Starting phenix.real_space_refine on Fri Jul 3 23:39:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmc_37649/07_2026/8wmc_37649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmc_37649/07_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_37649/07_2026/8wmc_37649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmc_37649/07_2026/8wmc_37649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wmc_37649/07_2026/8wmc_37649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmc_37649/07_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-dev-6108/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: 2.98, per 1000 atoms: 0.18 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: 1.36 Conformation dependent library (CDL) restraints added in 463.5 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: 1.74 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: 2.92 Time building geometry restraints manager: 1.80 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: 22886 1.68 - 3.35: 528 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: 1930 0.042 - 0.085: 416 0.085 - 0.127: 118 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.820 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- 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= 0.215 Angle : 0.682 8.383 23615 Z= 0.411 Chirality : 0.042 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 0.00381 / 0.21 (17384) covalent geometry : angle 0.67581 / 0.41 (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 : 0.479 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: 0.7088 time to fit residues: 175.3648 Evaluate side-chains 137 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.148643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111958 restraints weight = 22247.030| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.36 r_work: 0.3190 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17398 Z= 0.106 Angle : 0.496 7.469 23615 Z= 0.258 Chirality : 0.039 0.172 2501 Planarity : 0.004 0.046 2941 Dihedral : 11.524 89.540 2772 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.68 % Allowed : 8.09 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1959 helix: 2.02 (0.19), residues: 760 sheet: -0.02 (0.30), residues: 273 loop : -1.26 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.011 0.001 TYR B 188 PHE 0.012 0.001 PHE B 197 TRP 0.011 0.001 TRP A1466 HIS 0.005 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (17384) covalent geometry : angle 0.48939 / 0.26 (23600) hydrogen bonds : bond 0.04199 / 2.64 ( 669) hydrogen bonds : angle 4.55334 / 3.23 ( 1941) metal coordination : bond 0.00475 / 0.29 ( 14) metal coordination : angle 3.22331 / 2.35 ( 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 : 0.668 Fit side-chains REVERT: B 24 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6016 (mpp) REVERT: B 34 GLU cc_start: 0.7296 (tp30) cc_final: 0.6940 (mt-10) REVERT: B 150 MET cc_start: 0.7712 (mmt) cc_final: 0.7241 (mmt) REVERT: B 232 GLN cc_start: 0.8271 (mm110) cc_final: 0.7389 (tt0) REVERT: B 377 ARG cc_start: 0.6304 (mmp80) cc_final: 0.6093 (mmp80) REVERT: B 481 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6534 (p0) REVERT: B 667 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6575 (tm-30) REVERT: A 199 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8310 (ttt180) REVERT: A 361 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6967 (mp) REVERT: A 422 ASP cc_start: 0.7545 (t0) cc_final: 0.7338 (t0) REVERT: A 491 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8065 (mm-30) REVERT: A 513 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: A 609 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6811 (ttm110) REVERT: A 664 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6136 (pt0) REVERT: A 1299 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6700 (ptt90) outliers start: 29 outliers final: 12 residues processed: 164 average time/residue: 0.7789 time to fit residues: 139.9047 Evaluate side-chains 146 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 726 GLU Chi-restraints excluded: chain A residue 355 LEU 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: 5.9990 chunk 181 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 187 optimal weight: 0.0570 chunk 167 optimal weight: 10.0000 overall best weight: 2.3704 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.143739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106553 restraints weight = 22541.474| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.38 r_work: 0.3106 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17398 Z= 0.171 Angle : 0.544 8.231 23615 Z= 0.285 Chirality : 0.042 0.185 2501 Planarity : 0.004 0.042 2941 Dihedral : 11.534 91.429 2772 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.02 % Allowed : 9.88 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1959 helix: 1.90 (0.19), residues: 762 sheet: -0.05 (0.30), residues: 269 loop : -1.42 