Starting phenix.real_space_refine on Sun Aug 24 20:29:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9la1_62916/08_2025/9la1_62916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9la1_62916/08_2025/9la1_62916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9la1_62916/08_2025/9la1_62916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9la1_62916/08_2025/9la1_62916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9la1_62916/08_2025/9la1_62916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9la1_62916/08_2025/9la1_62916.map" } resolution = 3.15 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= 0.018 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 14234 2.51 5 N 3655 2.21 5 O 3951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21940 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: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} 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: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5482 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 20, 'TRANS': 654} Time building chain proxies: 5.16, per 1000 atoms: 0.24 Number of scatterers: 21940 At special positions: 0 Unit cell: (124.504, 124.504, 182.816, 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 3951 8.00 N 3655 7.00 C 14234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 885.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 12 sheets defined 69.8% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 62 through 89 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 116 removed outlier: 3.554A pdb=" N ASP A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.515A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.627A pdb=" N ARG A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 195 through 226 removed outlier: 4.087A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.592A 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 312 Processing helix chain 'A' and resid 314 through 333 Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.656A pdb=" N LEU A 361 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 383 through 388 removed outlier: 6.008A pdb=" N LEU A 386 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.880A pdb=" N ILE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 518 through 542 removed outlier: 3.611A pdb=" N ILE A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 566 through 574 removed outlier: 4.025A pdb=" N LEU A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 587 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.764A pdb=" N LEU A 615 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 663 through 672 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'B' and resid 62 through 89 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 97 through 116 removed outlier: 4.060A pdb=" N VAL B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 143 through 152 removed outlier: 3.777A pdb=" N ASP B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.810A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 195 through 226 removed outlier: 4.201A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.841A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 4.787A 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 282 through 313 removed outlier: 3.574A pdb=" N GLY B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 334 Processing helix chain 'B' and resid 336 through 354 Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.667A pdb=" N VAL B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 365 through 383 Proline residue: B 379 - end of helix removed outlier: 3.684A pdb=" N LYS B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 455 through 462 Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 492 through 506 removed outlier: 4.371A pdb=" N GLU B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 541 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 576 through 587 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 Processing helix chain 'B' and resid 640 through 650 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 674 through 684 Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 706 through 721 Processing helix chain 'C' and resid 62 through 89 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 116 removed outlier: 4.513A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 195 through 225 Processing helix chain 'C' and resid 227 through 234 removed outlier: 3.779A pdb=" N GLU C 231 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 4.545A 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: 3.599A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 336 through 354 Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.583A pdb=" N LEU C 361 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 377 Processing helix chain 'C' and resid 377 through 384 removed outlier: 3.667A pdb=" N LYS C 383 " --> pdb=" O PRO C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 455 through 462 Processing helix chain 'C' and resid 482 through 490 Processing helix chain 'C' and resid 492 through 510 Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 527 through 542 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 556 through 560 removed outlier: 3.564A pdb=" N LYS C 559 " --> pdb=" O ASP C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 575 Processing helix chain 'C' and resid 576 through 586 Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 627 through 639 Processing helix chain 'C' and resid 640 through 651 Processing helix chain 'C' and resid 663 through 672 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 696 through 705 Processing helix chain 'C' and resid 706 through 724 Processing helix chain 'D' and resid 62 through 89 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 97 through 117 removed outlier: 3.611A pdb=" N ASP D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 107 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.135A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 164 through 169' Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 197 through 225 removed outlier: 3.555A pdb=" N LYS D 203 " --> pdb=" O THR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 233 removed outlier: 4.391A pdb=" N GLY D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 313 removed outlier: 4.249A 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 Processing helix chain 'D' and resid 357 through 362 removed outlier: 3.973A pdb=" N LEU D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 357 through 362' Processing helix chain 'D' and resid 365 through 383 removed outlier: 4.287A pdb=" N LEU D 378 " --> pdb=" O GLN D 374 " (cutoff:3.500A) Proline residue: D 379 - end of helix removed outlier: 3.687A pdb=" N LYS D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 401 Processing helix chain 'D' and resid 455 through 462 removed outlier: 3.637A pdb=" N ILE D 459 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 492 Processing helix