Starting phenix.real_space_refine on Mon Nov 18 18:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/11_2024/8i4y_35188_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/11_2024/8i4y_35188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/11_2024/8i4y_35188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/11_2024/8i4y_35188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/11_2024/8i4y_35188_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/11_2024/8i4y_35188_trim.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 C 15374 2.51 5 N 4566 2.21 5 O 4682 1.98 5 H 24348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 292 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 24479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 24479 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 122, 'TRANS': 1564} Chain: "B" Number of atoms: 24479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 24479 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 122, 'TRANS': 1564} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'3HA': 1, 'ONF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ONF:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'3HA': 1, 'ONF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ONF:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 21.21, per 1000 atoms: 0.43 Number of scatterers: 49016 At special positions: 0 Unit cell: (195.8, 172.66, 121.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 O 4682 8.00 N 4566 7.00 C 15374 6.00 H 24348 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.76 Conformation dependent library (CDL) restraints added in 3.9 seconds 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 18 sheets defined 44.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.898A pdb=" N LEU A 81 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 111 through 129 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 174 through 184 removed outlier: 4.091A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.949A pdb=" N ARG A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.622A pdb=" N ILE A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.624A pdb=" N ALA A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 removed outlier: 4.411A pdb=" N SER A 411 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 491 removed outlier: 3.666A pdb=" N LEU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.877A pdb=" N THR A 504 " --> pdb=" O HIS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 533 Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.537A pdb=" N GLY A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.605A pdb=" N ALA A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.875A pdb=" N ALA A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 removed outlier: 4.021A pdb=" N ALA A 606 " --> pdb=" O PRO A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 619 through 640 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 665 through 686 removed outlier: 3.513A pdb=" N VAL A 673 " --> pdb=" O GLY A 669 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 4.094A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 729 through 744 removed outlier: 3.572A pdb=" N TRP A 740 " --> pdb=" O VAL A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 774 removed outlier: 3.685A pdb=" N GLU A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 774 " --> pdb=" O ARG A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 Processing helix chain 'A' and resid 801 through 811 removed outlier: 3.727A pdb=" N TRP A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS A 808 " --> pdb=" O HIS A 804 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.570A pdb=" N GLY A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 868 through 884 removed outlier: 4.126A pdb=" N ALA A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.309A pdb=" N GLN A 891 " --> pdb=" O ASP A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 960 removed outlier: 3.826A pdb=" N ALA A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 985 removed outlier: 3.551A pdb=" N ARG A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Proline residue: A1066 - end of helix Processing helix chain 'A' and resid 1073 through 1084 removed outlier: 3.817A pdb=" N GLN A1084 " --> pdb=" O ARG A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1093 Processing helix chain 'A' and resid 1123 through 1138 removed outlier: 3.665A pdb=" N SER A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1197 Processing helix chain 'A' and resid 1200 through 1205 removed outlier: 3.972A pdb=" N LEU A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1255 Processing helix chain 'A' and resid 1282 through 1296 removed outlier: 3.509A pdb=" N VAL A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A1292 " --> pdb=" O LYS A1288 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A1293 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A1294 " --> pdb=" O PHE A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1313 removed outlier: 3.694A pdb=" N ALA A1311 " --> pdb=" O ALA A1308 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG A1312 " --> pdb=" O GLY A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1344 removed outlier: 3.613A pdb=" N GLY A1330 " --> pdb=" O CYS A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1347 No H-bonds generated for 'chain 'A' and resid 1345 through 1347' Processing helix chain 'A' and resid 1367 through 1369 No H-bonds