Starting phenix.real_space_refine on Thu Aug 6 19:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmc_37649/08_2026/8wmc_37649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmc_37649/08_2026/8wmc_37649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wmc_37649/08_2026/8wmc_37649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmc_37649/08_2026/8wmc_37649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wmc_37649/08_2026/8wmc_37649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmc_37649/08_2026/8wmc_37649.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 37 5.49 5 S 75 5.16 5 C 10574 2.51 5 N 2982 2.21 5 O 3257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16929 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 6100 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 28, 'TRANS': 705} Chain breaks: 3 Chain: "A" Number of atoms: 10024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1249, 10024 Classifications: {'peptide': 1249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 69, 'TRANS': 1179} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9483 SG CYS A 463 41.138 48.304 52.348 1.00 67.66 S ATOM 9545 SG CYS A 472 41.211 49.211 48.693 1.00 56.85 S ATOM 9559 SG CYS A 474 37.862 48.869 50.447 1.00 54.69 S ATOM 9581 SG CYS A 477 39.928 51.836 51.198 1.00 48.17 S ATOM 11402 SG CYS A 706 48.213 32.538 77.785 1.00 75.16 S ATOM 11417 SG CYS A 708 44.842 32.617 79.503 1.00 62.30 S ATOM 11439 SG CYS A 711 46.273 35.796 78.048 1.00 59.36 S ATOM 13327 SG CYS A 965 53.998 37.341 116.916 1.00 51.96 S ATOM 13787 SG CYS A1312 55.837 36.299 113.552 1.00 53.87 S ATOM 14026 SG CYS A1342 52.994 34.240 115.261 1.00 48.21 S ATOM 14044 SG CYS A1345 52.230 37.325 113.386 1.00 43.09 S ATOM 7112 SG CYS A 123 42.070 72.923 25.592 1.00 77.33 S ATOM 7136 SG CYS A 126 44.927 71.978 26.346 1.00 74.46 S Time building chain proxies: 3.27, per 1000 atoms: 0.19 Number of scatterers: 16929 At special positions: 0 Unit cell: (102, 103.7, 169.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 75 16.00 P 37 15.00 O 3257 8.00 N 2982 7.00 C 10574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 658.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 472 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 477 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 706 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1312 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 123 " Number of angles added : 15 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 43.7% alpha, 15.1% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.642A pdb=" N THR B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.655A pdb=" N THR B 44 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 92 through 113 removed outlier: 4.957A pdb=" N ASN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.817A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.652A pdb=" N GLY B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.852A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.752A pdb=" N LEU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 277 through 293 removed outlier: 4.528A pdb=" N ASP B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 360 through 374 Processing helix chain 'B' and resid 376 through 393 removed outlier: 4.313A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.554A pdb=" N ARG B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 419 " --> pdb=" O PHE B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 419' Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 464 through 482 Processing helix chain 'B' and resid 485 through 500 Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.722A pdb=" N LYS B 505 " --> pdb=" O PHE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.780A pdb=" N LEU B 523 " --> pdb=" O HIS B 520 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 530 Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 554 through 558 removed outlier: 3.634A pdb=" N LEU B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 595 through 606 removed outlier: 3.725A pdb=" N ASN B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 625 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 675 through 683 removed outlier: 3.650A pdb=" N HIS B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 710 Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.619A pdb=" N ASN B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.638A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 57 through 76 removed outlier: 4.004A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 5.707A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.143A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.431A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.823A pdb=" N LEU A 832 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 963 removed