Starting phenix.real_space_refine on Sun May 18 04:33:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8or2_17115/05_2025/8or2_17115.cif Found real_map, /net/cci-nas-00/data/ceres_data/8or2_17115/05_2025/8or2_17115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8or2_17115/05_2025/8or2_17115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8or2_17115/05_2025/8or2_17115.map" model { file = "/net/cci-nas-00/data/ceres_data/8or2_17115/05_2025/8or2_17115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8or2_17115/05_2025/8or2_17115.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 99 5.16 5 C 10554 2.51 5 N 2816 2.21 5 O 3086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16558 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5651 Classifications: {'peptide': 689} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 677} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 8808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 8808 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 7 Chain: "F" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1365 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5876 SG CYS B 45 126.042 64.210 43.049 1.00 56.54 S ATOM 6171 SG CYS B 83 125.084 62.262 46.086 1.00 54.48 S ATOM 6100 SG CYS B 75 126.480 75.706 52.362 1.00 53.89 S ATOM 6267 SG CYS B 94 129.544 72.330 52.823 1.00 53.87 S ATOM 5943 SG CYS B 53 121.363 59.522 43.325 1.00 58.28 S ATOM 5966 SG CYS B 56 118.661 58.356 43.069 1.00 60.30 S ATOM 6050 SG CYS B 68 117.351 61.442 42.096 1.00 55.90 S Time building chain proxies: 9.61, per 1000 atoms: 0.58 Number of scatterers: 16558 At special positions: 0 Unit cell: (150.12, 133.92, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 99 16.00 O 3086 8.00 N 2816 7.00 C 10554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.27 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B4001 " pdb="ZN ZN B4001 " - pdb=" ND1 HIS B 80 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 45 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 83 " pdb=" ZN B4002 " pdb="ZN ZN B4002 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 94 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 75 " pdb=" ZN B4003 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 56 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 68 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 53 " 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3998 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 5 sheets defined 73.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.953A pdb=" N GLN A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.531A pdb=" N TYR A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 107 Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.756A pdb=" N ARG A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 191 removed outlier: 3.597A pdb=" N GLN A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 4.032A pdb=" N ILE A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.536A pdb=" N PHE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 255 removed outlier: 3.786A pdb=" N GLN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 279 removed outlier: 3.600A pdb=" N TYR A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.378A pdb=" N GLU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.564A pdb=" N GLU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.910A pdb=" N ARG A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 355 removed outlier: 3.643A pdb=" N CYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 385 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.900A pdb=" N ALA A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.861A pdb=" N LEU A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 481 through 496 removed outlier: 3.706A pdb=" N GLU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 525 Processing helix chain 'A' and resid 559 through 572 removed outlier: 3.604A pdb=" N TYR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 566 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 632 through 646 Processing helix chain 'A' and resid 690 through 722 removed outlier: 3.790A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.677A pdb=" N LEU A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 759 removed outlier: 3.776A pdb=" N LYS A 751 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS A 752 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.852A pdb=" N ASN B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.968A pdb=" N ASN B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.518A pdb=" N ARG C 23 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 36 Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 61 through 78 removed outlier: 3.893A pdb=" N GLY C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.742A pdb=" N SER C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 78 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.674A pdb=" N VAL C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 128 through 142 Processing helix chain 'C' and resid 148 through 165 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.860A pdb=" N MET C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 4.431A pdb=" N GLU C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 249 through 253 removed outlier: 4.050A pdb=" N LEU C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 270 through 285 removed outlier: 4.333A pdb=" N TYR C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 304 removed outlier: 3.556A pdb=" N VAL C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 removed outlier: 3.806A pdb=" N ARG C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL C 360 " --> pdb=" O CYS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 375 through 383 Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.633A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 443 removed outlier: 3.639A pdb=" N GLN C 431 " --> pdb=" O MET C 427 " (cutoff:3.500A) Proline residue: C 433 - end of helix removed outlier: 3.870A pdb=" N LYS C 437 " --> pdb=" O PRO C 433 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 438 " --> pdb=" O ASN C 434 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 441 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 465 Processing helix chain 'C' and resid 472 through 486 Proline residue: C 478 - end of helix Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'C' and resid 508 through 515 removed outlier: 6.121A pdb=" N GLN C 511 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N HIS C 514 " --> pdb=" O GLN C 511 " (cutoff:3.500A) Proline residue: C 515 - end of helix Processing helix chain 'C' and resid 516 through 529 Proline residue: C 522 - end of helix removed outlier: 3.548A pdb=" N GLY C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.518A pdb=" N LYS C 548 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 563 No H-bonds generated for 'chain 'C' and resid 561 through 563' Processing helix chain 'C' and resid 564 through 577 removed outlier: 4.197A pdb=" N ARG