generated for 'chain 'A' and resid 1367 through 1369' Processing helix chain 'A' and resid 1370 through 1384 removed outlier: 4.102A pdb=" N THR A1374 " --> pdb=" O GLN A1370 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP A1382 " --> pdb=" O THR A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1411 Processing helix chain 'A' and resid 1438 through 1444 removed outlier: 3.663A pdb=" N GLU A1442 " --> pdb=" O ALA A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1472 removed outlier: 4.078A pdb=" N GLU A1467 " --> pdb=" O ALA A1463 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP A1468 " --> pdb=" O ALA A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1497 Processing helix chain 'A' and resid 1512 through 1524 Processing helix chain 'A' and resid 1544 through 1548 Processing helix chain 'A' and resid 1549 through 1574 removed outlier: 4.332A pdb=" N GLY A1554 " --> pdb=" O GLY A1550 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1555 " --> pdb=" O ALA A1551 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY A1563 " --> pdb=" O GLY A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix removed outlier: 3.501A pdb=" N THR A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1592 No H-bonds generated for 'chain 'A' and resid 1590 through 1592' Processing helix chain 'A' and resid 1598 through 1617 removed outlier: 3.593A pdb=" N HIS A1615 " --> pdb=" O LEU A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1634 Processing helix chain 'A' and resid 1639 through 1648 Processing helix chain 'A' and resid 1654 through 1663 removed outlier: 3.583A pdb=" N MET A1658 " --> pdb=" O PRO A1654 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1669 Processing helix chain 'A' and resid 1683 through 1691 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.676A pdb=" N LEU B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.505A pdb=" N ARG B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 160 through 172 removed outlier: 3.981A pdb=" N HIS B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 184 removed outlier: 3.729A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 213 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 320 removed outlier: 3.609A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.690A pdb=" N VAL B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.807A pdb=" N GLN B 353 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.784A pdb=" N GLY B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 removed outlier: 4.430A pdb=" N SER B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 491 removed outlier: 3.553A pdb=" N LEU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.763A pdb=" N HIS B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 504 " --> pdb=" O HIS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 564 through 569 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.014A pdb=" N GLY B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 removed outlier: 4.000A pdb=" N ALA B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 599 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 619 through 640 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 665 through 685 removed outlier: 3.802A pdb=" N ARG B 678 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 682 " --> pdb=" O ARG B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.710A pdb=" N ALA B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 711 Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.555A pdb=" N ALA B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS B 743 " --> pdb=" O HIS B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 774 removed outlier: 3.554A pdb=" N GLU B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 772 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 774 " --> pdb=" O ARG B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing helix chain 'B' and resid 801 through 807 removed outlier: 3.712A pdb=" N TRP B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 826 Processing helix chain 'B' and resid 839 through 848 Processing helix chain 'B' and resid 868 through 884 removed outlier: 4.371A pdb=" N ALA B 872 " --> pdb=" O PRO B 868 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B 873 " --> pdb=" O PRO B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 4.509A pdb=" N GLN B 891 " --> pdb=" O ASP B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 960 removed outlier: 4.580A pdb=" N ALA B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY B 958 " --> pdb=" O GLY B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 1061 through 1069 Proline residue: B1066 - end of helix Processing helix chain 'B' and resid 1073 through 1083 Processing helix chain 'B' and resid 1090 through 1093 Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1123 through 1138 removed outlier: 4.093A pdb=" N SER B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1197 Processing helix chain 'B' and resid 1241 through 1255 removed outlier: 3.993A pdb=" N PHE B1255 " --> pdb=" O GLU B1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 1282 through 1297 removed outlier: 3.656A pdb=" N VAL B1286 " --> pdb=" O ASP B1282 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B1292 " --> pdb=" O LYS B1288 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B1293 " --> pdb=" O THR B1289 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B1294 " --> pdb=" O PHE B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'B' and