outlier: 3.938A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.559A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1242 " --> pdb=" O TYR A1238 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG A1243 " --> pdb=" O LYS A1239 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 4.046A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 removed outlier: 3.575A pdb=" N ARG A1310 " --> pdb=" O ALA A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1327 removed outlier: 4.206A pdb=" N ALA A1324 " --> pdb=" O ASP A1321 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A1326 " --> pdb=" O SER A1323 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA A1327 " --> pdb=" O ALA A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 removed outlier: 3.614A pdb=" N LYS A1331 " --> pdb=" O TYR A1328 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A1332 " --> pdb=" O PRO A1329 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1333 " --> pdb=" O GLU A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1399 Processing helix chain 'A' and resid 1420 through 1426 removed outlier: 3.648A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1476 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1539 through 1548 Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 4.395A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1595 removed outlier: 3.564A pdb=" N LYS A1592 " --> pdb=" O ASP A1588 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1595 " --> pdb=" O LYS A1591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 314 through 315 removed outlier: 6.763A pdb=" N TYR B 321 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU B 359 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER B 323 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 457 through 462 removed outlier: 3.523A pdb=" N GLN B 458 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 428 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 removed outlier: 4.009A pdb=" N GLU B 541 " --> pdb=" O LYS B 533 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 569 through 573 removed outlier: 6.761A pdb=" N THR B 570 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU B 613 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 572 " --> pdb=" O LEU B 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 615 through 617 removed outlier: 4.247A pdb=" N HIS B 615 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 633 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 150 removed outlier: 4.038A pdb=" N LYS A 6 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 238 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.501A pdb=" N MET A 17 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.040A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.976A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 557 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.976A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.936A pdb=" N ALA A 488 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 497 through 504 removed outlier: 11.065A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.450A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 659 through 663 removed outlier: 7.779A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 659 through 663 removed outlier: 7.779A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB8, first strand: chain 'A' and resid 739 through 740 Processing sheet with id=AB9, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AC1, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AC2, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 5.979A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A1502 " --> pdb=" O ARG A 896 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AC4, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.240A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.729A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2798 1.32 - 1.44: 4826 1.44 - 1.57: 9574 1.57 - 1.69: 74 1.69 - 1.82: 112 Bond restraints: 17384 Sorted by residual: bond pdb=" C PRO A 198 " pdb=" O PRO A 198 " ideal model delta sigma weight residual 1.239 1.193 0.046 1.22e-02 6.72e+03 1.45e+01 bond pdb=" C PHE B 197 " pdb=" O PHE B 197 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.22e-02 6.72e+03 1.34e+01 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.24e-02 6.50e+03 1.26e+01 bond pdb=" N ASP B 448 " pdb=" CA ASP B 448 " ideal model delta sigma weight residual 1.462 1.492 -0.031 9.30e-03 1.16e+04 1.08e+01 bond pdb=" N ARG A 199 " pdb=" CA ARG A 199 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.79e+00 ... (remaining 17379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 22819 1.68 - 3.35: 595 3.35 - 5.03: 166 5.03 - 6.71: 16 6.71 - 8.38: 4 Bond angle restraints: 23600 Sorted by residual: angle pdb=" N PRO B 449 " pdb=" CA