chain 'D' and resid 492 through 510 removed outlier: 3.522A pdb=" N GLY D 496 " --> pdb=" O TYR D 492 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER D 509 " --> pdb=" O GLU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 515 Processing helix chain 'D' and resid 517 through 527 removed outlier: 4.368A pdb=" N VAL D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 542 removed outlier: 3.512A pdb=" N LEU D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 566 through 575 removed outlier: 3.715A pdb=" N LEU D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 586 Processing helix chain 'D' and resid 599 through 608 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 684 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.706A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.390A pdb=" N HIS A 476 " --> pdb=" O CYS A 427 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.606A pdb=" N VAL A 469 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 433 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR A 446 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.769A 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 407 removed outlier: 6.635A pdb=" N HIS B 476 " --> pdb=" O CYS B 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 412 through 414 removed outlier: 6.726A pdb=" N VAL B 412 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 471 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 414 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 120 through 122 Processing sheet with id=AA8, first strand: chain 'C' and resid 402 through 407 removed outlier: 6.515A pdb=" N HIS C 476 " --> pdb=" O CYS C 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.856A pdb=" N VAL C 412 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 471 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 414 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 120 through 122 Processing sheet with id=AB2, first strand: chain 'D' and resid 403 through 407 removed outlier: 3.509A pdb=" N CYS D 475 " --> pdb=" O PHE D 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 431 through 433 1336 hydrogen bonds defined for protein. 3828 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: 3.72 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5254 1.33 - 1.45: 4823 1.45 - 1.57: 12223 1.57 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 22456 Sorted by residual: bond pdb=" N ILE D 723 " pdb=" CA ILE D 723 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N VAL D 280 " pdb=" CA VAL D 280 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N LYS A 595 " pdb=" CA LYS A 595 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.56e+00 bond pdb=" N ILE D 236 " pdb=" CA ILE D 236 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.38e+00 bond pdb=" N ILE C 524 " pdb=" CA ILE C 524 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.30e+00 ... (remaining 22451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 29142 2.07 - 4.14: 1103 4.14 - 6.22: 105 6.22 - 8.29: 22 8.29 - 10.36: 7 Bond angle restraints: 30379 Sorted by residual: angle pdb=" N TYR D 355 " pdb=" CA TYR D 355 " pdb=" C TYR D 355 " ideal model delta sigma weight residual 112.38 106.49 5.89 1.22e+00 6.72e-01 2.33e+01 angle pdb=" N TRP C 693 " pdb=" CA TRP C 693 " pdb=" C TRP C 693 " ideal model delta sigma weight residual 113.55 107.76 5.79 1.26e+00 6.30e-01 2.11e+01 angle pdb=" CB LYS A 507 " pdb=" CG LYS A 507 " pdb=" CD LYS A 507 " ideal model delta sigma weight residual 111.30 121.66 -10.36 2.30e+00 1.89e-01 2.03e+01 angle pdb=" N THR D 358 " pdb=" CA THR D 358 " pdb=" C THR D 358 " ideal model delta sigma weight residual 112.87 107.89 4.98 1.20e+00 6.94e-01 1.72e+01 angle pdb=" N VAL D 687 " pdb=" CA VAL D 687 " pdb=" C VAL D 687 " ideal model delta sigma weight residual 112.83 108.74 4.09 9.90e-01 1.02e+00 1.71e+01 ... (remaining 30374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11672 17.96 - 35.93: 1208 35.93 - 53.89: 318 53.89 - 71.86: 99 71.86 - 89.82: 6 Dihedral angle restraints: 13303 sinusoidal: 5396 harmonic: 7907 Sorted by residual: dihedral pdb=" CA VAL D 272 " pdb=" C VAL D 272 " pdb=" N GLY D 273 " pdb=" CA GLY D 273 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA MET B 652 " pdb=" C MET B 652 " pdb=" N ASN B 653 " pdb=" CA ASN B 653 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP B 627 " pdb=" CB ASP B 627 " pdb=" CG ASP B 627 " pdb=" OD1 ASP B 627 " ideal model delta sinusoidal sigma weight residual -30.00 -92.20 62.20 1 2.00e+01 2.50e-03 1.28e+01 ... (remaining 13300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2749 0.065 - 0.130: 543 0.130 - 0.195: 63 0.195 - 0.261: 20 0.261 - 0.326: 1 Chirality restraints: 3376 Sorted by residual: chirality pdb=" CB VAL D 435 " pdb=" CA VAL D 435 " pdb=" CG1 VAL D 435 " pdb=" CG2 VAL D 435 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ILE B 277 " pdb=" N ILE B 277 " pdb=" C ILE B 277 " pdb=" CB ILE B 277 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 3373 not shown) Planarity restraints: 3831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 75 " -0.029 2.00e-02 2.50e+03 2.80e-02 1.96e+01 pdb=" CG TRP D 75 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP D 75 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP D 75 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 75 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 75 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 75 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 75 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 75 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP D 75 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 152 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO D 153 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 484 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C SER A 484 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 484 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 485 " 0.014 2.00e-02 2.50e+03 ... (remaining 3828 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2377 2.74 - 3.28: 24873 3.28 - 3.82: 39649 3.82 - 4.36: 48970 4.36 - 4.90: 77006 Nonbonded interactions: 192875 Sorted by model distance: nonbonded pdb=" O PHE D 90 " pdb=" NH2 ARG D 168 " model vdw 2.201 3.120 nonbonded pdb=" OH TYR A 126 " pdb=" OD2 ASP D 352 " model vdw 2.207 3.040 nonbonded pdb=" O TRP A 255 " pdb=" OG1 THR A 259 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASP C 658 " pdb=" N ARG C 662 " model vdw 2.213 3.120 nonbonded pdb=" NE2 HIS D 569 " pdb=" O LEU D 592 " model vdw 2.224 3.120 ... (remaining 192870 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 51 through 725) selection = (chain 'B' and resid 51 through 725) selection = (chain 'C' and resid 51 through 725) selection = chain 'D' } 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.470 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.062 22456 Z= 0.363 Angle : 0.864 10.358 30379 Z= 0.537 Chirality : 0.054 0.326 3376 