resid 1311 through 1317 Processing helix chain 'B' and resid 1320 through 1344 removed outlier: 3.939A pdb=" N ARG B1328 " --> pdb=" O ALA B1324 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B1330 " --> pdb=" O CYS B1326 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B1331 " --> pdb=" O ARG B1327 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1347 No H-bonds generated for 'chain 'B' and resid 1345 through 1347' Processing helix chain 'B' and resid 1367 through 1369 No H-bonds generated for 'chain 'B' and resid 1367 through 1369' Processing helix chain 'B' and resid 1370 through 1384 removed outlier: 3.939A pdb=" N THR B1374 " --> pdb=" O GLN B1370 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP B1382 " --> pdb=" O THR B1378 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B1383 " --> pdb=" O SER B1379 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1412 removed outlier: 3.545A pdb=" N LEU B1406 " --> pdb=" O THR B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1444 Processing helix chain 'B' and resid 1458 through 1472 removed outlier: 3.799A pdb=" N ALA B1464 " --> pdb=" O ARG B1460 " (cutoff:3.500A) Processing helix chain 'B' and resid 1481 through 1486 removed outlier: 3.535A pdb=" N GLU B1485 " --> pdb=" O ALA B1482 " (cutoff:3.500A) Processing helix chain 'B' and resid 1489 through 1496 Processing helix chain 'B' and resid 1512 through 1524 removed outlier: 3.574A pdb=" N ALA B1520 " --> pdb=" O VAL B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1549 through 1574 removed outlier: 3.872A pdb=" N ALA B1558 " --> pdb=" O GLY B1554 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY B1563 " --> pdb=" O GLY B1559 " (cutoff:3.500A) Proline residue: B1564 - end of helix removed outlier: 3.501A pdb=" N THR B1572 " --> pdb=" O THR B1568 " (cutoff:3.500A) Processing helix chain 'B' and resid 1590 through 1592 No H-bonds generated for 'chain 'B' and resid 1590 through 1592' Processing helix chain 'B' and resid 1598 through 1618 removed outlier: 3.619A pdb=" N HIS B1615 " --> pdb=" O LEU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1634 Processing helix chain 'B' and resid 1639 through 1649 Processing helix chain 'B' and resid 1654 through 1663 Processing helix chain 'B' and resid 1683 through 1690 Processing helix chain 'B' and resid 1715 through 1719 Processing sheet with id=AA1, first strand: chain 'A' and resid 414 through 416 removed outlier: 3.786A pdb=" N ALA A 328 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 435 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 443 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE A 291 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N HIS A 445 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 289 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 447 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 284 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 268 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 41 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET A 266 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS A 43 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA A 264 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N VAL A 191 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 142 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 193 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 144 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N VAL B 191 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 142 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 193 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 144 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 141 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLY B 222 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR B 143 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ALA B 224 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY B 145 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 264 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N CYS B 43 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET B 266 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 41 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 268 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 284 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 447 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 289 " --> pdb=" O HIS B 445 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS B 445 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE B 291 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN B 443 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 328 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 364 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 361 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA4, first strand: chain 'A' and resid 467 through 473 removed outlier: 3.825A pdb=" N GLY A 517 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.558A pdb=" N THR A 647 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR A 550 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N LEU A 648 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 552 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N HIS A 650 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE A 554 " --> pdb=" O HIS A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 713 through 720 removed outlier: 6.747A pdb=" N VAL A 725 