PRO B 449 " pdb=" C PRO B 449 " ideal model delta sigma weight residual 113.84 122.22 -8.38 1.30e+00 5.92e-01 4.16e+01 angle pdb=" CA ASP A 162 " pdb=" C ASP A 162 " pdb=" O ASP A 162 " ideal model delta sigma weight residual 120.55 114.00 6.55 1.06e+00 8.90e-01 3.82e+01 angle pdb=" CA PHE A 200 " pdb=" C PHE A 200 " pdb=" O PHE A 200 " ideal model delta sigma weight residual 121.44 114.71 6.73 1.17e+00 7.31e-01 3.30e+01 angle pdb=" C PRO B 449 " pdb=" CA PRO B 449 " pdb=" CB PRO B 449 " ideal model delta sigma weight residual 111.85 104.60 7.25 1.42e+00 4.96e-01 2.61e+01 angle pdb=" CA ILE B 446 " pdb=" C ILE B 446 " pdb=" O ILE B 446 " ideal model delta sigma weight residual 121.93 116.46 5.47 1.12e+00 7.97e-01 2.39e+01 ... (remaining 23595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.79: 9569 18.79 - 37.57: 850 37.57 - 56.36: 127 56.36 - 75.14: 63 75.14 - 93.93: 15 Dihedral angle restraints: 10624 sinusoidal: 4873 harmonic: 5751 Sorted by residual: dihedral pdb=" CA TYR B 447 " pdb=" C TYR B 447 " pdb=" N ASP B 448 " pdb=" CA ASP B 448 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP A1404 " pdb=" CB ASP A1404 " pdb=" CG ASP A1404 " pdb=" OD1 ASP A1404 " ideal model delta sinusoidal sigma weight residual -30.00 -89.69 59.69 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA TYR B 209 " pdb=" C TYR B 209 " pdb=" N ASP B 210 " pdb=" CA ASP B 210 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 10621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1893 0.042 - 0.085: 427 0.085 - 0.127: 144 0.127 - 0.170: 33 0.170 - 0.212: 4 Chirality restraints: 2501 Sorted by residual: chirality pdb=" CA GLU A 857 " pdb=" N GLU A 857 " pdb=" C GLU A 857 " pdb=" CB GLU A 857 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE B 446 " pdb=" N ILE B 446 " pdb=" C ILE B 446 " pdb=" CB ILE B 446 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA ILE B 205 " pdb=" N ILE B 205 " pdb=" C ILE B 205 " pdb=" CB ILE B 205 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 2498 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 420 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C ALA A 420 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA A 420 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 421 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 904 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1376 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A1377 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " 0.030 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 227 2.67 - 3.23: 14718 3.23 - 3.78: 23795 3.78 - 4.34: 33413 4.34 - 4.90: 57427 Nonbonded interactions: 129580 Sorted by model distance: nonbonded pdb=" O2' G R 33 " pdb=" O4' G R 34 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 435 " pdb=" OD1 ASP A 437 " model vdw 2.234 3.040 nonbonded pdb=" NZ LYS A1580 " pdb=" OP2 C R 30 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 876 " pdb=" O ASP A1308 " model vdw 2.242 3.120 nonbonded pdb=" O GLU B 344 " pdb=" OG1 THR B 347 " model vdw 2.255 3.040 ... (remaining 129575 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.310 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17398 Z= 0.216 Angle : 0.695 8.383 23615 Z= 0.431 Chirality : 0.043 0.212 2501 Planarity : 0.004 0.058 2941 Dihedral : 14.804 93.927 6904 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1959 helix: 1.56 (0.19), residues: 765 sheet: -0.30 (0.30), residues: 277 loop : -1.37 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 290 TYR 0.031 0.001 TYR B 209 PHE 0.023 0.001 PHE A 197 TRP 0.011 0.001 TRP B 457 HIS 0.009 0.001 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.22 (17384) covalent geometry : angle 0.68894 / 0.43 (23600) hydrogen bonds : bond 0.17304 / 11.21 ( 669) hydrogen bonds : angle 6.10985 / 4.25 ( 1941) metal coordination : bond 0.01786 / 1.13 ( 14) metal coordination : angle 3.77492 / 2.75 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.663 Fit side-chains REVERT: B 232 GLN cc_start: 0.8095 (mm110) cc_final: 0.7488 (tt0) REVERT: A 664 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6278 (pt0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.7381 time to fit residues: 182.8050 Evaluate side-chains 138 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 365 ASN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1366 ASN A1452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112171 restraints weight = 22245.520| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.36 r_work: 0.3192 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17398 Z= 0.105 Angle : 0.499 7.852 23615 Z= 0.259 Chirality : 0.039 0.149 2501 Planarity : 0.004 0.045 2941 Dihedral : 11.501 88.313 2772 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.68 % Allowed : 8.20 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1959 helix: 2.01 (0.19), residues: 761 sheet: -0.02 (0.30), residues: 273 loop : -1.25 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 25 TYR 0.012 0.001 TYR B 188 PHE 0.011 0.001 PHE B 558 TRP 0.011 0.001 TRP A1466 HIS 0.005 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (17384) covalent geometry : angle 0.49260 / 0.26 (23600) hydrogen bonds : bond 0.04016 / 2.52 ( 669) hydrogen bonds : angle 4.51139 / 3.20 ( 1941) metal coordination : bond 0.00442 / 0.27 ( 14) metal coordination : angle 3.19812 / 2.