Planarity : 0.006 0.092 3831 Dihedral : 16.119 89.822 8231 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.10 % Allowed : 20.14 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2695 helix: 0.10 (0.12), residues: 1697 sheet: -0.83 (0.51), residues: 72 loop : -0.20 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 646 TYR 0.036 0.002 TYR B 562 PHE 0.030 0.003 PHE D 108 TRP 0.074 0.003 TRP D 75 HIS 0.015 0.002 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00627 (22456) covalent geometry : angle 0.86370 (30379) hydrogen bonds : bond 0.13725 ( 1336) hydrogen bonds : angle 6.65778 ( 3828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 495 time to evaluate : 0.838 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: A 61 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8678 (tmmt) REVERT: A 168 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7652 (ttp80) REVERT: A 210 TYR cc_start: 0.7470 (t80) cc_final: 0.7265 (t80) REVERT: A 320 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8224 (mmm160) REVERT: A 323 MET cc_start: 0.8834 (tpt) cc_final: 0.8539 (tpp) REVERT: A 348 ARG cc_start: 0.7295 (ttt180) cc_final: 0.7047 (ttt180) REVERT: A 421 ASP cc_start: 0.7878 (p0) cc_final: 0.7494 (p0) REVERT: A 523 HIS cc_start: 0.8555 (m-70) cc_final: 0.7780 (t-170) REVERT: A 598 HIS cc_start: 0.7118 (m-70) cc_final: 0.6607 (m-70) REVERT: A 676 MET cc_start: 0.8267 (mmt) cc_final: 0.7955 (ttt) REVERT: A 695 ASN cc_start: 0.4785 (OUTLIER) cc_final: 0.4104 (t0) REVERT: B 96 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.7609 (tmt170) REVERT: B 131 LYS cc_start: 0.8517 (tppt) cc_final: 0.8277 (ttmt) REVERT: B 272 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.7601 (p) REVERT: B 281 ASN cc_start: 0.7231 (t0) cc_final: 0.6908 (t0) REVERT: B 296 MET cc_start: 0.8909 (ttp) cc_final: 0.8643 (ttt) REVERT: B 408 LEU cc_start: 0.8131 (tt) cc_final: 0.7851 (pp) REVERT: B 477 LEU cc_start: 0.8248 (mp) cc_final: 0.7879 (mt) REVERT: B 482 LYS cc_start: 0.9199 (tttm) cc_final: 0.8907 (tptp) REVERT: B 577 GLU cc_start: 0.8511 (pt0) cc_final: 0.8292 (mm-30) REVERT: B 643 PHE cc_start: 0.8426 (t80) cc_final: 0.8208 (t80) REVERT: B 679 MET cc_start: 0.8849 (mtm) cc_final: 0.8637 (pmm) REVERT: B 711 LYS cc_start: 0.9385 (tttt) cc_final: 0.8983 (tppt) REVERT: B 714 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7850 (tm-30) REVERT: C 72 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8222 (tp) REVERT: C 96 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.7632 (tpt170) REVERT: C 101 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6252 (p0) REVERT: C 371 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8798 (mtmm) REVERT: C 380 TYR cc_start: 0.7872 (m-80) cc_final: 0.7457 (m-10) REVERT: C 411 GLU cc_start: 0.6940 (mp0) cc_final: 0.6666 (mp0) REVERT: C 418 ASN cc_start: 0.7436 (t0) cc_final: 0.7220 (t0) REVERT: C 421 ASP cc_start: 0.8476 (p0) cc_final: 0.7486 (t0) REVERT: C 456 ASP cc_start: 0.7786 (t70) cc_final: 0.7436 (t0) REVERT: C 592 LEU cc_start: 0.8312 (tp) cc_final: 0.8064 (mt) REVERT: C 630 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8074 (t0) REVERT: C 708 LYS cc_start: 0.7730 (ptmt) cc_final: 0.7439 (ptpp) REVERT: D 64 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.6431 (m100) REVERT: D 233 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7595 (t80) REVERT: D 253 ASP cc_start: 0.6543 (OUTLIER) cc_final: 0.6342 (t0) REVERT: D 320 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8404 (mmm160) REVERT: D 322 LYS cc_start: 0.7073 (pttt) cc_final: 0.6681 (mttp) REVERT: D 534 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8335 (pttp) REVERT: D 568 LEU cc_start: 0.8546 (tp) cc_final: 0.8122 (mt) REVERT: D 676 MET cc_start: 0.8470 (mtm) cc_final: 0.8214 (mtt) outliers start: 74 outliers final: 30 residues processed: 550 average time/residue: 0.1710 time to fit residues: 142.2476 Evaluate side-chains 364 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 274 TYR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 630 ASN Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 64 TRP Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 630 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 115 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 695 ASN B 502 ASN B 653 ASN B 718 ASN C 59 HIS C 62 ASN C 105 GLN C 143 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN ** C 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN D 62 ASN D 115 GLN D 350 GLN D 451 HIS D 527 GLN D 695 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.164772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118177 restraints weight = 39682.650| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.66 r_work: 0.3484 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22456 Z= 0.183 Angle : 0.648 9.344 30379 Z= 0.340 Chirality : 0.044 0.327 3376 Planarity : 0.005 0.059 3831 Dihedral : 6.611 59.389 3058 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.19 % Allowed : 20.18 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2695 helix: 0.76 (0.12), residues: 1729 sheet: -1.06 (0.48), residues: 78 loop : 0.22 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 187 TYR 0.022 0.002 TYR B 78 PHE 0.031 0.002 PHE A 108 TRP 0.030 0.002 TRP D 75 HIS 0.018 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00401 (22456) covalent geometry : angle 0.64785 (30379) hydrogen bonds : bond 0.05112 ( 1336) hydrogen bonds : angle 5.16272 ( 3828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 382 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8659 (tmmt) REVERT: A 194 ILE cc_start: 0.8146 (mm) cc_final: 0.7790 (mp) REVERT: A 348 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6959 (ttt180) REVERT: A 421 ASP cc_start: 0.7955 (p0) cc_final: 0.7573 (p0) REVERT: A 523 HIS cc_start: 0.8613 (m-70) cc_final: 0.7956 (t-170) REVERT: B 96 ARG cc_start: 0.8655 (ttm-80) cc_final: 0.7564 (tmt170) REVERT: B 121 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7846 (mtp180) REVERT: B 131 LYS cc_start: 0.8392 (tppt) cc_final: 0.8173 (ttmt) REVERT: B 189 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7596 (mm-30) REVERT: B 196 TYR cc_start: 0.7383 (t80) cc_final: 0.6866 (t80) REVERT: B 206 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7534 (t80) REVERT: B 210 TYR cc_start: 0.6931 (t80) cc_final: 0.5702 (t80) REVERT: B 281 ASN cc_start: 0.7197 (t0) cc_final: 0.6906 (t0) REVERT: B 320 ARG cc_start: 0.8220 (ttp-170) cc_final: 0.7852 (tpt170) REVERT: B 406 TYR cc_start: 0.7630 (m-80) cc_final: 0.7210 (m-80) REVERT: B 416 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.6389 (pm20) REVERT: B 477 LEU cc_start: 0.8322 (mp) cc_final: 0.8042 (mt) REVERT: B 482 LYS cc_start: 0.9062 (tttm) cc_final: 0.8794 (tptp) REVERT: B 643 PHE cc_start: 0.8390 (t80) cc_final: 0.8106 (t80) REVERT: B 692 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.5047 (ttm170) REVERT: C 96 ARG cc_start: 0.8310 (ttt-90) cc_final: 0.7542 (tpt170) REVERT: C 101 