C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 600 Processing helix chain 'C' and resid 606 through 621 removed outlier: 4.700A pdb=" N ASN C 610 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 617 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 651 through 657 Processing helix chain 'C' and resid 658 through 660 No H-bonds generated for 'chain 'C' and resid 658 through 660' Processing helix chain 'C' and resid 663 through 681 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 723 Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.768A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 766 removed outlier: 3.829A pdb=" N SER C 753 " --> pdb=" O GLY C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 780 Processing helix chain 'C' and resid 792 through 810 Processing helix chain 'C' and resid 813 through 826 removed outlier: 3.858A pdb=" N VAL C 817 " --> pdb=" O GLU C 813 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 818 " --> pdb=" O GLY C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 846 Processing helix chain 'C' and resid 856 through 866 removed outlier: 3.588A pdb=" N VAL C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C 866 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 887 removed outlier: 3.603A pdb=" N VAL C 885 " --> pdb=" O GLY C 881 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY C 886 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 887 " --> pdb=" O ILE C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 Proline residue: C 893 - end of helix removed outlier: 3.725A pdb=" N THR C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 920 removed outlier: 3.873A pdb=" N HIS C 911 " --> pdb=" O TYR C 907 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 918 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 929 through 941 removed outlier: 4.365A pdb=" N GLU C 941 " --> pdb=" O LEU C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 959 Processing helix chain 'C' and resid 962 through 977 Proline residue: C 968 - end of helix removed outlier: 3.511A pdb=" N LEU C 974 " --> pdb=" O LEU C 970 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 975 " --> pdb=" O LYS C 971 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER C 976 " --> pdb=" O GLY C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 991 removed outlier: 3.871A pdb=" N PHE C 991 " --> pdb=" O THR C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1014 removed outlier: 4.248A pdb=" N GLY C1009 " --> pdb=" O LYS C1005 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP C1010 " --> pdb=" O ASN C1006 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C1011 " --> pdb=" O CYS C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1037 Processing helix chain 'C' and resid 1044 through 1057 Proline residue: C1050 - end of helix removed outlier: 3.938A pdb=" N LYS C1057 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1092 removed outlier: 3.662A pdb=" N ARG C1082 " --> pdb=" O GLY C1078 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1113 removed outlier: 3.620A pdb=" N ASN C1107 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N HIS C1108 " --> pdb=" O GLU C1104 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C1109 " --> pdb=" O PHE C1105 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1131 Processing helix chain 'C' and resid 1134 through 1140 removed outlier: 3.600A pdb=" N VAL C1138 " --> pdb=" O CYS C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1154 Proline residue: C1148 - end of helix Processing helix chain 'C' and resid 1162 through 1185 removed outlier: 3.596A pdb=" N PHE C1166 " --> pdb=" O VAL C1162 " (cutoff:3.500A) Processing helix chain 'C' and resid 1201 through 1204 Processing helix chain 'C' and resid 1205 through 1210 Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 99 through 109 removed outlier: 4.161A pdb=" N LEU F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 109 " --> pdb=" O ILE F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 Proline residue: F 142 - end of helix removed outlier: 3.859A pdb=" N GLU F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 166 removed outlier: 3.822A pdb=" N ASP F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN F 163 " --> pdb=" O GLN F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 removed outlier: 3.548A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 199 Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.709A pdb=" N TRP F 213 " --> pdb=" O PRO F 209 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU F 217 " --> pdb=" O TRP F 213 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP F 218 " --> pdb=" O ASN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 251 Proline residue: F 249 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 541 removed outlier: 6.686A pdb=" N SER A 536 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA B 31 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN A 538 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP B 33 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 540 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N TRP B 35 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL B 24 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 10.748A pdb=" N GLY A 588 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 12.651A pdb=" N LYS B 26 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N SER A 586 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 11.359A pdb=" N ASN B 28 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLN A 584 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 30 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 600 " --> pdb=" O VAL A 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 726 Processing sheet with id=AA3, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.691A pdb=" N ARG B 99 " --> pdb=" O CYS B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1063 through 1066 removed outlier: 3.727A pdb=" N VAL C1066 " --> pdb=" O HIS C1073 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS C1073 " --> pdb=" O VAL C1066 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2862 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: 5.22 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2763 1.28 - 1.41: 3876 1.41 - 1.54: 10033 1.54 - 1.68: 15 1.68 - 1.81: 148 Bond restraints: 16835 Sorted by residual: bond pdb=" C VAL A 724 " pdb=" O VAL A 724 " ideal model delta sigma weight residual 1.236 1.145 0.091 1.19e-02 7.06e+03 5.91e+01 bond pdb=" CA ILE A 755 " pdb=" C ILE A 755 " ideal model delta sigma weight residual 1.524 1.425 0.099 1.30e-02 5.92e+03 5.77e+01 bond pdb=" C ARG B 91 " pdb=" N GLN B 92 " ideal model delta sigma weight residual 1.333 1.450 -0.117 1.55e-02 4.16e+03 5.69e+01 bond pdb=" C LYS A 720 " pdb=" O LYS A 720 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.19e-02 7.06e+03 4.98e+01 bond pdb=" C PRO F 209 " pdb=" O PRO F 209 " ideal model delta sigma weight residual 1.233 1.151 0.082 1.18e-02 7.18e+03 4.87e+01 ... (remaining 