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.624 Fit side-chains REVERT: B 24 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6013 (mpp) REVERT: B 34 GLU cc_start: 0.7316 (tp30) cc_final: 0.6960 (mt-10) REVERT: B 150 MET cc_start: 0.7715 (mmt) cc_final: 0.7231 (mmt) REVERT: B 182 ARG cc_start: 0.6746 (tpm-80) cc_final: 0.6087 (tpp80) REVERT: B 190 GLU cc_start: 0.6774 (tp30) cc_final: 0.6510 (tp30) REVERT: B 232 GLN cc_start: 0.8269 (mm110) cc_final: 0.7391 (tt0) REVERT: B 377 ARG cc_start: 0.6305 (mmp80) cc_final: 0.6093 (mmp80) REVERT: B 481 ASN cc_start: 0.6944 (OUTLIER) cc_final: 0.6533 (p0) REVERT: B 620 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6758 (ptp) REVERT: B 667 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6568 (tm-30) REVERT: A 199 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8307 (ttt180) REVERT: A 361 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6964 (mp) REVERT: A 422 ASP cc_start: 0.7544 (t0) cc_final: 0.7318 (t0) REVERT: A 491 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: A 513 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: A 609 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6842 (ttm110) REVERT: A 664 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6113 (pt0) REVERT: A 1299 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6706 (ptt90) outliers start: 29 outliers final: 12 residues processed: 163 average time/residue: 0.7449 time to fit residues: 132.8706 Evaluate side-chains 149 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 171 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 187 optimal weight: 0.0670 chunk 167 optimal weight: 0.3980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111478 restraints weight = 22412.484| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.37 r_work: 0.3182 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17398 Z= 0.095 Angle : 0.459 7.202 23615 Z= 0.238 Chirality : 0.038 0.171 2501 Planarity : 0.004 0.038 2941 Dihedral : 11.381 89.085 2772 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.08 % Allowed : 9.24 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 1959 helix: 2.15 (0.19), residues: 759 sheet: 0.18 (0.30), residues: 275 loop : -1.23 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.010 0.001 TYR A 492 PHE 0.011 0.001 PHE B 743 TRP 0.009 0.001 TRP A1466 HIS 0.004 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (17384) covalent geometry : angle 0.45228 / 0.24 (23600) hydrogen bonds : bond 0.03715 / 2.35 ( 669) hydrogen bonds : angle 4.17686 / 2.99 ( 1941) metal coordination : bond 0.00317 / 0.21 ( 14) metal coordination : angle 3.10912 / 2.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.654 Fit side-chains REVERT: B 24 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6013 (mpp) REVERT: B 91 GLN cc_start: 0.7000 (tt0) cc_final: 0.6109 (tm-30) REVERT: B 150 MET cc_start: 0.7828 (mmt) cc_final: 0.7259 (mmt) REVERT: B 162 ASP cc_start: 0.7131 (m-30) cc_final: 0.6756 (m-30) REVERT: B 166 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: B 229 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6281 (ptm) REVERT: B 232 GLN cc_start: 0.8270 (mm110) cc_final: 0.7353 (tt0) REVERT: B 481 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6607 (p0) REVERT: B 620 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6843 (ptp) REVERT: B 667 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6637 (tm-30) REVERT: A 199 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8293 (ttt180) REVERT: A 267 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: A 422 ASP cc_start: 0.7733 (t0) cc_final: 0.7471 (t0) REVERT: A 491 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8052 (mm-30) REVERT: A 513 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: A 642 ASP cc_start: 0.7448 (t0) cc_final: 0.7077 (m-30) REVERT: A 664 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6814 (mm-30) REVERT: A 1299 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6646 (ptt90) REVERT: A 1321 ASP cc_start: 0.7986 (p0) cc_final: 0.7725 (p0) outliers start: 36 outliers final: 8 residues processed: 164 average time/residue: 0.7334 time to fit residues: 131.9923 Evaluate side-chains 151 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105520 restraints weight = 22400.114| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.29 