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL A 718 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR A 723 " --> pdb=" O VAL A 718 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 935 through 936 removed outlier: 5.869A pdb=" N GLY A1032 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU A1042 " --> pdb=" O GLY A1032 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY A1045 " --> pdb=" O ILE A 997 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A 997 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP A1149 " --> pdb=" O GLY A 996 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG A 998 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER A1147 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1148 " --> pdb=" O LEU A1191 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A1191 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU A1185 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG A1184 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER A1179 " --> pdb=" O ARG A1184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A1186 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA A1173 " --> pdb=" O GLY A1190 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A1161 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A1097 " --> pdb=" O LEU A1108 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A1098 " --> pdb=" O LEU A1072 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 968 through 969 removed outlier: 3.655A pdb=" N GLN A 962 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1274 through 1276 removed outlier: 9.392A pdb=" N GLU A1274 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A1261 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A1276 " --> pdb=" O ALA A1261 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA A1263 " --> pdb=" O VAL A1276 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A1239 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY A1264 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER A1234 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A1303 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A1236 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A1305 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A1238 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA A1301 " --> pdb=" O ARG A1349 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL A1351 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A1303 " --> pdb=" O VAL A1351 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS A1353 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A1305 " --> pdb=" O CYS A1353 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ALA A1355 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A1350 " --> pdb=" O ALA A1390 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A1392 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A1352 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU A1394 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER A1354 " --> pdb=" O LEU A1394 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS A1389 " --> pdb=" O GLY A1417 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU A1419 " --> pdb=" O CYS A1389 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN A1391 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A1421 " --> pdb=" O GLN A1391 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP A1393 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 15.484A pdb=" N ALA A1416 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N LEU A1431 " --> pdb=" O ALA A1416 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG A1418 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A1676 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 10.845A pdb=" N ALA A1677 " --> pdb=" O VAL A1622 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA A1624 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A1679 " --> pdb=" O ALA A1624 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA A1626 " --> pdb=" O LEU A1679 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A1531 " --> pdb=" O PHE A1582 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N VAL A1584 " --> pdb=" O ARG A1531 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A1533 " --> pdb=" O VAL A1584 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N SER A1586 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LEU A1535 " --> pdb=" O SER A1586 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N SER A1588 " --> pdb=" O LEU A1535 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A1451 " --> pdb=" O GLY A1532 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N LEU A1534 " --> pdb=" O THR A1451 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A1453 " --> pdb=" O LEU A1534 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AB2, first strand: chain 'B' and resid 393 through 394 Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 473 removed outlier: 3.684A pdb=" N GLY B 517 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.606A pdb=" N THR B 647 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR B 550 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N LEU B 648 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 552 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS B 650 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE B 554 " --> pdb=" O HIS B 650 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 751 through 752 removed outlier: 