydrogen bonds : angle 4.63257 ( 3807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9757.15 seconds wall clock time: 166 minutes 52.62 seconds (10012.62 seconds total)