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6459 (p0) REVERT: C 154 TRP cc_start: 0.8724 (m100) cc_final: 0.8425 (m100) REVERT: C 164 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6364 (m-70) REVERT: C 421 ASP cc_start: 0.8340 (p0) cc_final: 0.7535 (t0) REVERT: C 547 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7859 (pt) REVERT: D 64 TRP cc_start: 0.7373 (m-90) cc_final: 0.6463 (m100) REVERT: D 254 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8325 (tp) REVERT: D 568 LEU cc_start: 0.8566 (tp) cc_final: 0.8156 (mt) outliers start: 100 outliers final: 52 residues processed: 447 average time/residue: 0.1509 time to fit residues: 105.2294 Evaluate side-chains 364 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 304 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 274 TYR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 164 HIS Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 427 CYS Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 622 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 560 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 224 optimal weight: 0.5980 chunk 223 optimal weight: 0.7980 chunk 201 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN C 51 HIS C 59 HIS ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS C 418 ASN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.165209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.114886 restraints weight = 39439.843| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.96 r_work: 0.3508 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22456 Z= 0.147 Angle : 0.586 9.900 30379 Z= 0.307 Chirality : 0.041 0.213 3376 Planarity : 0.004 0.056 3831 Dihedral : 5.711 59.885 3022 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.85 % Allowed : 19.89 % Favored : 76.26 % 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: 0.94 (0.16), residues: 2695 helix: 0.97 (0.12), residues: 1733 sheet: -1.05 (0.48), residues: 77 loop : 0.33 (0.23), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 479 TYR 0.020 0.002 TYR B 492 PHE 0.028 0.002 PHE C 540 TRP 0.022 0.001 TRP D 75 HIS 0.012 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00314 (22456) covalent geometry : angle 0.58608 (30379) hydrogen bonds : bond 0.04678 ( 1336) hydrogen bonds : angle 4.87386 ( 3828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 355 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8777 (mtpp) cc_final: 0.8559 (tmmt) REVERT: A 323 MET cc_start: 0.8733 (tpt) cc_final: 0.8482 (tpp) REVERT: A 348 ARG cc_start: 0.7331 (ttt180) cc_final: 0.6981 (ttt180) REVERT: A 421 ASP cc_start: 0.7917 (p0) cc_final: 0.7578 (p0) REVERT: A 483 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8360 (tp40) REVERT: A 520 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9032 (pt) REVERT: A 523 HIS cc_start: 0.8666 (m-70) cc_final: 0.8055 (t-170) REVERT: A 561 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 624 ASN cc_start: 0.7372 (m-40) cc_final: 0.6945 (m-40) REVERT: B 96 ARG cc_start: 0.8639 (ttm-80) cc_final: 0.7460 (tmt170) REVERT: B 189 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7507 (mm-30) REVERT: B 196 TYR cc_start: 0.7269 (t80) cc_final: 0.6824 (t80) REVERT: B 206 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7385 (t80) REVERT: B 210 TYR cc_start: 0.6772 (t80) cc_final: 0.5525 (t80) REVERT: B 320 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7861 (tpt170) REVERT: B 406 TYR cc_start: 0.7510 (m-80) cc_final: 0.7174 (m-80) REVERT: B 482 LYS cc_start: 0.9069 (tttm) cc_final: 0.8787 (tptp) REVERT: B 643 PHE cc_start: 0.8412 (t80) cc_final: 0.8159 (t80) REVERT: B 665 LEU cc_start: 0.8164 (tp) cc_final: 0.7959 (tp) REVERT: B 692 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5195 (ttm170) REVERT: C 72 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7814 (tp) REVERT: C 96 ARG cc_start: 0.8116 (ttt-90) cc_final: 0.7404 (tpt170) REVERT: C 101 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6431 (p0) REVERT: C 154 TRP cc_start: 0.8686 (m100) cc_final: 0.8458 (m100) REVERT: C 295 ASP cc_start: 0.8327 (t0) cc_final: 0.8084 (t0) REVERT: C 364 ILE cc_start: 0.8492 (mp) cc_final: 0.8206 (tt) REVERT: C 421 ASP cc_start: 0.8186 (p0) cc_final: 0.7460 (t0) REVERT: C 714 GLU cc_start: 0.8722 (tp30) cc_final: 0.8500 (mt-10) REVERT: D 64 TRP cc_start: 0.7308 (m-90) cc_final: 0.6436 (m100) REVERT: D 96 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7518 (tmt170) REVERT: D 140 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7942 (mt) REVERT: D 254 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 568 LEU cc_start: 0.8579 (tp) cc_final: 0.8192 (mt) REVERT: D 603 GLU cc_start: 0.8901 (tp30) cc_final: 0.8603 (tp30) REVERT: D 676 MET cc_start: 0.8465 (mtm) cc_final: 0.7976 (mtt) outliers start: 92 outliers final: 47 residues processed: 422 average time/residue: 0.1486 time to fit residues: 99.1697 Evaluate side-chains 356 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 274 TYR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 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 = 0.4276 r_free = 0.4276 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109521 restraints weight = 40021.505| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.49 r_work: 0.3372 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22456 Z= 0.264 Angle : 0.652 12.557 30379 Z= 0.345 Chirality : 0.045 0.238 3376 Planarity : 0.005 0.048 3831 Dihedral : 5.859 58.650 3021 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.74 % Allowed : 19.26 % Favored : 75.00 % 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: 0.76 (0.16), residues: 2695 helix: 0.78 (0.12), residues: 1735 sheet: -1.12 (0.46), residues: 78 loop : 0.40 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 479 TYR 0.028 0.002 TYR C 380 PHE 0.035 0.002 PHE D 287 TRP 0.021 0.002 TRP D 75 HIS 0.009 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00613 (22456) covalent geometry : angle 0.65178 (30379) hydrogen bonds : bond 0.04857 ( 1336) hydrogen bonds : angle 4.95931 ( 3828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 316 time to evaluate : 0.758 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: A 61 LYS cc_start: 0.8979 (mtpp) cc_final: 0.8681 (tmmt) REVERT: A 269 MET cc_start: 0.8882 (ttp) cc_final: 0.8639 (ttp) REVERT: A 323 MET cc_start: 0.8788 (tpt) cc_final: 0.8563 (tpp) REVERT: A 348 ARG cc_start: 0.7432 (ttt180) cc_final: 0.7017 (ttt180) REVERT: A 421 ASP cc_start: 0.7980 (p0) cc_final: 0.7639 (p0) REVERT: A 523 HIS cc_start: 0.8757 (m-70) cc_final: 0.8128 (t-170) REVERT: B 121 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7623 (mtp180) REVERT: B 189 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7736 (mm-30) REVERT: B 196 TYR cc_start: 0.7456 (t80) cc_final: 0.7167 (t80) REVERT: B 206 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 210 TYR cc_start: 0.6881 (t80) cc_final: 0.5518 (t80) REVERT: B 320 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7750 (tpt170) REVERT: B 406 TYR cc_start: 0.7518 (m-80) cc_final: 0.7192 (m-80) REVERT: B 643 PHE cc_start: 0.8531 (t80) cc_final: 0.8199 (t80) REVERT: B 692 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.5032 (ttm170) REVERT: B 709 LEU cc_start: 0.7880 (tp) cc_final: 0.7563 (tp) REVERT: C 72 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8229 (tp) REVERT: C 101 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6621 (p0) REVERT: C 154 TRP cc_start: 0.8868 (m100) cc_final: 0.8641 (m100) REVERT: C 281 ASN cc_start: 0.8616 (m110) cc_final: 0.8055 (m-40) REVERT: C 364 ILE cc_start: 0.8372 (mp) cc_final: 0.8058 (tt) REVERT: C 421 ASP cc_start: 0.8347 (p0) cc_final: 0.7568 (t0) REVERT: C 546 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8185 (tm-30) REVERT: C 547 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7807 (pt) REVERT: C 592 LEU cc_start: 0.8398 (tp) cc_final: 0.8164 (pt) REVERT: C 714 GLU cc_start: 0.8745 (tp30) cc_final: 0.8419 (mt-10) REVERT: D 64 TRP cc_start: 0.7474 (m-90) cc_final: 0.6732 (m100) REVERT: D 96 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7471 (ptt180) REVERT: D 109 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8599 (tp) REVERT: D 140 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7921 (mt) REVERT: D 530 GLU cc_start: 0.7312 (tt0) cc_final: 0.6980 (pm20) REVERT: D 562 TYR cc_start: 0.7313 (p90) cc_final: 0.7029 (p90) REVERT: D 568 LEU cc_start: 0.8559 (tp) cc_final: 0.8169 (mt) REVERT: D 676 MET cc_start: 0.8367 (mtm) cc_final: 0.8107 (mtt) outliers start: 137 outliers final: 88 residues processed: 417 average time/residue: 0.1302 time to fit residues: 88.1996 Evaluate side-chains 387 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 290 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 692 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 164 HIS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 560 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 19 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 197 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 219 optimal weight: 0.5980 chunk 221 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 265 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.163511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.111910 restraints weight = 39711.108| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.01 r_work: 0.3485 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22456 Z= 0.128 Angle : 0.568 12.203 30379 Z= 0.294 Chirality : 0.040 0.294 3376 Planarity : 0.004 0.045 3831 Dihedral : 5.555 58.416 3017 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 3.81 % Allowed : 20.98 % Favored : 75.21 % 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: 1.10 (0.16), residues: 2695 helix: 1.08 (0.12), residues: 1734 sheet: -0.93 (0.47), residues: 78 loop : 0.42 (0.23), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 177 TYR 0.021 0.001 TYR B 492 PHE 0.030 0.002 PHE C 544 TRP 0.016 0.001 TRP C 68 HIS 0.007 0.001 HIS C 569 Details of bonding type rmsd covalent geometry : bond 0.00275 (22456) covalent geometry : angle 0.56841 (30379) hydrogen bonds : bond 0.04317 ( 1336) hydrogen bonds : angle 4.68170 ( 3828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 339 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8624 (tmmt) REVERT: A 281 ASN cc_start: 0.7568 (t0) cc_final: 0.7238 (m-40) REVERT: A 323 MET cc_start: 0.8798 (tpt) cc_final: 0.8591 (tpp) REVERT: A 348 ARG cc_start: 0.7354 (ttt180) cc_final: 0.6911 (ttt180) REVERT: A 421 ASP cc_start: 0.8000 (p0) cc_final: 0.7695 (p0) REVERT: A 521 VAL cc_start: 0.8594 (t) cc_final: 0.8375 (p) REVERT: A 523 HIS cc_start: 0.8623 (m-70) cc_final: 0.8059 (t-170) REVERT: A 646 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7668 (mtm180) REVERT: B 189 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7524 (mm-30) REVERT: B 196 TYR cc_start: 0.7233 (t80) cc_final: 0.6857 (t80) REVERT: B 206 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7409 (t80) REVERT: B 210 TYR cc_start: 0.6792 (t80) cc_final: 0.5535 (t80) REVERT: B 320 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.7856 (tpt170) REVERT: B 401 ARG cc_start: 0.8532 (mtt90) cc_final: 0.8319 (mtm-85) REVERT: B 406 TYR cc_start: 0.7439 (m-80) cc_final: 0.7114 (m-80) REVERT: B 477 LEU cc_start: 0.8251 (mp) cc_final: 0.7918 (mt) REVERT: B 643 PHE cc_start: 0.8538 (t80) cc_final: 0.8194 (t80) REVERT: B 709 LEU cc_start: 0.7962 (tp) cc_final: 0.7631 (tp) REVERT: C 101 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6508 (p0) REVERT: C 154 TRP cc_start: 0.8742 (m100) cc_final: 0.8274 (m100) REVERT: C 295 ASP cc_start: 0.8306 (t70) cc_final: 0.8092 (t0) REVERT: C 421 ASP cc_start: 0.8275 (p0) cc_final: 0.7511 (t0) REVERT: C 547 LEU cc_start: 0.8021 (pt) cc_final: 0.7723 (pt) REVERT: C 714 GLU cc_start: 0.8741 (tp30) cc_final: 0.8411 (mt-10) REVERT: D 64 TRP cc_start: 0.7445 (m-90) cc_final: 0.6611 (m100) REVERT: D 96 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7544 (tmt170) REVERT: D 140 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7899 (mt) REVERT: D 173 ILE cc_start: 0.9181 (mm) cc_final: 0.8976 (mm) REVERT: D 527 GLN cc_start: 0.7227 (tp-100) cc_final: 0.6601 (tp-100) REVERT: D 530 GLU cc_start: 0.7250 (tt0) cc_final: 0.6950 (pm20) REVERT: D 562 TYR cc_start: 0.7217 (p90) cc_final: 0.7004 (p90) REVERT: D 568 LEU cc_start: 0.8521 (tp) cc_final: 0.8207 (mt) REVERT: D 676 MET cc_start: 0.8323 (mtm) cc_final: 0.7913 (mtt) outliers start: 91 outliers final: 63 residues processed: 399 average time/residue: 0.1397 time to fit residues: 89.8539 Evaluate side-chains 360 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 293 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 164 HIS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 480 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 148 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 141 optimal weight: 0.0020 chunk 189 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN C 305 ASN ** C 483 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 = 0.4295 r_free = 0.4295 target = 0.163251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.112002 restraints weight = 39712.314| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.98 r_work: 0.3471 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22456 Z= 0.131 Angle : 0.587 14.411 30379 Z= 0.298 Chirality : 0.040 0.254 3376 Planarity : 0.004 0.044 3831 Dihedral : 5.210 58.358 3011 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 3.81 % Allowed : 22.53 % Favored : 73.66 % 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: 1.19 (0.16), residues: 2695 helix: 1.14 (0.12), residues: 1740 sheet: -0.72 (0.49), residues: 77 loop : 0.45 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 177 TYR 0.020 0.001 TYR B 492 PHE 0.048 0.002 PHE B 674 TRP 0.018 0.001 TRP B 693 HIS 0.006 0.001 HIS C 569 Details of bonding type rmsd covalent geometry : bond 0.00283 (22456) covalent geometry : angle 0.58705 (30379) hydrogen bonds : bond 0.04206 ( 1336) hydrogen bonds : angle 4.58083 ( 