8.692A pdb=" N THR B 723 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL B 718 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 725 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 935 through 936 removed outlier: 5.906A pdb=" N GLY B1032 " --> pdb=" O GLU B1042 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU B1042 " --> pdb=" O GLY B1032 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY B1045 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 997 " --> pdb=" O GLY B1045 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B1149 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG B 998 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER B1147 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B1148 " --> pdb=" O LEU B1191 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B1191 " --> pdb=" O VAL B1148 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU B1185 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG B1184 " --> pdb=" O SER B1179 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N SER B1179 " --> pdb=" O ARG B1184 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA B1173 " --> pdb=" O GLY B1190 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B1097 " --> pdb=" O LEU B1108 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B1098 " --> pdb=" O LEU B1072 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 967 through 969 removed outlier: 3.797A pdb=" N GLN B 962 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1274 through 1276 removed outlier: 9.247A pdb=" N GLU B1274 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B1261 " --> pdb=" O GLU B1274 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL B1276 " --> pdb=" O ALA B1261 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA B1263 " --> pdb=" O VAL B1276 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B1239 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY B1264 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER B1234 " --> pdb=" O VAL B1300 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B1302 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA B1301 " --> pdb=" O ARG B1349 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL B1351 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B1303 " --> pdb=" O VAL B1351 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS B1353 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B1305 " --> pdb=" O CYS B1353 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B1350 " --> pdb=" O ALA B1390 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL B1392 " --> pdb=" O ILE B1350 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B1352 " --> pdb=" O VAL B1392 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 15.293A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B1425 " --> pdb=" O ARG B1422 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N ALA B1677 " --> pdb=" O VAL B1622 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA B1624 " --> pdb=" O ALA B1677 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B1679 " --> pdb=" O ALA B1624 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA B1626 " --> pdb=" O LEU B1679 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ARG B1681 " --> pdb=" O ALA B1626 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B1582 " --> pdb=" O ARG B1531 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR B1451 " --> pdb=" O LEU B1530 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B1532 " --> pdb=" O THR B1451 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1274 through 1276 removed outlier: 9.247A pdb=" N GLU B1274 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B1261 " --> pdb=" O GLU B1274 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL B1276 " --> pdb=" O ALA B1261 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA B1263 " --> pdb=" O VAL B1276 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B1239 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY B1264 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER B1234 " --> pdb=" O VAL B1300 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B1302 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA B1301 " --> pdb=" O ARG B1349 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N VAL B1351 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B1303 " --> pdb=" O VAL B1351 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS B1353 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B1305 " --> pdb=" O CYS B1353 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B1350 " --> pdb=" O ALA B1390 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL B1392 " --> pdb=" O ILE B1350 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B1352 " --> pdb=" O VAL B1392 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 15.293A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B1425 " --> pdb=" O ARG B1422 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG B1681 " --> pdb=" O TYR B1651 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.02 Time building geometry restraints manager: 14.