16830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 22351 2.58 - 5.17: 305 5.17 - 7.75: 49 7.75 - 10.33: 16 10.33 - 12.92: 10 Bond angle restraints: 22731 Sorted by residual: angle pdb=" N ALA F 235 " pdb=" CA ALA F 235 " pdb=" C ALA F 235 " ideal model delta sigma weight residual 113.01 125.11 -12.10 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N VAL A 658 " pdb=" CA VAL A 658 " pdb=" C VAL A 658 " ideal model delta sigma weight residual 110.72 120.81 -10.09 1.01e+00 9.80e-01 9.99e+01 angle pdb=" N VAL F 238 " pdb=" CA VAL F 238 " pdb=" C VAL F 238 " ideal model delta sigma weight residual 112.98 125.45 -12.47 1.25e+00 6.40e-01 9.95e+01 angle pdb=" N SER C 17 " pdb=" CA SER C 17 " pdb=" C SER C 17 " ideal model delta sigma weight residual 112.54 124.11 -11.57 1.22e+00 6.72e-01 8.99e+01 angle pdb=" O GLN B 92 " pdb=" C GLN B 92 " pdb=" N VAL B 93 " ideal model delta sigma weight residual 122.46 109.60 12.86 1.37e+00 5.33e-01 8.82e+01 ... (remaining 22726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9213 17.99 - 35.98: 952 35.98 - 53.97: 158 53.97 - 71.96: 26 71.96 - 89.95: 14 Dihedral angle restraints: 10363 sinusoidal: 4245 harmonic: 6118 Sorted by residual: dihedral pdb=" N TYR A 772 " pdb=" C TYR A 772 " pdb=" CA TYR A 772 " pdb=" CB TYR A 772 " ideal model delta harmonic sigma weight residual 122.80 107.11 15.69 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C VAL F 238 " pdb=" N VAL F 238 " pdb=" CA VAL F 238 " pdb=" CB VAL F 238 " ideal model delta harmonic sigma weight residual -122.00 -137.16 15.16 0 2.50e+00 1.60e-01 3.68e+01 dihedral pdb=" N VAL F 238 " pdb=" C VAL F 238 " pdb=" CA VAL F 238 " pdb=" CB VAL F 238 " ideal model delta harmonic sigma weight residual 123.40 138.07 -14.67 0 2.50e+00 1.60e-01 3.45e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2583 0.139 - 0.278: 34 0.278 - 0.418: 13 0.418 - 0.557: 5 0.557 - 0.696: 6 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CA ALA F 235 " pdb=" N ALA F 235 " pdb=" C ALA F 235 " pdb=" CB ALA F 235 " both_signs ideal model delta sigma weight residual False 2.48 1.79 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA VAL F 238 " pdb=" N VAL F 238 " pdb=" C VAL F 238 " pdb=" CB VAL F 238 " both_signs ideal model delta sigma weight residual False 2.44 1.77 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA THR F 212 " pdb=" N THR F 212 " pdb=" C THR F 212 " pdb=" CB THR F 212 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2638 not shown) Planarity restraints: 2869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 772 " 0.075 2.00e-02 2.50e+03 3.81e-02 2.91e+01 pdb=" CG TYR A 772 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 772 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 772 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 772 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 772 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 772 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 772 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 681 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C ARG A 681 " 0.084 2.00e-02 2.50e+03 pdb=" O ARG A 681 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL A 682 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1060 " -0.024 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C LYS C1060 " 0.083 2.00e-02 2.50e+03 pdb=" O LYS C1060 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU C1061 " -0.028 2.00e-02 2.50e+03 ... (remaining 2866 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 52 2.42 - 3.04: 11075 3.04 - 3.66: 24143 3.66 - 4.28: 33845 4.28 - 4.90: 57547 Nonbonded interactions: 126662 Sorted by model distance: nonbonded pdb=" CB HIS A 727 " pdb=" OD1 ASP A 770 " model vdw 1.805 3.440 nonbonded pdb=" O ILE C 654 " pdb=" OG SER C 657 " model vdw 2.105 3.040 nonbonded pdb=" O PRO C 893 " pdb=" NE2 GLN C 897 " model vdw 2.125 3.120 nonbonded pdb=" O GLN A 463 " pdb=" OH TYR A 500 " model vdw 2.137 3.040 nonbonded pdb=" O THR C 624 " pdb=" OG1 THR C 628 " model vdw 2.139 3.040 ... (remaining 126657 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 0.010 Normalize map: mean=0, sd=1: 3.080 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 40.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 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 : 0.007 0.127 16844 Z= 0.461 Angle : 0.761 12.916 22731 Z= 0.486 Chirality : 0.058 0.696 2641 Planarity : 0.004 0.049 2869 Dihedral : 14.647 89.947 6365 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.24 % Allowed : 1.50 % Favored : 97.26 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 2032 helix: 2.50 (0.15), residues: 1388 sheet: -1.91 (1.31), residues: 12 loop : -1.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 213 HIS 0.004 0.000 HIS C 847 PHE 0.029 0.001 PHE C 24 TYR 0.075 0.002 TYR A 772 ARG 0.014 0.000 ARG A 764 Details of bonding type rmsd hydrogen bonds : bond 0.16105 ( 965) hydrogen bonds : angle 5.38273 ( 2862) metal coordination : bond 0.00359 ( 9) covalent geometry : bond 0.00717 (16835) covalent geometry : angle 0.76102 (22731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 341 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 GLU cc_start: 0.7052 (tp30) cc_final: 0.6822 (tp30) REVERT: A 518 ASN cc_start: 0.7411 (t0) cc_final: 0.7191 (t0) REVERT: A 655 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5359 (t0) REVERT: A 657 ASN cc_start: 0.6500 (OUTLIER) cc_final: 0.5299 (t0) REVERT: A 659 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5670 (m-30) REVERT: A 676 LYS cc_start: 0.6028 (mmmt) cc_final: 0.5682 (mmtt) REVERT: C 20 LYS cc_start: 0.7553 (tmtm) cc_final: 0.7315 (ttmt) REVERT: C 21 ASP cc_start: 0.6796 (m-30) cc_final: 0.6493 (m-30) REVERT: C 348 LYS cc_start: 0.6996 (ptpp) cc_final: 0.6734 (ptpp) REVERT: C 441 LYS cc_start: 0.7947 (mptt) cc_final: 0.7687 (mptt) REVERT: C 457 MET cc_start: 0.7055 (tpp) cc_final: 0.6606 (tpp) REVERT: C 834 ILE cc_start: 0.6783 (mp) cc_final: 0.6559 (mp) REVERT: C 890 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6896 (tm-30) REVERT: C 1106 LEU cc_start: 0.7687 (mp) cc_final: 0.6607 (tt) outliers start: 23 outliers final: 13 residues processed: 359 average time/residue: 0.3108 time to fit residues: 165.2358 Evaluate side-chains 335 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 319 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 PRO Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 657 ASN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 HIS C 848 HIS C1108 HIS F 159 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.155872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139380 restraints weight = 24693.731| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.87 r_work: 0.3782 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16844 Z= 0.206 Angle : 0.677 10.924 22731 Z= 0.346 Chirality : 0.043 0.165 2641 Planarity : 0.005 0.061 2869 Dihedral : 4.764 56.103 2247 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.61 % Allowed : 8.81 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2032 