3828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 317 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ARG cc_start: 0.7299 (ttt180) cc_final: 0.6805 (ttt180) REVERT: A 421 ASP cc_start: 0.7943 (p0) cc_final: 0.7667 (p0) REVERT: A 521 VAL cc_start: 0.8597 (t) cc_final: 0.8376 (p) REVERT: A 523 HIS cc_start: 0.8562 (m-70) cc_final: 0.8042 (t-170) REVERT: A 646 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7634 (mtm180) REVERT: B 189 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7551 (mm-30) REVERT: B 196 TYR cc_start: 0.7265 (t80) cc_final: 0.6891 (t80) REVERT: B 206 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7395 (t80) REVERT: B 210 TYR cc_start: 0.6767 (t80) cc_final: 0.5623 (t80) REVERT: B 320 ARG cc_start: 0.8284 (ttp-170) cc_final: 0.7996 (tpt90) REVERT: B 351 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5691 (t80) REVERT: B 401 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8281 (mtm-85) REVERT: B 406 TYR cc_start: 0.7431 (m-80) cc_final: 0.7119 (m-80) REVERT: B 477 LEU cc_start: 0.8258 (mp) cc_final: 0.7971 (mt) REVERT: B 577 GLU cc_start: 0.8605 (pt0) cc_final: 0.8398 (mm-30) REVERT: B 596 PHE cc_start: 0.7097 (m-80) cc_final: 0.6868 (m-80) REVERT: B 618 LYS cc_start: 0.8815 (tttm) cc_final: 0.8539 (ptmm) REVERT: B 623 PHE cc_start: 0.7334 (m-10) cc_final: 0.6766 (m-10) REVERT: B 643 PHE cc_start: 0.8539 (t80) cc_final: 0.8236 (t80) REVERT: B 709 LEU cc_start: 0.7843 (tp) cc_final: 0.7501 (tp) REVERT: C 72 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7796 (tp) REVERT: C 96 ARG cc_start: 0.8103 (ttt-90) cc_final: 0.7303 (tpt170) REVERT: C 101 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6627 (p0) REVERT: C 154 TRP cc_start: 0.8662 (m100) cc_final: 0.8441 (m100) REVERT: C 295 ASP cc_start: 0.8112 (t70) cc_final: 0.7907 (t0) REVERT: C 421 ASP cc_start: 0.8229 (p0) cc_final: 0.7432 (t0) REVERT: C 714 GLU cc_start: 0.8748 (tp30) cc_final: 0.8409 (mt-10) REVERT: D 64 TRP cc_start: 0.7437 (m-90) cc_final: 0.6630 (m100) REVERT: D 96 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7440 (ptt180) REVERT: D 140 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7936 (mt) REVERT: D 175 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8730 (mp) REVERT: D 351 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5233 (t80) REVERT: D 527 GLN cc_start: 0.7264 (tp-100) cc_final: 0.6427 (tp-100) REVERT: D 530 GLU cc_start: 0.7184 (tt0) cc_final: 0.6894 (pm20) REVERT: D 556 ASP cc_start: 0.5820 (t70) cc_final: 0.5139 (t0) REVERT: D 562 TYR cc_start: 0.7226 (p90) cc_final: 0.7021 (p90) REVERT: D 568 LEU cc_start: 0.8575 (tp) cc_final: 0.8231 (mt) REVERT: D 676 MET cc_start: 0.8232 (mtm) cc_final: 0.7935 (mtt) outliers start: 91 outliers final: 60 residues processed: 378 average time/residue: 0.1509 time to fit residues: 92.1191 Evaluate side-chains 364 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 296 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 596 PHE Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 566 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 17 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 231 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.162253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112359 restraints weight = 39680.568| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.61 r_work: 0.3422 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22456 Z= 0.159 Angle : 0.608 12.451 30379 Z= 0.307 Chirality : 0.041 0.261 3376 Planarity : 0.004 0.041 3831 Dihedral : 5.226 58.552 3011 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 3.94 % Allowed : 22.74 % Favored : 73.32 % 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: 1.22 (0.16), residues: 2695 helix: 1.16 (0.12), residues: 1742 sheet: -0.61 (0.49), residues: 77 loop : 0.47 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 470 TYR 0.018 0.001 TYR B 492 PHE 0.043 0.002 PHE C 387 TRP 0.011 0.001 TRP B 693 HIS 0.007 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00362 (22456) covalent geometry : angle 0.60842 (30379) hydrogen bonds : bond 0.04206 ( 1336) hydrogen bonds : angle 4.57039 ( 3828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 303 time to evaluate : 0.937 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: A 140 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8924 (mp) REVERT: A 339 LEU cc_start: 0.8866 (pt) cc_final: 0.8336 (mt) REVERT: A 348 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6724 (ttt180) REVERT: A 421 ASP cc_start: 0.7950 (p0) cc_final: 0.7668 (p0) REVERT: A 521 VAL cc_start: 0.8576 (t) cc_final: 0.8366 (p) REVERT: A 523 HIS cc_start: 0.8622 (m-70) cc_final: 0.8080 (t-170) REVERT: A 550 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 189 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7637 (mm-30) REVERT: B 196 TYR cc_start: 0.7431 (t80) cc_final: 0.6994 (t80) REVERT: B 206 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7448 (t80) REVERT: B 210 TYR cc_start: 0.6911 (t80) cc_final: 0.5803 (t80) REVERT: B 320 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.7914 (tpt90) REVERT: B 351 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.5729 (t80) REVERT: B 360 MET cc_start: 0.8188 (mmm) cc_final: 0.7834 (ppp) REVERT: B 401 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8313 (mtm-85) REVERT: B 406 TYR cc_start: 0.7517 (m-80) cc_final: 0.7207 (m-80) REVERT: B 477 LEU cc_start: 0.8292 (mp) cc_final: 0.8003 (mt) REVERT: B 618 LYS cc_start: 0.8854 (tttm) cc_final: 0.8587 (ptmm) REVERT: B 623 PHE cc_start: 0.7090 (m-10) cc_final: 0.6668 (m-10) REVERT: B 652 MET cc_start: 0.5380 (ptp) cc_final: 0.2560 (tpp) REVERT: B 676 MET cc_start: 0.8579 (mtp) cc_final: 0.8258 (mmm) REVERT: B 709 LEU cc_start: 0.7932 (tp) cc_final: 0.7642 (tp) REVERT: C 72 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.7866 (tp) REVERT: C 96 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7289 (tpt170) REVERT: C 154 TRP cc_start: 0.8734 (m100) cc_final: 0.8472 (m100) REVERT: C 202 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8618 (mp) REVERT: C 421 ASP cc_start: 0.8335 (p0) cc_final: 0.7487 (t0) REVERT: C 644 LEU cc_start: 0.9041 (tt) cc_final: 0.8625 (tp) REVERT: C 714 GLU cc_start: 0.8725 (tp30) cc_final: 0.8419 (mt-10) REVERT: D 64 TRP cc_start: 0.7453 (m-90) cc_final: 0.6638 (m100) REVERT: D 96 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7452 (ptt180) REVERT: D 140 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7937 (mt) REVERT: D 175 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8761 (mp) REVERT: D 351 TYR cc_start: 0.6280 (OUTLIER) cc_final: 0.5431 (t80) REVERT: D 437 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7067 (mmmm) REVERT: D 527 GLN cc_start: 0.7210 (tp-100) cc_final: 0.6362 (tp-100) REVERT: D 530 GLU cc_start: 0.7160 (tt0) cc_final: 0.6844 (pm20) REVERT: D 556 ASP cc_start: 0.5873 (t70) cc_final: 0.5257 (t0) REVERT: D 562 TYR cc_start: 0.7314 (p90) cc_final: 0.7075 (p90) REVERT: D 568 LEU cc_start: 0.8571 (tp) cc_final: 