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 394 TYR 0.014 0.002 TYR B 551 PHE 0.016 0.002 PHE A1456 TRP 0.013 0.001 TRP A1466 HIS 0.007 0.001 HIS A1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (17384) covalent geometry : angle 0.53761 / 0.28 (23600) hydrogen bonds : bond 0.05235 / 3.31 ( 669) hydrogen bonds : angle 4.36765 / 3.12 ( 1941) metal coordination : bond 0.00597 / 0.39 ( 14) metal coordination : angle 3.34887 / 2.42 ( 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 174 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.617 Fit side-chains REVERT: B 24 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6101 (mpp) REVERT: B 34 GLU cc_start: 0.7792 (tp30) cc_final: 0.7533 (tp30) REVERT: B 145 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7131 (mtt180) REVERT: B 162 ASP cc_start: 0.7124 (m-30) cc_final: 0.6796 (m-30) REVERT: B 229 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6361 (ptm) REVERT: B 378 ARG cc_start: 0.5441 (tmt170) cc_final: 0.5149 (tpt90) REVERT: B 432 GLU cc_start: 0.7276 (tm-30) cc_final: 0.7073 (tm-30) REVERT: B 667 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 361 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7075 (mp) REVERT: A 422 ASP cc_start: 0.7941 (t0) cc_final: 0.7686 (t0) REVERT: A 513 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: A 816 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8178 (mm-40) REVERT: A 1299 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.6912 (ptt90) REVERT: A 1321 ASP cc_start: 0.8007 (p0) cc_final: 0.7730 (p0) REVERT: A 1395 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7341 (mmt90) REVERT: A 1578 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (pp20) outliers start: 35 outliers final: 14 residues processed: 163 average time/residue: 0.7786 time to fit residues: 138.9507 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 : 0.593 ------------------------------------------------------------------------------- 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 179 MET 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 338 MET 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 660 SER 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 1395 ARG Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.143341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106450 restraints weight = 22415.023| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.31 r_work: 0.3107 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17398 Z= 0.154 Angle : 0.511 7.855 23615 Z= 0.269 Chirality : 0.041 0.173 2501 Planarity : 0.004 0.049 2941 Dihedral : 11.570 92.354 2772 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.66 % Allowed : 10.34 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1959 helix: 1.91 (0.19), residues: 756 sheet: -0.11 (0.30), residues: 270 loop : -1.43 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1393 TYR 0.012 0.001 TYR B 478 PHE 0.012 0.001 PHE A 15 TRP 0.013 0.001 TRP B 693 HIS 0.005 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (17384) covalent geometry : angle 0.50503 / 0.27 (23600) hydrogen bonds : bond 0.04785 / 3.02 ( 669) hydrogen bonds : angle 4.23053 / 3.03 ( 1941) metal coordination : bond 0.00499 / 0.34 ( 14) metal coordination : angle 3.20492 / 2.33 ( 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 180 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.669 Fit side-chains REVERT: B 24 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6078 (mpp) REVERT: B 34 GLU cc_start: 0.7601 (tp30) cc_final: 0.7026 (mt-10) REVERT: B 145 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7041 (mtt180) REVERT: B 229 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6456 (ptm) REVERT: B 232 GLN cc_start: 0.8370 (mm110) cc_final: 0.7221 (tt0) REVERT: B 378 ARG cc_start: 0.5447 (tmt170) cc_final: 0.5069 (tpt90) REVERT: B 542 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7755 (mm) REVERT: B 667 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6695 (tm-30) REVERT: A 267 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: A 290 ARG cc_start: 0.7161 (tmm160) cc_final: 0.6942 (tmm160) REVERT: A 361 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6995 (mp) REVERT: A 422 ASP cc_start: 0.8102 (t0) cc_final: 0.7827 (t0) REVERT: A 491 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: A 513 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: A 816 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: A 1299 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6989 (ptt90) REVERT: A 1321 ASP cc_start: 0.7972 (p0) cc_final: 0.7645 (p0) REVERT: A 1395 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.6866 (mmm160) REVERT: A 1578 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7512 (pp20) outliers start: 46 outliers final: 15 residues processed: 168 average time/residue: 0.7561 time to fit residues: 139.2385 Evaluate side-chains 155 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 