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 24324 1.12 - 1.29: 4361 1.29 - 1.47: 8860 1.47 - 1.64: 11933 1.64 - 1.82: 68 Bond restraints: 49546 Sorted by residual: bond pdb=" N ALA B 323 " pdb=" H ALA B 323 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" CD1 PHE A 627 " pdb=" HD1 PHE A 627 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" N LEU A1151 " pdb=" H LEU A1151 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" N ALA A 107 " pdb=" H ALA A 107 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" NH1 ARG B 912 " pdb="HH11 ARG B 912 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 49541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 75146 2.62 - 5.23: 11336 5.23 - 7.85: 3082 7.85 - 10.47: 76 10.47 - 13.08: 24 Bond angle restraints: 89664 Sorted by residual: angle pdb=" C VAL A 916 " pdb=" N PRO A 917 " pdb=" CA PRO A 917 " ideal model delta sigma weight residual 119.66 124.23 -4.57 7.30e-01 1.88e+00 3.91e+01 angle pdb=" CA ASP B 64 " pdb=" CB ASP B 64 " pdb=" CG ASP B 64 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.89e+01 angle pdb=" N SER A 250 " pdb=" CA SER A 250 " pdb=" C SER A 250 " ideal model delta sigma weight residual 111.33 118.54 -7.21 1.21e+00 6.83e-01 3.55e+01 angle pdb=" N PRO A 928 " pdb=" CA PRO A 928 " pdb=" C PRO A 928 " ideal model delta sigma weight residual 110.70 117.95 -7.25 1.22e+00 6.72e-01 3.53e+01 angle pdb=" C VAL B 916 " pdb=" N PRO B 917 " pdb=" CA PRO B 917 " ideal model delta sigma weight residual 119.66 123.53 -3.87 7.20e-01 1.93e+00 2.89e+01 ... (remaining 89659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 21611 21.54 - 43.07: 1151 43.07 - 64.61: 522 64.61 - 86.14: 36 86.14 - 107.68: 8 Dihedral angle restraints: 23328 sinusoidal: 12976 harmonic: 10352 Sorted by residual: dihedral pdb=" CA LYS A 249 " pdb=" C LYS A 249 " pdb=" N SER A 250 " pdb=" CA SER A 250 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA THR A 397 " pdb=" C THR A 397 " pdb=" N VAL A 398 " pdb=" CA VAL A 398 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLY A1279 " pdb=" C GLY A1279 " pdb=" N THR A1280 " pdb=" CA THR A1280 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 23325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2571 0.091 - 0.183: 1075 0.183 - 0.274: 185 0.274 - 0.365: 24 0.365 - 0.457: 13 Chirality restraints: 3868 Sorted by residual: chirality pdb=" CA ASP B1222 " pdb=" N ASP B1222 " pdb=" C ASP B1222 " pdb=" CB ASP B1222 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA VAL B 862 " pdb=" N VAL B 862 " pdb=" C VAL B 862 " pdb=" CB VAL B 862 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA GLN B 33 " pdb=" N GLN B 33 " pdb=" C GLN B 33 " pdb=" CB GLN B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 3865 not shown) Planarity restraints: 7786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1337 " -0.239 9.50e-02 1.11e+02 1.31e-01 2.47e+02 pdb=" NE ARG B1337 " -0.111 2.00e-02 2.50e+03 pdb=" CZ ARG B1337 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG B1337 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG B1337 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B1337 " 0.184 2.00e-02 2.50e+03 pdb="HH12 ARG B1337 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG B1337 " 0.190 2.00e-02 2.50e+03 pdb="HH22 ARG B1337 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1337 " 0.239 9.50e-02 1.11e+02 1.30e-01 2.42e+02 pdb=" NE ARG A1337 " 0.086 2.00e-02 2.50e+03 pdb=" CZ ARG A1337 " 0.076 2.00e-02 2.50e+03 pdb=" NH1 ARG A1337 " 0.056 2.00e-02 2.50e+03 pdb=" NH2 ARG A1337 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARG A1337 " -0.182 2.00e-02 2.50e+03 pdb="HH12 ARG A1337 " 0.033 2.00e-02 2.50e+03 pdb="HH21 ARG A1337 " -0.192 2.00e-02 2.50e+03 pdb="HH22 ARG A1337 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1651 " -0.202 2.00e-02 2.50e+03 8.92e-02 2.39e+02 pdb=" CG TYR B1651 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B1651 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR B1651 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR B1651 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR B1651 " 0.063 2.00e-02 2.50e+03 pdb=" CZ TYR B1651 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B1651 " -0.189 2.00e-02 2.50e+03 pdb=" HD1 TYR B1651 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 TYR B1651 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR B1651 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR B1651 " 0.029 2.00e-02 2.50e+03 ... (remaining 7783 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3469 2.19 - 2.79: 86465 2.79 - 3.40: 135734 3.40 - 4.00: 179207 4.00 - 4.60: 262347 Nonbonded interactions: 667222 Sorted by model distance: nonbonded pdb=" HG SER A1591 " pdb=" OD2 ASP A1605 " model vdw 1.590 2.450 nonbonded pdb=" OE1 GLU B 654 " pdb=" HG SER B 787 " model vdw 1.596 2.450 nonbonded pdb=" HG SER B1512 " pdb=" OD1 ASP B1515 " model vdw 1.597 2.450 nonbonded pdb=" HG SER B 665 " pdb=" OD2 ASP B 668 " model vdw 1.597 2.450 nonbonded pdb=" OD1 ASP B 408 " pdb=" HG SER B 410 " model vdw 1.600 2.450 ... (remaining 667217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 2.800 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: 0.850 Extract box with map and model: 1.640 Check model and map are aligned: 0.320 Set scattering table: 0.410 Process input model: 99.730 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.012 0.053 25198 Z= 0.831 Angle : 1.826 9.054 34402 Z= 1.229 Chirality : 0.097 0.457 3868 Planarity : 0.016 0.161 4658 Dihedral : 12.825 107.677 9074 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.16 % Allowed : 2.89 % Favored : 95.95 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3370 helix: -1.03 (0.12), residues: 1214 sheet: 1.08 (0.25), residues: 440 loop : -0.48 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.021 TRP A 122 HIS 0.024 0.003 HIS A1461 