helix: 1.64 (0.14), residues: 1422 sheet: -1.84 (1.14), residues: 12 loop : -1.68 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 236 HIS 0.008 0.001 HIS A 476 PHE 0.027 0.002 PHE A 569 TYR 0.035 0.002 TYR A 377 ARG 0.009 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 965) hydrogen bonds : angle 3.95652 ( 2862) metal coordination : bond 0.00933 ( 9) covalent geometry : bond 0.00469 (16835) covalent geometry : angle 0.67661 (22731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 345 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.5793 (mmt) cc_final: 0.5340 (mmt) REVERT: A 204 VAL cc_start: 0.7949 (t) cc_final: 0.7510 (m) REVERT: A 209 VAL cc_start: 0.8185 (p) cc_final: 0.7895 (t) REVERT: A 518 ASN cc_start: 0.7683 (t0) cc_final: 0.7447 (t0) REVERT: A 643 LEU cc_start: 0.8003 (mm) cc_final: 0.7758 (mp) REVERT: A 676 LYS cc_start: 0.6626 (mmmt) cc_final: 0.6408 (mmtt) REVERT: B 47 ASN cc_start: 0.8329 (m110) cc_final: 0.8075 (m-40) REVERT: C 21 ASP cc_start: 0.7385 (m-30) cc_final: 0.7097 (m-30) REVERT: C 85 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7658 (mm-30) REVERT: C 156 ASP cc_start: 0.7776 (m-30) cc_final: 0.7559 (m-30) REVERT: C 691 ASP cc_start: 0.7918 (t0) cc_final: 0.7145 (t0) REVERT: C 695 ASP cc_start: 0.7560 (m-30) cc_final: 0.7103 (m-30) REVERT: C 743 ARG cc_start: 0.7185 (ptp90) cc_final: 0.6936 (ptp90) REVERT: C 890 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 1052 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7987 (tt) REVERT: C 1106 LEU cc_start: 0.7738 (mp) cc_final: 0.6725 (tt) REVERT: C 1121 MET cc_start: 0.6591 (mtp) cc_final: 0.6174 (mmm) REVERT: C 1142 LEU cc_start: 0.7804 (tt) cc_final: 0.7526 (tp) REVERT: F 208 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7523 (pp) REVERT: F 238 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7318 (t) outliers start: 30 outliers final: 14 residues processed: 361 average time/residue: 0.2957 time to fit residues: 155.8226 Evaluate side-chains 331 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 314 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 142 optimal weight: 0.4980 chunk 164 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN A 737 GLN C 511 GLN C 603 ASN C 847 HIS C1164 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.151520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.134968 restraints weight = 24225.174| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.85 r_work: 0.3727 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16844 Z= 0.163 Angle : 0.577 11.165 22731 Z= 0.295 Chirality : 0.039 0.158 2641 Planarity : 0.004 0.053 2869 Dihedral : 4.125 56.648 2228 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.04 % Allowed : 12.30 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2032 helix: 1.64 (0.14), residues: 1423 sheet: -1.69 (1.13), residues: 12 loop : -1.71 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 213 HIS 0.006 0.001 HIS A 476 PHE 0.025 0.002 PHE C 482 TYR 0.031 0.002 TYR C1117 ARG 0.006 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.05048 ( 965) hydrogen bonds : angle 3.77387 ( 2862) metal coordination : bond 0.00704 ( 9) covalent geometry : bond 0.00378 (16835) covalent geometry : angle 0.57742 (22731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 336 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.6139 (mmt) cc_final: 0.5528 (mmt) REVERT: A 125 ASP cc_start: 0.7424 (m-30) cc_final: 0.7214 (m-30) REVERT: A 143 HIS cc_start: 0.5766 (OUTLIER) cc_final: 0.5496 (m90) REVERT: A 204 VAL cc_start: 0.7917 (t) cc_final: 0.7512 (m) REVERT: A 209 VAL cc_start: 0.8417 (p) cc_final: 0.8116 (t) REVERT: A 377 TYR cc_start: 0.7479 (m-10) cc_final: 0.7271 (m-80) REVERT: A 397 LYS cc_start: 0.8456 (ptpp) cc_final: 0.8240 (ptpp) REVERT: A 518 ASN cc_start: 0.7644 (t0) cc_final: 0.7402 (t0) REVERT: A 643 LEU cc_start: 0.8029 (mm) cc_final: 0.7736 (mp) REVERT: A 645 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7874 (ttmm) REVERT: B 47 ASN cc_start: 0.8338 (m110) cc_final: 0.8064 (m-40) REVERT: C 20 LYS cc_start: 0.7514 (tmtm) cc_final: 0.7255 (ttmt) REVERT: C 21 ASP cc_start: 0.7283 (m-30) cc_final: 0.7059 (m-30) REVERT: C 156 ASP cc_start: 0.7796 (m-30) cc_final: 0.7544 (m-30) REVERT: C 457 MET cc_start: 0.7562 (tpp) cc_final: 0.7181 (tpp) REVERT: C 481 ILE cc_start: 0.7922 (mm) cc_final: 0.7636 (mt) REVERT: C 691 ASP cc_start: 0.7875 (t0) cc_final: 0.7137 (t0) REVERT: C 695 ASP cc_start: 0.7518 (m-30) cc_final: 0.6928 (m-30) REVERT: C 748 GLN cc_start: 0.7895 (pp30) cc_final: 0.7607 (pp30) REVERT: C 826 LYS cc_start: 0.7550 (mtpp) cc_final: 0.7249 (mtmm) REVERT: C 890 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7956 (tp30) REVERT: C 897 GLN cc_start: 0.7851 (mp10) cc_final: 0.7398 (tm-30) REVERT: C 907 TYR cc_start: 0.6740 (t80) cc_final: 0.6480 (t80) REVERT: C 909 LEU cc_start: 0.7900 (mp) cc_final: 0.7696 (mt) REVERT: C 957 LYS cc_start: 0.8293 (mmtp) cc_final: 0.8088 (mmtm) REVERT: C 1011 PHE cc_start: 0.7476 (m-80) cc_final: 0.7161 (m-80) REVERT: C 1017 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5314 (m-30) REVERT: C 1052 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8002 (tt) REVERT: C 1106 LEU cc_start: 0.7890 (mp) cc_final: 0.6957 (tt) REVERT: C 1121 MET cc_start: 0.6643 (mtp) cc_final: 0.6160 (mmm) REVERT: C 1142 LEU cc_start: 0.7859 (tt) cc_final: 0.7619 (tp) REVERT: C 1168 LYS cc_start: 0.7422 (mmmm) cc_final: 0.7063 (mtpp) REVERT: F 145 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6329 (mt-10) REVERT: F 208 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7603 (pp) REVERT: F 238 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7171 (t) outliers start: 38 outliers final: 26 residues processed: 355 average time/residue: 0.3018 time to fit residues: 156.8055 Evaluate side-chains 349 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 318 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 238 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 11 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 130 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 chunk 58 optimal weight: 0.0270 chunk 141 optimal weight: 0.6980 chunk 112 optimal weight: 0.0010 chunk 132 optimal weight: 0.6980 overall best weight: 0.