r_work: 0.3101 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17398 Z= 0.182 Angle : 0.565 8.010 23615 Z= 0.294 Chirality : 0.043 0.163 2501 Planarity : 0.005 0.048 2941 Dihedral : 11.523 91.252 2772 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.25 % Allowed : 10.34 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 1959 helix: 1.84 (0.19), residues: 762 sheet: -0.02 (0.30), residues: 265 loop : -1.42 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.014 0.002 TYR B 551 PHE 0.016 0.002 PHE A1454 TRP 0.014 0.002 TRP B 693 HIS 0.007 0.001 HIS A1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (17384) covalent geometry : angle 0.55901 / 0.29 (23600) hydrogen bonds : bond 0.05388 / 3.39 ( 669) hydrogen bonds : angle 4.29710 / 3.08 ( 1941) metal coordination : bond 0.00663 / 0.42 ( 14) metal coordination : angle 3.30188 / 2.34 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.604 Fit side-chains REVERT: B 24 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6041 (mpp) REVERT: B 34 GLU cc_start: 0.7747 (tp30) cc_final: 0.7448 (tp30) REVERT: B 145 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.5990 (mtp180) REVERT: B 229 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6411 (ptm) REVERT: B 378 ARG cc_start: 0.5422 (tmt170) cc_final: 0.5079 (tpt90) REVERT: B 667 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6757 (tm-30) REVERT: A 267 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: A 290 ARG cc_start: 0.7156 (tmm160) cc_final: 0.6953 (tmm160) REVERT: A 361 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6949 (mp) REVERT: A 422 ASP cc_start: 0.8031 (t0) cc_final: 0.7792 (t0) REVERT: A 513 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 816 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8119 (mm-40) REVERT: A 1299 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6942 (ptt90) REVERT: A 1321 ASP cc_start: 0.7976 (p0) cc_final: 0.7645 (p0) outliers start: 39 outliers final: 12 residues processed: 163 average time/residue: 0.7565 time to fit residues: 134.9027 Evaluate side-chains 150 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 157 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106323 restraints weight = 22300.253| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.24 r_work: 0.3111 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17398 Z= 0.148 Angle : 0.504 7.722 23615 Z= 0.265 Chirality : 0.041 0.156 2501 Planarity : 0.004 0.051 2941 Dihedral : 11.567 91.544 2772 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.48 % Allowed : 11.03 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1959 helix: 1.95 (0.19), residues: 755 sheet: -0.02 (0.30), residues: 267 loop : -1.41 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.012 0.001 TYR B 478 PHE 0.012 0.001 PHE A 776 TRP 0.012 0.001 TRP A1466 HIS 0.006 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (17384) covalent geometry : angle 0.49807 / 0.26 (23600) hydrogen bonds : bond 0.04678 / 2.95 ( 669) hydrogen bonds : angle 4.17175 / 3.00 ( 1941) metal coordination : bond 0.00479 / 0.33 ( 14) metal coordination : angle 3.19344 / 2.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.502 Fit side-chains REVERT: B 24 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6069 (mpp) REVERT: B 34 GLU cc_start: 0.7664 (tp30) cc_final: 0.7077 (mt-10) REVERT: B 91 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: B 145 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.5879 (mtp180) REVERT: B 190 GLU cc_start: 0.6762 (tp30) cc_final: 0.6455 (tp30) REVERT: B 229 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6485 (ptm) REVERT: B 232 GLN cc_start: 0.8411 (mm110) cc_final: 0.7211 (tt0) REVERT: B 378 ARG cc_start: 0.5438 (tmt170) cc_final: 0.5085 (tpt90) REVERT: A 290 ARG cc_start: 0.7214 (tmm160) cc_final: 0.6998 (tmm160) REVERT: A 361 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6943 (mp) REVERT: A 422 ASP cc_start: 0.8023 (t0) cc_final: 0.7769 (t0) REVERT: A 491 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: A 513 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 816 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8124 (mm-40) REVERT: A 1299 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7014 (ptt90) REVERT: A 1321 ASP cc_start: 0.7995 (p0) cc_final: 0.7639 (p0) outliers start: 43 outliers final: 13 residues processed: 168 average time/residue: 0.6694 time to fit residues: 123.9572 Evaluate side-chains 155 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 99 optimal weight: 0.0570 chunk 128 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 80 optimal weight: 0.0970 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 475 GLN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107416 restraints weight = 22278.980| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.24 