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 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 338 MET 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 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 421 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 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 1395 ARG Chi-restraints excluded: chain A residue 1578 GLU 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: 8.9990 chunk 68 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.138181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.101343 restraints weight = 22524.871| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.32 r_work: 0.3021 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 17398 Z= 0.351 Angle : 0.721 9.162 23615 Z= 0.379 Chirality : 0.050 0.210 2501 Planarity : 0.006 0.064 2941 Dihedral : 11.872 95.817 2772 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.24 % Allowed : 11.21 % Favored : 85.56 % 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: -0.60 (0.18), residues: 1959 helix: 1.21 (0.19), residues: 762 sheet: -0.32 (0.30), residues: 269 loop : -1.87 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 499 TYR 0.020 0.002 TYR B 551 PHE 0.022 0.003 PHE A 150 TRP 0.016 0.002 TRP A1466 HIS 0.011 0.002 HIS A1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.35 (17384) covalent geometry : angle 0.71501 / 0.38 (23600) hydrogen bonds : bond 0.07779 / 4.93 ( 669) hydrogen bonds : angle 4.75652 / 3.40 ( 1941) metal coordination : bond 0.01468 / 0.87 ( 14) metal coordination : angle 3.67855 / 2.74 ( 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 189 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 133 time to evaluate : 0.656 Fit side-chains REVERT: B 24 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6125 (mpp) REVERT: B 34 GLU cc_start: 0.7820 (tp30) cc_final: 0.7235 (mt-10) REVERT: B 145 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7221 (mtt90) REVERT: B 229 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6553 (ptm) REVERT: B 542 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7825 (mm) REVERT: B 632 ASN cc_start: 0.7767 (t0) cc_final: 0.7525 (t0) REVERT: B 667 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6815 (tm-30) REVERT: A 199 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8541 (ttt180) REVERT: A 290 ARG cc_start: 0.7393 (tmm160) cc_final: 0.7118 (tmm160) REVERT: A 361 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7034 (mp) REVERT: A 422 ASP cc_start: 0.8196 (t0) cc_final: 0.7914 (t0) REVERT: A 513 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: A 519 MET cc_start: 0.8483 (ttp) cc_final: 0.8153 (ttp) REVERT: A 651 ARG cc_start: 0.6732 (mtm-85) cc_final: 0.6331 (mtp180) REVERT: A 740 ASP cc_start: 0.8552 (p0) cc_final: 0.8263 (p0) REVERT: A 816 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: A 1299 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7207 (ptt90) REVERT: A 1321 ASP cc_start: 0.8000 (p0) cc_final: 0.7716 (p0) REVERT: A 1395 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7477 (mmt90) REVERT: A 1542 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 1578 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7610 (pp20) outliers start: 56 outliers final: 21 residues processed: 173 average time/residue: 0.7204 time to fit residues: 137.2818 Evaluate side-chains 158 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET 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 640 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 199 ARG 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 421 ILE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 699 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 Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1542 GLU Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1581 ASP Chi-restraints excluded: chain A residue 1588 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105841 restraints weight = 22330.545| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.28 r_work: 0.3101 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17398 Z= 0.119 Angle : 0.506 8.771 23615 Z= 0.269 Chirality : 0.040 0.177 2501 Planarity : 0.004 0.055 2941 Dihedral : 11.754 94.876 2772 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.37 % Allowed : 12.42 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1959 helix: 1.76 (0.19), residues: 753 sheet: -0.11 (0.30), residues: 271 loop : -1.61 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 645 TYR 0.014 0.001 TYR A 492 PHE 0.012 0.001 PHE A 776 TRP 0.013 0.001 TRP A1466 HIS 0.004 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17384) covalent geometry : angle 0.49921 / 0.27 (23600) hydrogen bonds : bond 0.04713 / 2.98 ( 669) hydrogen bonds : angle 4.27171 / 3.07 ( 1941) metal coordination : bond 0.00363 / 0.26 ( 14) metal coordination : angle 3.30873 / 2.36 ( 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: 41 poor density : 139 time to evaluate : 0.675 Fit side-chains REVERT: B 24 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5993 (mpp) REVERT: B 34 GLU cc_start: 0.7692 (tp30) cc_final: 0.7129 (mt-10) REVERT: B 145 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6950 (mtt90) REVERT: B 229 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6525 (ptm) REVERT: B 232 GLN cc_start: 0.8469 (mm110) cc_final: 0.7235 (tt0) REVERT: B 542 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7865 (mm) REVERT: B 667 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6823 (tm-30) REVERT: A 290 ARG cc_start: 0.7236 (tmm160) cc_final: 0.6984 (tmm160) REVERT: A 422 ASP cc_start: 0.8051 (t0) cc_final: 0.7760 (t0) REVERT: A 491 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: A 513 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: A 651 ARG cc_start: 0.6315 (mtm-85) cc_final: 0.5931 (mtp180) REVERT: A 740 ASP cc_start: 0.8374 (p0) cc_final: 0.8098 (p0) REVERT: A 816 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8148 (mm-40) REVERT: A 1299 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7114 (ptt90) REVERT: A 1321 ASP cc_start: 0.7893 (p0) cc_final: 0.7540 (p0) REVERT: A 1395 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7253 (mmt90) outliers start: 41 outliers final: 14 residues processed: 172 average time/residue: 0.7302 time to fit residues: 138.7899 Evaluate side-chains 154 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 3 THR 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 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 Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 13 optimal weight: 0.0570 chunk 11 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.7102 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.141108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104359 restraints weight = 22221.602| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.25 r_work: 0.3079 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17398 Z= 0.188 Angle : 0.551 8.116 23615 Z= 0.290 Chirality : 0.042 0.180 2501 Planarity : 0.005 0.058 2941 Dihedral : 11.704 95.240 2772 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.60 % Allowed : 12.82 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.70 (0.19), residues: 754 sheet: -0.12 (0.30), residues: 267 loop : -1.66 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 294 TYR 0.013 0.002 TYR A 492 PHE 0.015 0.002 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 0.00458 / 0.19 (17384) covalent geometry : angle 0.54442 / 0.29 (23600) hydrogen bonds : bond 0.05418 / 3.44 ( 669) hydrogen bonds : angle 4.32094 / 3.11 ( 1941) metal coordination : bond 0.00741 / 0.47 ( 14) metal coordination : angle 3.29935 / 2.45 ( 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 176 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.666 Fit side-chains REVERT: B 24 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6049 (mpp) REVERT: B 34 GLU cc_start: 0.7747 (tp30) cc_final: 0.7150 (mt-10) REVERT: B 145 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7142 (mtt180) REVERT: B 166 GLU cc_start: 0.7524 (mp0) cc_final: 0.6903 (pm20) REVERT: B 229 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6517 (ptm) REVERT: B 475 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: B 542 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7876 (mm) REVERT: B 632 ASN cc_start: 0.7832 (t0) cc_final: 0.7604 (t0) REVERT: B 667 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6843 (tm-30) REVERT: A 290 ARG cc_start: 0.7286 (tmm160) cc_final: 0.7035 (tmm160) REVERT: A 361 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6876 (mp) REVERT: A 422 ASP cc_start: 0.8106 (t0) cc_final: 0.7791 (t0) REVERT: A 491 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: A 513 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: A 651 ARG cc_start: 0.6509 (mtm-85) cc_final: 0.6103 (mtp180) REVERT: A 740 ASP cc_start: 0.8410 (p0) cc_final: 0.8138 (p0) REVERT: A 816 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8179 (mm-40) REVERT: A 1299 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7106 (ptt90) REVERT: A 1321 ASP cc_start: 0.7942 (p0) cc_final: 0.7574 (p0) REVERT: A 1395 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7302 (mmt90) outliers start: 45 outliers final: 20 residues processed: 167 average time/residue: 0.7458 time to fit residues: 137.4850 Evaluate side-chains 158 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 145 ARG Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 475 GLN 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 3 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 421 ILE 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 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 Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 146 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 156 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 151 