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 610 ASN C 662 ASN C 847 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.154545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137906 restraints weight = 24229.180| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.89 r_work: 0.3782 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16844 Z= 0.112 Angle : 0.533 12.811 22731 Z= 0.268 Chirality : 0.037 0.164 2641 Planarity : 0.004 0.043 2869 Dihedral : 3.719 55.836 2225 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.26 % Allowed : 14.39 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 2032 helix: 1.81 (0.14), residues: 1426 sheet: -1.75 (1.18), residues: 12 loop : -1.65 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 213 HIS 0.003 0.000 HIS C 247 PHE 0.029 0.001 PHE A 569 TYR 0.024 0.001 TYR C1117 ARG 0.003 0.000 ARG C 137 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 965) hydrogen bonds : angle 3.60861 ( 2862) metal coordination : bond 0.00280 ( 9) covalent geometry : bond 0.00237 (16835) covalent geometry : angle 0.53327 (22731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.6106 (mmt) cc_final: 0.5474 (mmt) REVERT: A 125 ASP cc_start: 0.7412 (m-30) cc_final: 0.7109 (m-30) REVERT: A 143 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.5426 (m90) REVERT: A 204 VAL cc_start: 0.7882 (t) cc_final: 0.7451 (m) REVERT: A 209 VAL cc_start: 0.8349 (p) cc_final: 0.8076 (t) REVERT: A 250 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 353 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7927 (tt0) REVERT: A 377 TYR cc_start: 0.7460 (m-10) cc_final: 0.7219 (m-80) REVERT: A 397 LYS cc_start: 0.8434 (ptpp) cc_final: 0.8183 (ptpp) REVERT: A 518 ASN cc_start: 0.7546 (t0) cc_final: 0.7325 (t0) REVERT: A 643 LEU cc_start: 0.7963 (mm) cc_final: 0.7727 (mp) REVERT: A 645 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7821 (ttmm) REVERT: A 770 ASP cc_start: 0.7050 (m-30) cc_final: 0.6526 (p0) REVERT: B 50 MET cc_start: 0.6979 (mmm) cc_final: 0.6760 (mmm) REVERT: C 46 GLU cc_start: 0.6957 (tp30) cc_final: 0.6746 (tp30) REVERT: C 116 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6919 (tm-30) REVERT: C 156 ASP cc_start: 0.7821 (m-30) cc_final: 0.7545 (m-30) REVERT: C 370 GLU cc_start: 0.6582 (pp20) cc_final: 0.6321 (tm-30) REVERT: C 429 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 430 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7650 (p) REVERT: C 457 MET cc_start: 0.7555 (tpp) cc_final: 0.7185 (tpp) REVERT: C 691 ASP cc_start: 0.7873 (t0) cc_final: 0.7175 (t0) REVERT: C 695 ASP cc_start: 0.7553 (m-30) cc_final: 0.6982 (m-30) REVERT: C 826 LYS cc_start: 0.7491 (mtpp) cc_final: 0.7207 (mtmm) REVERT: C 890 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7921 (tp30) REVERT: C 897 GLN cc_start: 0.7805 (mp10) cc_final: 0.7414 (tm-30) REVERT: C 957 LYS cc_start: 0.8284 (mmtp) cc_final: 0.8063 (mmtp) REVERT: C 1052 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7966 (tt) REVERT: C 1106 LEU cc_start: 0.7891 (mp) cc_final: 0.7036 (tt) REVERT: C 1121 MET cc_start: 0.6485 (mtp) cc_final: 0.6151 (mmm) REVERT: C 1142 LEU cc_start: 0.7871 (tt) cc_final: 0.7609 (tt) REVERT: C 1168 LYS cc_start: 0.7514 (mmmm) cc_final: 0.7222 (mtpp) REVERT: F 208 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7566 (pp) outliers start: 42 outliers final: 20 residues processed: 349 average time/residue: 0.3086 time to fit residues: 156.2335 Evaluate side-chains 341 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 317 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 602 GLN Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 21 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN C 847 HIS C 854 GLN F 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.147716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131012 restraints weight = 24280.312| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.90 r_work: 0.3663 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16844 Z= 0.192 Angle : 0.620 14.466 22731 Z= 0.313 Chirality : 0.041 0.163 2641 Planarity : 0.004 0.048 2869 Dihedral : 4.033 55.542 2224 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.90 % Allowed : 15.52 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2032 helix: 1.51 (0.14), residues: 1423 sheet: -0.28 (1.04), residues: 24 loop : -1.76 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 167 HIS 0.008 0.001 HIS A 476 PHE 0.019 0.002 PHE A 566 TYR 0.022 0.002 TYR C1117 ARG 0.006 0.001 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.05570 ( 965) hydrogen bonds : angle 3.87661 ( 2862) metal coordination : bond 0.00762 ( 9) covalent geometry : bond 0.00457 (16835) covalent geometry : angle 0.62036 (22731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.6593 (mmt) cc_final: 0.5850 (mmt) REVERT: A 125 ASP cc_start: 0.7721 (m-30) cc_final: 0.7449 (m-30) REVERT: A 143 HIS cc_start: 0.5703 (OUTLIER) cc_final: 0.5408 (m90) REVERT: A 204 VAL cc_start: 0.7955 (t) cc_final: 0.7577 (m) REVERT: A 209 VAL cc_start: 0.8495 (p) cc_final: 0.8251 (t) REVERT: A 250 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7425 (mm-30) REVERT: A 261 MET cc_start: 0.7730 (mtp) cc_final: 0.7507 (mtp) REVERT: A 353 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8042 (tt0) REVERT: A 397 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8273 (ptpp) REVERT: A 472 LYS cc_start: 0.8122 (tppt) cc_final: 0.7890 (ttmm) REVERT: A 614 TYR cc_start: 0.7821 (m-10) cc_final: 0.7595 (m-10) REVERT: A 643 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7880 (mp) REVERT: A 645 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7948 (ttmm) REVERT: B 47 ASN cc_start: 0.8424 (m110) cc_final: 0.8152 (m110) REVERT: C 156 ASP cc_start: 0.7893 (m-30) cc_final: 0.7565 (m-30) REVERT: C 279 PHE cc_start: 0.6648 (t80) cc_final: 0.6395 (t80) REVERT: C 348 LYS cc_start: 0.8045 (ptpp) cc_final: 0.7810 (ptpp) REVERT: C 429 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 457 MET cc_start: 0.7582 (tpp) cc_final: 0.7198 (tpp) REVERT: C 481 ILE cc_start: 0.8072 (mm) cc_final: 0.7869 (mt) REVERT: C 662 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7794 (p0) REVERT: C 691 ASP cc_start: 0.7894 (t0) cc_final: 0.7164 (t0) REVERT: C 695 ASP cc_start: 0.7624 (m-30) cc_final: 0.7041 (m-30) REVERT: C 762 LEU cc_start: 0.7516 (tp) cc_final: 0.7167 (tp) REVERT: C 826 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7372 (mtmm) REVERT: C 856 GLU cc_start: 0.6722 (tp30) cc_final: 0.6488 (tp30) REVERT: C 890 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7986 (tp30) REVERT: C 897 GLN cc_start: 0.7858 (mp10) cc_final: 0.7447 (tm-30) REVERT: C 957 LYS cc_start: 0.8461 (mmtp) cc_final: 0.8189 (mmtp) REVERT: C 1017 ASP cc_start: 0.6505 (OUTLIER) cc_final: 0.5256 (m-30) REVERT: C 1073 HIS cc_start: 0.7260 (t-90) cc_final: 0.6861 (t-170) REVERT: C 1106 LEU cc_start: 0.7873 (mp) cc_final: 0.7013 (tt) REVERT: C 1121 MET cc_start: 0.6750 (mtp) cc_final: 0.6484 (mmm) REVERT: C 1168 LYS cc_start: 0.7547 (mmmm) cc_final: 0.7012 (mmmm) REVERT: F 208 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7643 (pp) outliers start: 54 outliers final: 35 residues processed: 360 average time/residue: 0.2966 time to fit residues: 155.2489 Evaluate side-chains 358 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 204 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 121 optimal weight: 0.2980 chunk 90 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 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 346 ASN A 518 ASN C 244 GLN ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.131761 restraints weight = 24211.925| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.85 r_work: 0.3665 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16844 Z= 0.156 Angle : 0.593 14.011 22731 Z= 0.297 Chirality : 0.039 0.162 2641 Planarity : 0.004 0.048 2869 