r_work: 0.3135 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17398 Z= 0.109 Angle : 0.470 7.261 23615 Z= 0.247 Chirality : 0.039 0.154 2501 Planarity : 0.004 0.048 2941 Dihedral : 11.536 91.429 2772 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.31 % Allowed : 12.07 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1959 helix: 2.06 (0.19), residues: 755 sheet: 0.11 (0.30), residues: 272 loop : -1.35 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.011 0.001 TYR A 492 PHE 0.011 0.001 PHE A 776 TRP 0.011 0.001 TRP B 693 HIS 0.004 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (17384) covalent geometry : angle 0.46340 / 0.25 (23600) hydrogen bonds : bond 0.04036 / 2.56 ( 669) hydrogen bonds : angle 4.04105 / 2.91 ( 1941) metal coordination : bond 0.00347 / 0.25 ( 14) metal coordination : angle 3.15502 / 2.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.465 Fit side-chains REVERT: B 24 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6036 (mpp) REVERT: B 34 GLU cc_start: 0.7612 (tp30) cc_final: 0.7041 (mt-10) REVERT: B 91 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: B 145 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5864 (mtp180) REVERT: B 190 GLU cc_start: 0.6767 (tp30) cc_final: 0.6459 (tp30) REVERT: B 229 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6499 (ptm) REVERT: B 232 GLN cc_start: 0.8464 (mm110) cc_final: 0.7219 (tt0) REVERT: B 378 ARG cc_start: 0.5384 (tmt170) cc_final: 0.5029 (tpt90) REVERT: B 620 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6492 (ptm) REVERT: B 667 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6767 (tm-30) REVERT: A 267 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: A 290 ARG cc_start: 0.7153 (tmm160) cc_final: 0.6933 (tmm160) REVERT: A 361 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7125 (mp) REVERT: A 422 ASP cc_start: 0.8001 (t0) cc_final: 0.7685 (t0) REVERT: A 426 LYS cc_start: 0.7995 (mttt) cc_final: 0.7538 (mtmm) REVERT: A 491 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: A 513 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: A 740 ASP cc_start: 0.8321 (p0) cc_final: 0.8034 (p0) REVERT: A 816 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8110 (mm-40) REVERT: A 1299 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6949 (ptt90) REVERT: A 1321 ASP cc_start: 0.7998 (p0) cc_final: 0.7639 (p0) outliers start: 40 outliers final: 18 residues processed: 168 average time/residue: 0.6397 time to fit residues: 118.3724 Evaluate side-chains 161 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 178 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105468 restraints weight = 22169.110| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.24 r_work: 0.3102 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17398 Z= 0.166 Angle : 0.532 10.447 23615 Z= 0.277 Chirality : 0.041 0.164 2501 Planarity : 0.004 0.055 2941 Dihedral : 11.553 92.967 2772 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.77 % Allowed : 12.31 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1959 helix: 1.90 (0.19), residues: 756 sheet: 0.02 (0.30), residues: 269 loop : -1.43 (0.18), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 645 TYR 0.012 0.001 TYR B 478 PHE 0.013 0.002 PHE A 776 TRP 0.014 0.001 TRP B 693 HIS 0.005 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (17384) covalent geometry : angle 0.52633 / 0.28 (23600) hydrogen bonds : bond 0.04935 / 3.12 ( 669) hydrogen bonds : angle 4.18206 / 3.00 ( 1941) metal coordination : bond 0.00639 / 0.41 ( 14) metal coordination : angle 3.21950 / 2.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.572 Fit side-chains REVERT: B 24 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6028 (mpp) REVERT: B 34 GLU cc_start: 0.7670 (tp30) cc_final: 0.7065 (mt-10) REVERT: B 91 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: B 145 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.5867 (mtp180) REVERT: B 166 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6262 (pm20) REVERT: B 229 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6567 (ptm) REVERT: B 232 GLN cc_start: 0.8478 (mm110) cc_final: 0.7219 (tt0) REVERT: B 378 ARG cc_start: 0.5439 (tmt170) cc_final: 0.5120 (tpt90) REVERT: B 542 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 667 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6742 (tm-30) REVERT: A 267 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: A 290 ARG cc_start: 0.7246 (tmm160) cc_final: 0.7022 (tmm160) REVERT: A 361 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6880 (mp) REVERT: A 422 ASP cc_start: 0.8006 (t0) cc_final: 0.7682 (t0) REVERT: A 491 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8068 (mm-30) REVERT: A 513 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: A 740 ASP cc_start: 0.8382 (p0) cc_final: 0.8138 (p0) REVERT: A 816 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: A 1299 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7024 (ptt90) REVERT: A 1321 ASP cc_start: 0.7973 (p0) cc_final: 0.7592 (p0) outliers start: 48 outliers final: 20 residues processed: 177 average time/residue: 0.6373 time to fit residues: 124.2902 Evaluate side-chains 167 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 0.1980 chunk 21 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 11 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109185 restraints weight = 22454.723| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.23 r_work: 0.3162 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17398 Z= 0.089 Angle : 0.453 6.417 23615 Z= 0.238 Chirality : 0.038 0.152 2501 Planarity : 0.004 0.047 2941 Dihedral : 11.483 91.687 2772 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.79 % Allowed : 13.34 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 1959 helix: 2.12 (0.19), residues: 758 sheet: 0.16 (0.30), residues: 280 loop : -1.34 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.012 0.001 TYR A 661 PHE 0.010 0.001 PHE B 522 TRP 0.013 0.001 TRP B 693 HIS 0.003 0.000 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (17384) covalent geometry : angle 0.44646 / 0.24 (23600) hydrogen bonds : bond 0.03354 / 2.14 ( 669) hydrogen bonds : angle 3.91742 / 2.83 ( 1941) metal coordination : bond 0.00305 / 0.22 ( 14) metal coordination : angle 3.18834 / 2.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.449 Fit side-chains REVERT: B 24 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.5965 (mpp) REVERT: B 34 GLU cc_start: 0.7590 (tp30) cc_final: 0.7011 (mt-10) REVERT: B 91 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: B 166 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: B 190 GLU cc_start: 0.6760 (tp30) cc_final: 0.6458 (tp30) REVERT: B 229 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6513 (ptm) REVERT: B 232 GLN cc_start: 0.8449 (mm110) cc_final: 0.7177 (tt0) REVERT: B 378 ARG cc_start: 0.5406 (tmt170) cc_final: 0.5119 (tpt90) REVERT: B 458 GLN cc_start: 0.7992 (mt0) cc_final: 0.7753 (tt0) REVERT: B 620 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6402 (ptm) REVERT: B 667 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 267 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: A 290 ARG cc_start: 0.7189 (tmm160) cc_final: 0.6978 (tmm160) REVERT: A 343 LYS cc_start: 0.7800 (tptp) cc_final: 0.7409 (tppp) REVERT: A 422 ASP cc_start: 0.7991 (t0) cc_final: 0.7698 (t0) REVERT: A 491 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: A 740 ASP cc_start: 0.8205 (p0) cc_final: 0.7981 (p0) REVERT: A 1321 ASP cc_start: 0.7936 (p0) cc_final: 0.7560 (p0) REVERT: A 1365 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7329 (mm-30) outliers start: 31 outliers final: 11 residues processed: 168 average time/residue: 0.5886 time to fit residues: 109.1625 Evaluate side-chains 151 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 742 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107823 restraints weight = 22332.117| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.24 r_work: 0.3135 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17398 Z= 0.124 Angle : 0.491 11.519 23615 Z= 0.252 Chirality : 0.040 0.159 2501 Planarity : 0.004 0.049 2941 Dihedral : 11.447 92.319 2772 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.56 % Allowed : 13.69 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1959 helix: 2.08 (0.19), residues: 760 sheet: 0.20 (0.30), residues: 274 loop : -1.33 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 25 TYR 0.011 0.001 TYR A 492 PHE 0.012 0.001 PHE A 776 TRP 0.016 0.001 TRP B 693 HIS 0.004 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 (17384) covalent geometry : angle 0.48514 / 0.25 (23600) hydrogen bonds : bond 0.03955 / 2.52 ( 669) hydrogen bonds : angle 3.96865 / 2.86 ( 1941) metal coordination : bond 0.00503 / 0.32 ( 14) metal coordination : angle 3.05257 / 2.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.453 Fit side-chains REVERT: B 34 GLU cc_start: 0.7597 (tp30) cc_final: 0.7020 (mt-10) REVERT: B 91 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: B 145 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5864 (mtp180) REVERT: B 166 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: B 229 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6491 (ptm) REVERT: B 232 GLN cc_start: 0.8453 (mm110) cc_final: 0.7194 (tt0) REVERT: B 243 LEU cc_start: 0.7188 (mt) cc_final: 0.6972 (tp) REVERT: B 378 ARG cc_start: 0.5416 (tmt170) cc_final: 0.5059 (tpt90) REVERT: B 667 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 267 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: A 290 ARG cc_start: 0.7229 (tmm160) cc_final: 0.7013 (tmm160) REVERT: A 343 LYS cc_start: 0.7847 (tptp) cc_final: 0.7459 (tppp) REVERT: A 361 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6734 (mp) REVERT: A 422 ASP cc_start: 0.7993 (t0) cc_final: 0.7674 (t0) REVERT: A 491 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8042 (mm-30) REVERT: A 513 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 740 ASP cc_start: 0.8262 (p0) cc_final: 0.8000 (p0) REVERT: A 1321 ASP cc_start: 0.7956 (p0) cc_final: 0.7569 (p0) REVERT: A 1365 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7329 (mm-30) outliers start: 27 outliers final: 15 residues processed: 154 average time/residue: 0.5893 time to fit residues: 99.9836 Evaluate side-chains 152 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 742 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 181 optimal weight: 0.0870 chunk 99 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106346 restraints weight = 22226.089| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.38 r_work: 0.3100 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17398 Z= 0.153 Angle : 0.521 10.953 23615 Z= 0.269 Chirality : 0.041 0.160 2501 Planarity : 0.004 0.053 2941 Dihedral : 11.480 93.371 2772 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.50 % Allowed : 13.81 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 1959 helix: 1.98 (0.19), residues: 762 sheet: 0.13 (0.30), residues: 269 loop : -1.38 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 25 TYR 0.012 0.001 TYR B 478 PHE 0.012 0.001 PHE A 776 TRP 0.018 0.001 TRP B 693 HIS 0.005 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (17384) covalent geometry : angle 0.51513 / 0.27 (23600) hydrogen bonds : bond 0.04637 / 2.94 ( 669) hydrogen bonds : angle 4.08423 / 2.94 ( 1941) metal coordination : bond 0.00685 / 0.42 ( 14) metal coordination : angle 3.11816 / 2.26 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.409 Fit side-chains REVERT: B 24 MET cc_start: 0.6462 (mpp) cc_final: 0.5999 (mpp) REVERT: B 34 GLU cc_start: 0.7702 (tp30) cc_final: 0.7119 (mt-10) REVERT: B 91 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6574 (tm-30) REVERT: B 118 ASP cc_start: 0.7680 (m-30) cc_final: 0.7239 (t0) REVERT: B 145 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.5828 (mtp180) REVERT: B 166 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6672 (pm20) REVERT: B 229 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6535 (ptm) REVERT: B 232 GLN cc_start: 0.8478 (mm110) cc_final: 0.7200 (tt0) REVERT: B 378 ARG cc_start: 0.5489 (tmt170) cc_final: 0.5241 (tpt90) REVERT: B 632 ASN cc_start: 0.7748 (t0) cc_final: 0.7513 (t0) REVERT: B 667 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 267 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: A 290 ARG cc_start: 0.7318 (tmm160) cc_final: 0.7100 (tmm160) REVERT: A 343 LYS cc_start: 0.7890 (tptp) cc_final: 0.7525 (tppp) REVERT: A 361 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7122 (mp) REVERT: A 422 ASP cc_start: 0.8047 (t0) cc_final: 0.7735 (t0) REVERT: A 426 LYS cc_start: 0.8084 (mttt) cc_final: 0.7679 (mtmp) REVERT: A 491 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: A 513 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: A 740 ASP cc_start: 0.8332 (p0) cc_final: 0.8070 (p0) REVERT: A 816 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8133 (mm-40) REVERT: A 1321 ASP cc_start: 0.7968 (p0) cc_final: 0.7574 (p0) outliers start: 26 outliers final: 15 residues processed: 155 average time/residue: 0.6634 time to fit residues: 112.8646 Evaluate side-chains 155 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 0.0060 chunk 55 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 168 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 overall best weight: 2.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105148 restraints weight = 22369.433| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.29 r_work: 0.3090 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17398 Z= 0.183 Angle : 0.560 13.548 23615 Z= 0.289 Chirality : 0.042 0.163 2501 Planarity : 0.004 0.057 2941 Dihedral : 11.537 94.614 2772 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.79 % Allowed : 13.58 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1959 helix: 1.84 (0.19), residues: 762 sheet: 0.06 (0.30), residues: 271 loop : -1.49 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1294 TYR 0.013 0.001 TYR B 478 PHE 0.013 0.002 PHE A 658 TRP 0.021 0.001 TRP B 693 HIS 0.006 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 (17384) covalent geometry : angle 0.55493 / 0.29 (23600) hydrogen bonds : bond 0.05162 / 3.27 ( 669) hydrogen bonds : angle 4.19284 / 3.02 ( 1941) metal coordination : bond 0.00749 / 0.46 ( 14) metal coordination : angle 3.16563 / 2.33 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5517.53 seconds wall clock time: 94 minutes 30.24 seconds (5670.24 seconds total)