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.144148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107342 restraints weight = 22502.355| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.43 r_work: 0.3119 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2062 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= 0.101 Angle : 0.487 11.653 23615 Z= 0.254 Chirality : 0.039 0.178 2501 Planarity : 0.004 0.048 2941 Dihedral : 11.637 94.224 2772 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.50 % Allowed : 14.33 % Favored : 84.17 % 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: 1.92 (0.19), residues: 757 sheet: 0.03 (0.30), residues: 282 loop : -1.53 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.014 0.001 TYR A 661 PHE 0.012 0.001 PHE B 522 TRP 0.011 0.001 TRP A1466 HIS 0.003 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (17384) covalent geometry : angle 0.48001 / 0.25 (23600) hydrogen bonds : bond 0.03893 / 2.48 ( 669) hydrogen bonds : angle 4.08286 / 2.95 ( 1941) metal coordination : bond 0.00347 / 0.25 ( 14) metal coordination : angle 3.24400 / 2.34 ( 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 167 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.669 Fit side-chains REVERT: B 24 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6009 (mpp) REVERT: B 34 GLU cc_start: 0.7666 (tp30) cc_final: 0.7034 (mt-10) REVERT: B 118 ASP cc_start: 0.7689 (m-30) cc_final: 0.7196 (t0) REVERT: B 145 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6967 (mtt180) REVERT: B 229 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6525 (ptm) REVERT: B 542 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7785 (mm) REVERT: B 632 ASN cc_start: 0.7769 (t0) cc_final: 0.7553 (t0) REVERT: B 663 VAL cc_start: 0.7689 (t) cc_final: 0.7164 (p) REVERT: A 290 ARG cc_start: 0.7224 (tmm160) cc_final: 0.6977 (tmm160) REVERT: A 343 LYS cc_start: 0.7887 (tptp) cc_final: 0.7546 (tppp) REVERT: A 422 ASP cc_start: 0.7948 (t0) cc_final: 0.7641 (t0) REVERT: A 491 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (mm-30) REVERT: A 513 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: A 740 ASP cc_start: 0.8302 (p0) cc_final: 0.8039 (p0) REVERT: A 1321 ASP cc_start: 0.7885 (p0) cc_final: 0.7525 (p0) REVERT: A 1365 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 1395 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6853 (mmm160) outliers start: 26 outliers final: 13 residues processed: 161 average time/residue: 0.7118 time to fit residues: 126.4901 Evaluate side-chains 153 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 145 ARG Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 483 ILE 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 1395 ARG Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 66 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.143534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107076 restraints weight = 22303.569| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.27 r_work: 0.3114 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17398 Z= 0.119 Angle : 0.493 7.614 23615 Z= 0.258 Chirality : 0.039 0.170 2501 Planarity : 0.004 0.049 2941 Dihedral : 11.565 94.249 2772 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.56 % Allowed : 14.56 % Favored : 83.88 % 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: 1.95 (0.19), residues: 759 sheet: 0.03 (0.30), residues: 282 loop : -1.51 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 25 TYR 0.012 0.001 TYR A 492 PHE 0.013 0.001 PHE A 776 TRP 0.014 0.001 TRP B 693 HIS 0.004 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17384) covalent geometry : angle 0.48636 / 0.26 (23600) hydrogen bonds : bond 0.04178 / 2.66 ( 669) hydrogen bonds : angle 4.07600 / 2.95 ( 1941) metal coordination : bond 0.00435 / 0.30 ( 14) metal coordination : angle 3.14149 / 2.29 ( 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 162 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.697 Fit side-chains REVERT: B 24 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6002 (mpp) REVERT: B 34 GLU cc_start: 0.7697 (tp30) cc_final: 0.7106 (mt-10) REVERT: B 118 ASP cc_start: 0.7603 (m-30) cc_final: 0.7160 (t0) REVERT: B 145 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7044 (mtt90) REVERT: B 229 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6560 (ptm) REVERT: B 542 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7845 (mm) REVERT: B 632 ASN cc_start: 0.7723 (t0) cc_final: 0.7519 (t0) REVERT: B 663 VAL cc_start: 0.7699 (t) cc_final: 0.7162 (p) REVERT: B 667 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6835 (tm-30) REVERT: A 267 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: A 290 ARG cc_start: 0.7270 (tmm160) cc_final: 0.7021 (tmm160) REVERT: A 343 LYS cc_start: 0.7901 (tptp) cc_final: 0.7561 (tppp) REVERT: A 361 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7068 (mp) REVERT: A 422 ASP cc_start: 0.7993 (t0) cc_final: 0.7671 (t0) REVERT: A 426 