Dihedral : 4.019 53.381 2224 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.22 % Allowed : 15.68 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 2032 helix: 1.54 (0.14), residues: 1425 sheet: -0.17 (1.10), residues: 24 loop : -1.77 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 213 HIS 0.005 0.001 HIS A 476 PHE 0.018 0.001 PHE A 566 TYR 0.036 0.002 TYR C1117 ARG 0.004 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 965) hydrogen bonds : angle 3.82922 ( 2862) metal coordination : bond 0.00671 ( 9) covalent geometry : bond 0.00364 (16835) covalent geometry : angle 0.59322 (22731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 324 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.6755 (mmt) cc_final: 0.6040 (mmt) REVERT: A 125 ASP cc_start: 0.7687 (m-30) cc_final: 0.7441 (m-30) REVERT: A 143 HIS cc_start: 0.5616 (OUTLIER) cc_final: 0.5409 (m90) REVERT: A 204 VAL cc_start: 0.7925 (t) cc_final: 0.7530 (m) REVERT: A 250 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 302 ILE cc_start: 0.7824 (tp) cc_final: 0.7610 (tt) REVERT: A 353 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7971 (tt0) REVERT: A 397 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8205 (ptpp) REVERT: A 614 TYR cc_start: 0.7784 (m-10) cc_final: 0.7515 (m-10) REVERT: A 643 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 645 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7883 (ttmm) REVERT: A 770 ASP cc_start: 0.7020 (m-30) cc_final: 0.6529 (p0) REVERT: B 47 ASN cc_start: 0.8292 (m110) cc_final: 0.8007 (m110) REVERT: C 116 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6911 (tm-30) REVERT: C 156 ASP cc_start: 0.7796 (m-30) cc_final: 0.7457 (m-30) REVERT: C 221 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6196 (tp30) REVERT: C 279 PHE cc_start: 0.6639 (t80) cc_final: 0.6379 (t80) REVERT: C 290 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6530 (t) REVERT: C 348 LYS cc_start: 0.8139 (ptpp) cc_final: 0.7874 (ptpp) REVERT: C 429 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7814 (tm-30) REVERT: C 430 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7640 (p) REVERT: C 481 ILE cc_start: 0.8078 (mm) cc_final: 0.7874 (mt) REVERT: C 662 ASN cc_start: 0.8085 (p0) cc_final: 0.7798 (p0) REVERT: C 691 ASP cc_start: 0.7932 (t0) cc_final: 0.7221 (t0) REVERT: C 695 ASP cc_start: 0.7620 (m-30) cc_final: 0.7040 (m-30) REVERT: C 826 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7319 (mtmm) REVERT: C 844 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7405 (mm-30) REVERT: C 856 GLU cc_start: 0.6581 (tp30) cc_final: 0.6353 (tp30) REVERT: C 890 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8061 (tp30) REVERT: C 897 GLN cc_start: 0.7747 (mp10) cc_final: 0.7354 (tm-30) REVERT: C 957 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8178 (mmtp) REVERT: C 1073 HIS cc_start: 0.7226 (t-90) cc_final: 0.6870 (t-170) REVERT: C 1106 LEU cc_start: 0.7774 (mp) cc_final: 0.6926 (tt) REVERT: C 1121 MET cc_start: 0.6747 (mtp) cc_final: 0.6449 (mmm) REVERT: F 208 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7686 (pp) outliers start: 60 outliers final: 38 residues processed: 358 average time/residue: 0.3016 time to fit residues: 157.7549 Evaluate side-chains 362 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 318 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1068 MET Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 30 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 203 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 518 ASN ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.147252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.130871 restraints weight = 24014.475| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.88 r_work: 0.3655 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16844 Z= 0.159 Angle : 0.614 15.013 22731 Z= 0.306 Chirality : 0.040 0.193 2641 Planarity : 0.004 0.047 2869 Dihedral : 4.042 50.179 2224 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.33 % Allowed : 16.38 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2032 helix: 1.50 (0.14), residues: 1430 sheet: -0.40 (1.11), residues: 24 loop : -1.78 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 213 HIS 0.005 0.001 HIS A 476 PHE 0.021 0.002 PHE A 566 TYR 0.014 0.002 TYR C 797 ARG 0.004 0.000 ARG C1174 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 965) hydrogen bonds : angle 3.86959 ( 2862) metal coordination : bond 0.00633 ( 9) covalent geometry : bond 0.00373 (16835) covalent geometry : angle 0.61366 (22731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 324 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.6958 (mmt) cc_final: 0.6226 (mmt) REVERT: A 121 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7048 (mt0) REVERT: A 125 ASP cc_start: 0.7622 (m-30) cc_final: 0.7373 (m-30) REVERT: A 173 ARG cc_start: 0.4595 (OUTLIER) cc_final: 0.4151 (ptp-170) REVERT: A 204 VAL cc_start: 0.7921 (t) cc_final: 0.7550 (m) REVERT: A 302 ILE cc_start: 0.7925 (tp) cc_final: 0.7710 (tt) REVERT: A 353 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7986 (tt0) REVERT: A 397 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8218 (ptpp) REVERT: A 472 LYS cc_start: 0.8062 (tppt) cc_final: 0.7847 (ttmm) REVERT: A 614 TYR cc_start: 0.7771 (m-80) cc_final: 0.7515 (m-10) REVERT: A 643 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 645 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7866 (ttmm) REVERT: A 742 PHE cc_start: 0.7567 (p90) cc_final: 0.7191 (p90) REVERT: A 770 ASP cc_start: 0.7047 (m-30) cc_final: 0.6580 (p0) REVERT: B 47 ASN cc_start: 0.8258 (m110) cc_final: 0.7980 (m110) REVERT: C 46 GLU cc_start: 0.7054 (tp30) cc_final: 0.6593 (tp30) REVERT: C 54 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7894 (mm) REVERT: C 116 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6875 (tm-30) REVERT: C 156 ASP cc_start: 0.7797 (m-30) cc_final: 0.7426 (m-30) REVERT: C 348 LYS cc_start: 0.8209 (ptpp) cc_final: 0.7993 (ptpp) REVERT: C 429 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8089 (tm-30) REVERT: C 612 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7749 (tt) REVERT: C 617 GLU cc_start: 0.7405 (tp30) cc_final: 0.7190 (tp30) REVERT: C 691 ASP cc_start: 0.7935 (t0) cc_final: 0.7169 (t0) REVERT: C 695 ASP cc_start: 0.7636 (m-30) cc_final: 0.6864 (m-30) REVERT: C 696 GLU cc_start: 0.6535 (mp0) cc_final: 0.6264 (mp0) REVERT: C 748 GLN cc_start: 0.7840 (pp30) cc_final: 0.7603 (pp30) REVERT: C 826 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7372 (mtmm) REVERT: C 844 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7389 (mm-30) REVERT: C 856 GLU cc_start: 0.6593 (tp30) cc_final: 0.6366 (tp30) REVERT: C 890 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8022 (tp30) REVERT: C 897 GLN cc_start: 0.7734 (mp10) cc_final: 0.7386 (tm-30) REVERT: C 957 LYS cc_start: 0.8493 (mmtp) cc_final: 0.8206 (mmtp) REVERT: C 1073 HIS cc_start: 0.7211 (t-90) cc_final: 0.6978 (t-170) REVERT: C 1106 LEU cc_start: 0.7861 (mp) cc_final: 0.6979 (tt) REVERT: C 1121 