0.8237 (mt) REVERT: D 676 MET cc_start: 0.8243 (mtm) cc_final: 0.7986 (mtt) outliers start: 94 outliers final: 65 residues processed: 368 average time/residue: 0.1562 time to fit residues: 91.8164 Evaluate side-chains 376 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 300 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 91 ARG 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 319 PHE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 596 PHE Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 480 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 263 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS C 362 GLN ** C 483 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 = 0.4270 r_free = 0.4270 target = 0.161085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110608 restraints weight = 39546.151| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.58 r_work: 0.3389 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22456 Z= 0.189 Angle : 0.643 20.763 30379 Z= 0.322 Chirality : 0.042 0.301 3376 Planarity : 0.004 0.042 3831 Dihedral : 5.264 58.802 3009 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Rotamer: Outliers : 4.06 % Allowed : 22.57 % Favored : 73.37 % 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: 1.19 (0.16), residues: 2695 helix: 1.12 (0.12), residues: 1738 sheet: -0.55 (0.50), residues: 77 loop : 0.48 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 646 TYR 0.018 0.002 TYR B 492 PHE 0.035 0.002 PHE C 387 TRP 0.012 0.001 TRP D 75 HIS 0.006 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00437 (22456) covalent geometry : angle 0.64307 (30379) hydrogen bonds : bond 0.04308 ( 1336) hydrogen bonds : angle 4.61647 ( 3828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 315 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8965 (mp) REVERT: A 348 ARG cc_start: 0.7134 (ttt180) cc_final: 0.6603 (ttt180) REVERT: A 421 ASP cc_start: 0.7958 (p0) cc_final: 0.7686 (p0) REVERT: A 523 HIS cc_start: 0.8646 (m-70) cc_final: 0.8090 (t-170) REVERT: A 550 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7567 (mm) REVERT: A 646 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7486 (ttm170) REVERT: B 189 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7689 (mm-30) REVERT: B 196 TYR cc_start: 0.7541 (t80) cc_final: 0.6785 (t80) REVERT: B 206 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7536 (t80) REVERT: B 210 TYR cc_start: 0.6969 (t80) cc_final: 0.5823 (t80) REVERT: B 320 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.7886 (tpt90) REVERT: B 351 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5749 (t80) REVERT: B 360 MET cc_start: 0.8191 (mmm) cc_final: 0.7946 (ppp) REVERT: B 361 LEU cc_start: 0.8307 (mt) cc_final: 0.8015 (mt) REVERT: B 406 TYR cc_start: 0.7496 (m-80) cc_final: 0.7176 (m-80) REVERT: B 477 LEU cc_start: 0.8327 (mp) cc_final: 0.8002 (mt) REVERT: B 618 LYS cc_start: 0.8879 (tttm) cc_final: 0.8632 (ptmm) REVERT: B 623 PHE cc_start: 0.7221 (m-10) cc_final: 0.6804 (m-10) REVERT: B 652 MET cc_start: 0.5439 (ptp) cc_final: 0.2409 (tpp) REVERT: B 676 MET cc_start: 0.8631 (mtp) cc_final: 0.8291 (mmm) REVERT: B 709 LEU cc_start: 0.7949 (tp) cc_final: 0.7651 (tp) REVERT: B 711 LYS cc_start: 0.9195 (tttt) cc_final: 0.8980 (ptpp) REVERT: C 72 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.7892 (tp) REVERT: C 154 TRP cc_start: 0.8775 (m100) cc_final: 0.8471 (m100) REVERT: C 202 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8659 (mp) REVERT: C 421 ASP cc_start: 0.8342 (p0) cc_final: 0.7496 (t0) REVERT: C 679 MET cc_start: 0.8606 (ptm) cc_final: 0.8360 (ppp) REVERT: C 714 GLU cc_start: 0.8706 (tp30) cc_final: 0.8416 (mt-10) REVERT: D 64 TRP cc_start: 0.7491 (m-90) cc_final: 0.6680 (m100) REVERT: D 96 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7557 (tmt170) REVERT: D 140 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7933 (mt) REVERT: D 175 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8764 (mp) REVERT: D 351 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5470 (t80) REVERT: D 497 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8247 (mtm110) REVERT: D 527 GLN cc_start: 0.7162 (tp-100) cc_final: 0.6644 (tp-100) REVERT: D 530 GLU cc_start: 0.7189 (tt0) cc_final: 0.6849 (pm20) REVERT: D 556 ASP cc_start: 0.5897 (t70) cc_final: 0.5284 (t0) REVERT: D 568 LEU cc_start: 0.8595 (tp) cc_final: 0.8264 (mt) outliers start: 97 outliers final: 71 residues processed: 383 average time/residue: 0.1461 time to fit residues: 89.0574 Evaluate side-chains 379 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 298 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 596 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 56 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 228 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 122 optimal weight: 0.2980 chunk 249 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN C 354 HIS C 362 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.161709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112774 restraints weight = 39802.095| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.64 r_work: 0.3401 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22456 Z= 0.179 Angle : 0.641 12.664 30379 Z= 0.324 Chirality : 0.042 0.240 3376 Planarity : 0.004 0.041 3831 Dihedral : 5.202 58.954 3005 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 4.06 % Allowed : 22.32 % Favored : 73.62 % 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: 1.17 (0.16), residues: 2695 helix: 1.11 (0.12), residues: 1737 sheet: -0.46 (0.50), residues: 77 loop : 0.46 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 470 TYR 0.027 0.002 TYR A 576 PHE 0.042 0.002 PHE C 387 TRP 0.012 0.001 TRP D 75 HIS 0.006 0.001 HIS B 569 Details of bonding type rmsd covalent geometry : bond 0.00412 (22456) covalent geometry : angle 0.64126 (30379) hydrogen bonds : bond 0.04304 ( 1336) hydrogen bonds : angle 4.63357 ( 3828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 308 time to evaluate : 0.888 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: A 140 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8981 (mp) REVERT: A 193 ARG cc_start: 0.7653 (mmt-90) cc_final: 0.7451 (mpt180) REVERT: A 348 ARG cc_start: 0.7122 (ttt180) cc_final: 0.6583 (ttt180) REVERT: A 421 ASP cc_start: 0.7989 (p0) cc_final: 0.7701 (p0) REVERT: A 523 HIS cc_start: 0.8669 (m-70) cc_final: 0.8122 (t-170) REVERT: B 189 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7654 (mm-30) REVERT: B 206 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7489 (t80) REVERT: B 210 TYR cc_start: 0.6909 (t80) cc_final: 0.5747 (t80) REVERT: B 320 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.7829 (tpt90) REVERT: B 351 TYR cc_start: 0.6285 (OUTLIER) cc_final: 0.5667 (t80) REVERT: B 361 LEU cc_start: 0.8350 (mt) cc_final: 0.8078 (mt) REVERT: B 406 TYR cc_start: 0.7485 (m-80) cc_final: 0.7162 (m-80) REVERT: B 477 LEU cc_start: 0.8308 (mp) cc_final: 0.7976 (mt) REVERT: B 618 LYS cc_start: 0.8871 (tttm) cc_final: 