LYS cc_start: 0.8091 (mttt) cc_final: 0.7681 (mtmp) REVERT: A 513 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: A 740 ASP cc_start: 0.8357 (p0) cc_final: 0.8104 (p0) REVERT: A 1321 ASP cc_start: 0.7895 (p0) cc_final: 0.7520 (p0) REVERT: A 1365 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 1395 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7298 (mmt90) outliers start: 27 outliers final: 15 residues processed: 155 average time/residue: 0.7518 time to fit residues: 128.4147 Evaluate side-chains 157 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 145 ARG Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 3 THR 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 513 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 99 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.145344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108803 restraints weight = 22223.711| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.23 r_work: 0.3151 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2070 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= 0.091 Angle : 0.475 13.300 23615 Z= 0.245 Chirality : 0.038 0.178 2501 Planarity : 0.004 0.045 2941 Dihedral : 11.509 93.660 2772 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.56 % Allowed : 14.73 % Favored : 83.71 % 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: 0.32 (0.19), residues: 1959 helix: 2.03 (0.19), residues: 759 sheet: 0.17 (0.30), residues: 280 loop : -1.41 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.014 0.001 TYR A 661 PHE 0.011 0.001 PHE A 776 TRP 0.014 0.001 TRP B 693 HIS 0.003 0.000 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (17384) covalent geometry : angle 0.46890 / 0.25 (23600) hydrogen bonds : bond 0.03497 / 2.24 ( 669) hydrogen bonds : angle 3.94754 / 2.86 ( 1941) metal coordination : bond 0.00307 / 0.22 ( 14) metal coordination : angle 3.12046 / 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 169 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.509 Fit side-chains REVERT: B 24 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5965 (mpp) REVERT: B 34 GLU cc_start: 0.7608 (tp30) cc_final: 0.7006 (mt-10) REVERT: B 118 ASP cc_start: 0.7661 (m-30) cc_final: 0.7202 (t0) REVERT: B 145 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6924 (mtt90) REVERT: B 229 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6641 (ptm) REVERT: B 232 GLN cc_start: 0.8395 (mm110) cc_final: 0.7181 (tt0) REVERT: B 289 MET cc_start: 0.7026 (ttp) cc_final: 0.6821 (tmt) REVERT: B 542 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 632 ASN cc_start: 0.7673 (t0) cc_final: 0.7471 (t0) REVERT: B 663 VAL cc_start: 0.7578 (t) cc_final: 0.7061 (p) REVERT: A 267 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: A 290 ARG cc_start: 0.7244 (tmm160) cc_final: 0.7006 (tmm160) REVERT: A 343 LYS cc_start: 0.7839 (tptp) cc_final: 0.7522 (tppp) REVERT: A 361 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7070 (mp) REVERT: A 422 ASP cc_start: 0.7906 (t0) cc_final: 0.7571 (t0) REVERT: A 426 LYS cc_start: 0.8034 (mttt) cc_final: 0.7656 (mtmm) REVERT: A 513 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 740 ASP cc_start: 0.8231 (p0) cc_final: 0.7999 (p0) REVERT: A 1321 ASP cc_start: 0.7871 (p0) cc_final: 0.7516 (p0) REVERT: A 1365 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 1395 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.6822 (mmm160) outliers start: 27 outliers final: 14 residues processed: 160 average time/residue: 0.6533 time to fit residues: 115.2761 Evaluate side-chains 160 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 145 ARG Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET 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 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 513 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.144227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107656 restraints weight = 22327.387| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.25 r_work: 0.3132 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17398 Z= 0.116 Angle : 0.495 11.734 23615 Z= 0.254 Chirality : 0.039 0.171 2501 Planarity : 0.004 0.045 2941 Dihedral : 11.470 93.874 2772 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.50 % Allowed : 15.14 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1959 helix: 2.03 (0.19), residues: 759 sheet: 0.17 (0.30), residues: 282 loop : -1.41 (0.19), residues: 918 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 0.015 0.001 TRP B 693 HIS 0.004 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (17384) covalent geometry : angle 0.48872 / 0.25 (23600) hydrogen bonds : bond 0.03935 / 2.52 ( 669) hydrogen bonds : angle 3.98297 / 2.88 ( 1941) metal coordination : bond 0.00426 / 0.29 ( 14) metal coordination : angle 3.04945 / 2.22 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5806.64 seconds wall clock time: 99 minutes 34.57 seconds (5974.57 seconds total)