MET cc_start: 0.6610 (mtp) cc_final: 0.6268 (mmm) REVERT: C 1168 LYS cc_start: 0.7484 (mmmm) cc_final: 0.7147 (mtpp) REVERT: F 208 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7681 (pp) outliers start: 62 outliers final: 42 residues processed: 360 average time/residue: 0.3090 time to fit residues: 163.1935 Evaluate side-chains 365 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1068 MET Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 153 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 190 optimal weight: 0.1980 chunk 110 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 204 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 346 ASN A 518 ASN ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130043 restraints weight = 24105.672| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.86 r_work: 0.3665 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16844 Z= 0.160 Angle : 0.615 14.813 22731 Z= 0.307 Chirality : 0.040 0.168 2641 Planarity : 0.004 0.047 2869 Dihedral : 4.024 46.419 2224 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.54 % Allowed : 16.70 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 2032 helix: 1.49 (0.14), residues: 1430 sheet: 0.02 (1.02), residues: 29 loop : -1.81 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 213 HIS 0.006 0.001 HIS A 476 PHE 0.028 0.002 PHE F 160 TYR 0.021 0.002 TYR C 797 ARG 0.006 0.000 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 965) hydrogen bonds : angle 3.88771 ( 2862) metal coordination : bond 0.00672 ( 9) covalent geometry : bond 0.00376 (16835) covalent geometry : angle 0.61503 (22731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7054 (mt0) REVERT: A 125 ASP cc_start: 0.7639 (m-30) cc_final: 0.7389 (m-30) REVERT: A 173 ARG cc_start: 0.4737 (OUTLIER) cc_final: 0.4294 (ptp-170) REVERT: A 204 VAL cc_start: 0.7926 (t) cc_final: 0.7551 (m) REVERT: A 302 ILE cc_start: 0.7932 (tp) cc_final: 0.7718 (tt) REVERT: A 353 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7996 (tt0) REVERT: A 397 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8208 (ptpp) REVERT: A 472 LYS cc_start: 0.8040 (tppt) cc_final: 0.7835 (ttmm) REVERT: A 565 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7922 (mmm160) REVERT: A 614 TYR cc_start: 0.7804 (m-80) cc_final: 0.7547 (m-10) REVERT: A 643 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7888 (mp) REVERT: A 645 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7843 (ttmm) REVERT: A 770 ASP cc_start: 0.7031 (m-30) cc_final: 0.6583 (p0) REVERT: B 102 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: C 54 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7880 (mm) REVERT: C 116 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6873 (tm-30) REVERT: C 156 ASP cc_start: 0.7784 (m-30) cc_final: 0.7397 (m-30) REVERT: C 290 VAL cc_start: 0.6958 (OUTLIER) cc_final: 0.6582 (t) REVERT: C 348 LYS cc_start: 0.8261 (ptpp) cc_final: 0.8013 (ptpp) REVERT: C 429 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8098 (tm-30) REVERT: C 430 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7648 (p) REVERT: C 612 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7838 (tt) REVERT: C 661 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7643 (ptpp) REVERT: C 679 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8399 (mtpp) REVERT: C 691 ASP cc_start: 0.7931 (t0) cc_final: 0.7163 (t0) REVERT: C 695 ASP cc_start: 0.7639 (m-30) cc_final: 0.6853 (m-30) REVERT: C 696 GLU cc_start: 0.6529 (mp0) cc_final: 0.6238 (mp0) REVERT: C 748 GLN cc_start: 0.7822 (pp30) cc_final: 0.7592 (pp30) REVERT: C 826 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7385 (mtmm) REVERT: C 890 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8010 (tp30) REVERT: C 897 GLN cc_start: 0.7735 (mp10) cc_final: 0.7450 (tm-30) REVERT: C 907 TYR cc_start: 0.6940 (t80) cc_final: 0.6739 (t80) REVERT: C 915 GLU cc_start: 0.8390 (mp0) cc_final: 0.8126 (mp0) REVERT: C 957 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8204 (mmtp) REVERT: C 1106 LEU cc_start: 0.7761 (mp) cc_final: 0.6841 (tt) REVERT: C 1121 MET cc_start: 0.6631 (mtp) cc_final: 0.6313 (mmm) REVERT: C 1168 LYS cc_start: 0.7463 (mmmm) cc_final: 0.7242 (mtpp) REVERT: F 208 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7655 (pp) outliers start: 66 outliers final: 46 residues processed: 363 average time/residue: 0.3141 time to fit residues: 166.7803 Evaluate side-chains 379 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 191 optimal weight: 0.6980 chunk 73 optimal weight: 0.0570 chunk 97 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 518 ASN C 610 ASN C1073 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131892 restraints weight = 24037.751| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.86 r_work: 0.3669 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16844 Z= 0.134 Angle : 0.608 14.812 22731 Z= 0.303 Chirality : 0.039 0.192 2641 Planarity : 0.004 0.047 2869 Dihedral : 3.938 41.798 2224 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.28 % Allowed : 17.24 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2032 helix: 1.57 (0.14), residues: 1431 sheet: 0.18 (1.04), residues: 29 loop : -1.78 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 213 HIS 0.008 0.001 HIS C1073 PHE 0.021 0.001 PHE F 160 TYR 0.019 0.001 TYR C 797 ARG 0.005 0.000 ARG A 565 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 965) hydrogen bonds : angle 3.83593 ( 2862) metal coordination : bond 0.00446 ( 9) covalent geometry : bond 0.00304 (16835) covalent geometry : angle 0.60837 (22731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASP cc_start: 0.7631 (m-30) cc_final: 0.7385 (m-30) REVERT: A 173 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.4316 (ptp-170) REVERT: A 204 VAL cc_start: 0.7895 (t) cc_final: 0.7512 (m) REVERT: A 302 ILE cc_start: 0.7913 (tp) cc_final: 0.7698 (tt) REVERT: A 353 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7966 (tt0) REVERT: A 452 VAL cc_start: 0.6894 (OUTLIER) cc_final: 0.6686 (p) REVERT: A 472 LYS cc_start: 0.8064 (tppt) cc_final: 0.7829 (ttmm) REVERT: A 565 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7917 (mmm160) REVERT: A 589 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 614 TYR cc_start: 0.7717 (m-80) cc_final: 0.7474 (m-10) REVERT: A 643 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 697 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 770 ASP cc_start: 0.6984 (m-30) cc_final: 0.6563 (p0) REVERT: B 102 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: C 54 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7851 (mm) REVERT: C 116 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6829 (tm-30) REVERT: C 156 ASP cc_start: 0.7781 (m-30) cc_final: 0.7399 (m-30) REVERT: C 290 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6721 (t) REVERT: C 429 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8082 (tm-30) REVERT: C 457 MET cc_start: 0.7599 (tpp) cc_final: 0.7015 (tpp) REVERT: C 612 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7806 (tt) REVERT: C 