0.8655 (ptmm) REVERT: B 623 PHE cc_start: 0.7247 (m-10) cc_final: 0.6896 (m-10) REVERT: B 652 MET cc_start: 0.5352 (ptp) cc_final: 0.4908 (ppp) REVERT: B 676 MET cc_start: 0.8644 (mtp) cc_final: 0.8343 (mmm) REVERT: B 711 LYS cc_start: 0.9181 (tttt) cc_final: 0.8976 (ptpp) REVERT: C 72 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7902 (tp) REVERT: C 202 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 330 MET cc_start: 0.8482 (mtm) cc_final: 0.8173 (mtm) REVERT: C 421 ASP cc_start: 0.8361 (p0) cc_final: 0.7511 (t0) REVERT: C 588 VAL cc_start: 0.7021 (t) cc_final: 0.6683 (p) REVERT: C 671 GLU cc_start: 0.9218 (tt0) cc_final: 0.8898 (pp20) REVERT: C 714 GLU cc_start: 0.8704 (tp30) cc_final: 0.8410 (mt-10) REVERT: D 64 TRP cc_start: 0.7469 (m-90) cc_final: 0.6665 (m100) REVERT: D 96 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7519 (ptt180) REVERT: D 140 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7921 (mt) REVERT: D 175 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8777 (mp) REVERT: D 351 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.5524 (t80) REVERT: D 497 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8269 (mtm110) REVERT: D 527 GLN cc_start: 0.7128 (tp-100) cc_final: 0.6601 (tp-100) REVERT: D 530 GLU cc_start: 0.7212 (tt0) cc_final: 0.6851 (pm20) REVERT: D 556 ASP cc_start: 0.5951 (t70) cc_final: 0.5442 (t0) REVERT: D 568 LEU cc_start: 0.8592 (tp) cc_final: 0.8261 (mt) outliers start: 97 outliers final: 72 residues processed: 377 average time/residue: 0.1457 time to fit residues: 88.4125 Evaluate side-chains 377 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 296 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 596 PHE Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 666 HIS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 504 MET Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 181 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN B 653 ASN C 354 HIS C 362 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.163077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.111880 restraints weight = 39675.492| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.99 r_work: 0.3479 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22456 Z= 0.138 Angle : 0.637 12.538 30379 Z= 0.320 Chirality : 0.041 0.230 3376 Planarity : 0.004 0.041 3831 Dihedral : 5.150 59.204 3005 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 3.31 % Allowed : 23.28 % Favored : 73.41 % 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: 1.19 (0.16), residues: 2695 helix: 1.14 (0.12), residues: 1734 sheet: -0.63 (0.49), residues: 87 loop : 0.47 (0.23), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 470 TYR 0.023 0.001 TYR A 576 PHE 0.044 0.002 PHE C 544 TRP 0.013 0.001 TRP C 68 HIS 0.012 0.001 HIS C 666 Details of bonding type rmsd covalent geometry : bond 0.00306 (22456) covalent geometry : angle 0.63704 (30379) hydrogen bonds : bond 0.04190 ( 1336) hydrogen bonds : angle 4.57008 ( 3828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5390 Ramachandran restraints generated. 2695 Oldfield, 0 Emsley, 2695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 303 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8962 (mp) REVERT: A 210 TYR cc_start: 0.7143 (t80) cc_final: 0.6942 (t80) REVERT: A 348 ARG cc_start: 0.7066 (ttt180) cc_final: 0.6533 (ttt180) REVERT: A 421 ASP cc_start: 0.8008 (p0) cc_final: 0.7719 (p0) REVERT: A 523 HIS cc_start: 0.8605 (m-70) cc_final: 0.8082 (t-170) REVERT: B 189 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7515 (mm-30) REVERT: B 206 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 210 TYR cc_start: 0.6771 (t80) cc_final: 0.5630 (t80) REVERT: B 319 PHE cc_start: 0.8234 (t80) cc_final: 0.7933 (t80) REVERT: B 320 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.7749 (tpt90) REVERT: B 351 TYR cc_start: 0.6311 (OUTLIER) cc_final: 0.5658 (t80) REVERT: B 406 TYR cc_start: 0.7421 (m-80) cc_final: 0.7100 (m-80) REVERT: B 477 LEU cc_start: 0.8238 (mp) cc_final: 0.7928 (mt) REVERT: B 618 LYS cc_start: 0.8873 (tttm) cc_final: 0.8672 (ptmm) REVERT: B 623 PHE cc_start: 0.7184 (m-10) cc_final: 0.6894 (m-10) REVERT: B 676 MET cc_start: 0.8609 (mtp) cc_final: 0.8314 (mmm) REVERT: C 72 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.7769 (tp) REVERT: C 154 TRP cc_start: 0.8742 (m100) cc_final: 0.8438 (m100) REVERT: C 330 MET cc_start: 0.8387 (mtm) cc_final: 0.8175 (mtm) REVERT: C 421 ASP cc_start: 0.8301 (p0) cc_final: 0.7480 (t0) REVERT: C 671 GLU cc_start: 0.9255 (tt0) cc_final: 0.8894 (pp20) REVERT: C 714 GLU cc_start: 0.8708 (tp30) cc_final: 0.8399 (mt-10) REVERT: D 64 TRP cc_start: 0.7408 (m-90) cc_final: 0.6607 (m100) REVERT: D 96 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7509 (tmt170) REVERT: D 140 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7910 (mt) REVERT: D 175 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8738 (mp) REVERT: D 351 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5493 (t80) REVERT: D 465 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7938 (tp-100) REVERT: D 497 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8296 (mtm110) REVERT: D 527 GLN cc_start: 0.7092 (tp-100) cc_final: 0.6613 (tp-100) REVERT: D 530 GLU cc_start: 0.7163 (tt0) cc_final: 0.6810 (pm20) REVERT: D 556 ASP cc_start: 0.5855 (t70) cc_final: 0.5421 (t0) REVERT: D 568 LEU cc_start: 0.8533 (tp) cc_final: 0.8215 (mt) outliers start: 79 outliers final: 62 residues processed: 357 average time/residue: 0.1263 time to fit residues: 72.5734 Evaluate side-chains 361 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 291 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 596 PHE Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 666 HIS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 141 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 483 GLN C 354 HIS C 362 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.160632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111856 restraints weight = 39639.193| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.93 r_work: 0.3382 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22456 Z= 0.211 Angle : 0.685 13.285 30379 Z= 0.344 Chirality : 0.044 0.331 3376 Planarity : 0.004 0.043 3831 Dihedral : 5.221 59.626 3005 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 3.14 % Allowed : 23.74 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.15 (0.16), residues: 2695 helix: 1.06 (0.12), residues: 1737 sheet: -0.38 (0.51), residues: 77 loop : 0.52 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 470 TYR 0.023 0.002 TYR A 576 PHE 0.042 0.002 PHE C 387 TRP 0.013 0.002 TRP D 75 HIS 0.015 0.001 HIS C 666 Details of bonding type rmsd covalent geometry : bond 0.00493 (22456) covalent geometry : angle 0.68481 (30379) hydrogen bonds : bond 0.04365 ( 1336) hydrogen bonds : angle 4.66413 ( 3828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8624.17 seconds wall clock time: 147 minutes 40.92 seconds (8860.92 seconds total)