661 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7661 (ptpp) REVERT: C 679 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8351 (mtpp) REVERT: C 691 ASP cc_start: 0.7910 (t0) cc_final: 0.7178 (t0) REVERT: C 695 ASP cc_start: 0.7591 (m-30) cc_final: 0.6860 (m-30) REVERT: C 696 GLU cc_start: 0.6529 (mp0) cc_final: 0.6238 (mp0) REVERT: C 748 GLN cc_start: 0.7801 (pp30) cc_final: 0.7577 (pp30) REVERT: C 826 LYS cc_start: 0.7614 (mtpp) cc_final: 0.7333 (mtmm) REVERT: C 844 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7406 (mm-30) REVERT: C 890 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8001 (tp30) REVERT: C 897 GLN cc_start: 0.7736 (mp10) cc_final: 0.7448 (tm-30) REVERT: C 907 TYR cc_start: 0.6865 (t80) cc_final: 0.6616 (t80) REVERT: C 957 LYS cc_start: 0.8440 (mmtp) cc_final: 0.8152 (mmtp) REVERT: C 1106 LEU cc_start: 0.7760 (mp) cc_final: 0.6836 (tt) REVERT: C 1121 MET cc_start: 0.6539 (mtp) cc_final: 0.6224 (mmm) REVERT: C 1166 PHE cc_start: 0.7482 (m-80) cc_final: 0.7105 (m-80) REVERT: C 1168 LYS cc_start: 0.7442 (mmmm) cc_final: 0.7169 (mtpp) REVERT: F 208 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7651 (pp) outliers start: 61 outliers final: 41 residues processed: 362 average time/residue: 0.2982 time to fit residues: 157.8559 Evaluate side-chains 377 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 166 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 148 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 188 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 346 ASN A 518 ASN ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1073 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.147530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.131160 restraints weight = 24049.209| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.88 r_work: 0.3665 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16844 Z= 0.142 Angle : 0.624 15.061 22731 Z= 0.311 Chirality : 0.040 0.241 2641 Planarity : 0.004 0.047 2869 Dihedral : 3.935 40.769 2224 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.22 % Allowed : 17.56 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 2032 helix: 1.53 (0.14), residues: 1432 sheet: 0.35 (1.05), residues: 29 loop : -1.78 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 213 HIS 0.007 0.001 HIS C1073 PHE 0.025 0.002 PHE C 482 TYR 0.030 0.001 TYR C 797 ARG 0.007 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 965) hydrogen bonds : angle 3.86533 ( 2862) metal coordination : bond 0.00515 ( 9) covalent geometry : bond 0.00328 (16835) covalent geometry : angle 0.62441 (22731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 VAL cc_start: 0.7879 (t) cc_final: 0.7484 (m) REVERT: A 302 ILE cc_start: 0.7922 (tp) cc_final: 0.7707 (tt) REVERT: A 353 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7981 (tt0) REVERT: A 397 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8169 (ptpp) REVERT: A 452 VAL cc_start: 0.6925 (OUTLIER) cc_final: 0.6711 (p) REVERT: A 565 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7827 (mmm160) REVERT: A 589 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 614 TYR cc_start: 0.7594 (m-80) cc_final: 0.7341 (m-10) REVERT: A 643 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7856 (mp) REVERT: A 697 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 770 ASP cc_start: 0.6987 (m-30) cc_final: 0.6558 (p0) REVERT: C 20 LYS cc_start: 0.7454 (tmtm) cc_final: 0.7253 (ttmt) REVERT: C 54 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7883 (mm) REVERT: C 116 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6835 (tm-30) REVERT: C 156 ASP cc_start: 0.7771 (m-30) cc_final: 0.7379 (m-30) REVERT: C 290 VAL cc_start: 0.7077 (OUTLIER) cc_final: 0.6733 (t) REVERT: C 429 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 457 MET cc_start: 0.7595 (tpp) cc_final: 0.6997 (tpp) REVERT: C 612 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7815 (tt) REVERT: C 661 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7642 (ptpp) REVERT: C 679 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8367 (mtpp) REVERT: C 691 ASP cc_start: 0.7894 (t0) cc_final: 0.7201 (t0) REVERT: C 695 ASP cc_start: 0.7605 (m-30) cc_final: 0.6892 (m-30) REVERT: C 696 GLU cc_start: 0.6488 (mp0) cc_final: 0.6231 (mp0) REVERT: C 748 GLN cc_start: 0.7838 (pp30) cc_final: 0.7602 (pp30) REVERT: C 826 LYS cc_start: 0.7597 (mtpp) cc_final: 0.7329 (mtmm) REVERT: C 844 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7444 (mm-30) REVERT: C 890 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8101 (tp30) REVERT: C 897 GLN cc_start: 0.7749 (mp10) cc_final: 0.7453 (tm-30) REVERT: C 957 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8165 (mmtp) REVERT: C 1106 LEU cc_start: 0.7742 (mp) cc_final: 0.6803 (tt) REVERT: C 1121 MET cc_start: 0.6551 (mtp) cc_final: 0.6221 (mmm) REVERT: C 1166 PHE cc_start: 0.7450 (m-80) cc_final: 0.7084 (m-80) REVERT: C 1168 LYS cc_start: 0.7410 (mmmm) cc_final: 0.7181 (mtpp) REVERT: F 208 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7652 (pp) outliers start: 60 outliers final: 42 residues processed: 358 average time/residue: 0.3078 time to fit residues: 160.5779 Evaluate side-chains 375 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 304 TYR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 992 THR Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain C residue 1017 ASP Chi-restraints excluded: chain C residue 1052 LEU Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1119 ILE Chi-restraints excluded: chain F residue 192 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 231 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 159 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 123 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 188 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN A 518 ASN ** C 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 848 HIS C1073 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.147867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131510 restraints weight = 24023.506| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.86 r_work: 0.3677 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16844 Z= 0.138 Angle : 0.631 14.986 22731 Z= 0.314 Chirality : 0.039 0.221 2641 Planarity : 0.004 0.047 2869 Dihedral : 3.911 40.622 2224 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.06 % Allowed : 17.94 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2032 helix: 1.55 (0.14), residues: 1433 sheet: 0.52 (1.13), residues: 24 loop : -1.78 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 213 HIS 0.007 0.001 HIS C1073 PHE 0.033 0.002 PHE C 279 TYR 0.024 0.001 TYR C 797 ARG 0.007 0.000 ARG C 285 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 965) hydrogen bonds : angle 3.85467 ( 2862) metal coordination : bond 0.00464 ( 9) covalent geometry : bond 0.00317 (16835) covalent geometry : angle 0.63129 (22731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9914.83 seconds wall clock time: 172 minutes 37.74 seconds (10357.74 seconds total)