PHE 0.071 0.014 PHE B 778 TYR 0.185 0.025 TYR B1651 ARG 0.012 0.001 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 413 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLU cc_start: 0.8001 (tt0) cc_final: 0.7734 (tt0) REVERT: A 681 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7210 (mt-10) REVERT: A 806 LEU cc_start: 0.7349 (tp) cc_final: 0.7119 (tp) REVERT: A 1402 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7797 (p) REVERT: B 330 GLU cc_start: 0.8542 (tp30) cc_final: 0.7942 (tm-30) REVERT: B 387 MET cc_start: 0.9044 (mmm) cc_final: 0.8814 (mmm) REVERT: B 479 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7275 (tt) REVERT: B 497 ASP cc_start: 0.8156 (m-30) cc_final: 0.7891 (m-30) REVERT: B 806 LEU cc_start: 0.8287 (tp) cc_final: 0.7963 (tp) outliers start: 28 outliers final: 10 residues processed: 439 average time/residue: 1.1448 time to fit residues: 715.0222 Evaluate side-chains 157 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 305 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 183 GLN A 482 GLN A1461 HIS A1617 GLN ** B 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25198 Z= 0.263 Angle : 0.717 8.542 34402 Z= 0.382 Chirality : 0.044 0.210 3868 Planarity : 0.007 0.076 4658 Dihedral : 7.173 94.595 3755 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.45 % Allowed : 7.27 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3370 helix: -0.07 (0.14), residues: 1274 sheet: 0.86 (0.22), residues: 558 loop : -0.51 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 423 HIS 0.009 0.002 HIS B 399 PHE 0.022 0.002 PHE A 850 TYR 0.015 0.002 TYR B 151 ARG 0.005 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 ARG cc_start: 0.6914 (mtt180) cc_final: 0.6666 (mpt-90) REVERT: A 681 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7306 (mt-10) REVERT: A 1284 ASP cc_start: 0.7094 (t70) cc_final: 0.6676 (t0) REVERT: A 1343 TYR cc_start: 0.7513 (m-80) cc_final: 0.7120 (m-80) REVERT: A 1630 TRP cc_start: 0.7974 (m-10) cc_final: 0.7754 (m-10) REVERT: B 330 GLU cc_start: 0.8362 (tp30) cc_final: 0.7825 (tm-30) REVERT: B 479 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7054 (tt) REVERT: B 674 THR cc_start: 0.7631 (p) cc_final: 0.7345 (t) REVERT: B 1067 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5758 (mp0) outliers start: 35 outliers final: 22 residues processed: 182 average time/residue: 0.9989 time to fit residues: 272.3475 Evaluate side-chains 134 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1469 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1183 VAL Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1411 MET Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 369 ASN A1617 GLN B 374 GLN ** B 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25198 Z= 0.335 Angle : 0.641 7.944 34402 Z= 0.333 Chirality : 0.043 0.191 3868 Planarity : 0.006 0.055 4658 Dihedral : 6.261 86.376 3744 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.74 % Allowed : 7.40 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3370 helix: 0.40 (0.14), residues: 1280 sheet: 0.37 (0.21), residues: 568 loop : -0.70 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1124 HIS 0.013 0.002 HIS A 743 PHE 0.015 0.002 PHE A 95 TYR 0.021 0.002 TYR A1343 ARG 0.018 0.001 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 PHE cc_start: 0.7426 (m-10) cc_final: 0.6687 (m-10) REVERT: A 1199 ARG cc_start: 0.5085 (tpp80) cc_final: 0.4866 (tpp80) REVERT: A 1284 ASP cc_start: 0.7179 (t70) cc_final: 0.6973 (t0) REVERT: B 330 GLU cc_start: 0.8330 (tp30) cc_final: 0.7810 (tm-30) REVERT: B 479 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7152 (tt) REVERT: B 552 LEU cc_start: 0.8542 (tp) cc_final: 0.8331 (mt) REVERT: B 659 TYR cc_start: 0.8303 (t80) cc_final: 0.7923 (t80) REVERT: B 674 THR cc_start: 0.7622 (p) cc_final: 0.7350 (t) outliers start: 42 outliers final: 27 residues processed: 155 average time/residue: 0.9148 time to fit residues: 220.7005 Evaluate side-chains 129 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1617 GLN Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1716 GLN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1411 MET Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 33 optimal weight: 0.0870 chunk 145 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25198 Z= 0.187 Angle : 0.561 7.280 34402 Z= 0.285 Chirality : 0.041 0.173 3868 Planarity : 0.005 0.053 4658 Dihedral : 5.686 78.736 3744 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.99 % Allowed : 8.84 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3370 helix: 0.72 (0.15), residues: 1294 sheet: 0.50 (0.21), residues: 566 loop : -0.61 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.005 0.001 HIS A1497 PHE 0.010 0.001 PHE B1238 TYR 0.010 0.001 TYR A 659 ARG 0.010 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 GLU cc_start: 0.8324 (tp30) cc_final: 0.7761 (tm-30) REVERT: B 479 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7187 (tt) REVERT: B 552 LEU cc_start: 0.8549 (tp) cc_final: 0.8340 (mt) REVERT: B 674 THR cc_start: 0.7542 (p) cc_final: 0.7213 (t) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 0.8749 time to fit residues: 182.7233 Evaluate side-chains 119 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 1143 ARG Chi-restraints excluded: chain B residue 1411 MET Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 213 ASN A1370 GLN ** A1505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 369 ASN B 372 HIS ** B1505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25198 Z= 0.411 Angle : 0.660 7.433 34402 Z= 0.343 Chirality : 0.044 0.175 3868 Planarity : 0.006 0.054 4658 Dihedral : 5.878 72.875 3743 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.74 % Allowed : 9.01 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3370 helix: 0.51 (0.14), residues: 1286 sheet: -0.09 (0.21), residues: 594 loop : -0.89 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 914 HIS 0.020 0.002 HIS A1692 PHE 0.026 0.002 PHE A 778 TYR 0.020 0.002 TYR B 659 ARG 0.013 0.001 ARG A1433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.4879 (OUTLIER) cc_final: 0.3783 (mm-40) REVERT: B 330 GLU cc_start: 0.8423 (tp30) cc_final: 0.7963 (tm-30) REVERT: B 479 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7294 (tt) outliers start: 42 outliers final: 23 residues processed: 137 average time/residue: 0.8494 time to fit residues: 186.3224 Evaluate side-chains 116 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1633 SER Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25198 Z= 0.226 Angle : 0.567 11.435 34402 Z= 0.287 Chirality : 0.041 0.168 3868 Planarity : 0.005 0.055 4658 Dihedral : 5.500 65.428 3743 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.12 % Allowed : 9.96 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3370 helix: 0.76 (0.14), residues: 1298 sheet: 0.03 (0.21), residues: 588 loop : -0.85 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.013 0.001 HIS A1692 PHE 0.010 0.001 PHE B 815 TYR 0.009 0.001 TYR B1452 ARG 0.006 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 GLU cc_start: 0.8386 (tp30) cc_final: 0.7921 (tm-30) REVERT: B 479 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7297 (tt) REVERT: B 573 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6517 (mtp180) outliers start: 27 outliers final: 20 residues processed: 121 average time/residue: 0.8437 time to fit residues: 165.8811 Evaluate side-chains 109 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A1014 GLN B 804 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25198 Z= 0.220 Angle : 0.542 6.551 34402 Z= 0.273 Chirality : 0.041 0.219 3868 Planarity : 0.005 0.050 4658 Dihedral : 5.188 58.576 3743 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.99 % Allowed : 10.37 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3370 helix: 1.05 (0.15), residues: 1286 sheet: 0.10 (0.21), residues: 582 loop : -0.86 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1630 HIS 0.011 0.001 HIS A1692 PHE 0.010 0.001 PHE A1029 TYR 0.018 0.001 TYR B1706 ARG 0.016 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.4615 (OUTLIER) cc_final: 0.3145 (mm-40) REVERT: B 330 GLU cc_start: 0.8376 (tp30) cc_final: 0.7921 (tm-30) REVERT: B 479 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7286 (tt) REVERT: B 573 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6551 (mtp180) REVERT: B 674 THR cc_start: 0.7064 (p) cc_final: 0.6799 (t) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.8458 time to fit residues: 154.3228 Evaluate side-chains 112 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25198 Z= 0.271 Angle : 0.550 6.672 34402 Z= 0.279 Chirality : 0.041 0.166 3868 Planarity : 0.005 0.051 4658 Dihedral : 5.186 58.501 3741 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.95 % Allowed : 10.58 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 3370 helix: 1.02 (0.15), residues: 1292 sheet: 0.13 (0.21), residues: 572 loop : -0.92 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1630 HIS 0.009 0.001 HIS A1692 PHE 0.011 0.001 PHE B 815 TYR 0.009 0.001 TYR B 659 ARG 0.004 0.000 ARG A 829 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 GLU cc_start: 0.8401 (tp30) cc_final: 0.7942 (tm-30) REVERT: B 479 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7316 (tt) REVERT: B 573 ARG cc_start: 0.6946 (mtm-85) cc_final: 0.6545 (mtp180) REVERT: B 605 ARG cc_start: 0.8265 (mtp180) cc_final: 0.8022 (mtp180) REVERT: B 674 THR cc_start: 0.7203 (p) cc_final: 0.6889 (t) outliers start: 23 outliers final: 21 residues processed: 109 average time/residue: 0.8998 time to fit residues: 156.6298 Evaluate side-chains 110 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1580 THR Chi-restraints excluded: chain B residue 1632 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.7980 chunk 310 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 272 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25198 Z= 0.208 Angle : 0.526 7.223 34402 Z= 0.264 Chirality : 0.041 0.166 3868 Planarity : 0.005 0.050 4658 Dihedral : 5.005 58.347 3741 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.83 % Allowed : 10.66 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3370 helix: 1.19 (0.15), residues: 1290 sheet: 0.18 (0.21), residues: 572 loop : -0.89 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1630 HIS 0.009 0.001 HIS A1692 PHE 0.014 0.001 PHE A 778 TYR 0.009 0.001 TYR B 659 ARG 0.005 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 GLU cc_start: 0.8374 (tp30) cc_final: 0.7920 (tm-30) REVERT: B 479 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7237 (tt) REVERT: B 573 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6516 (mtp180) REVERT: B 1580 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8028 (t) outliers start: 20 outliers final: 17 residues processed: 112 average time/residue: 0.9207 time to fit residues: 164.1886 Evaluate side-chains 107 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1580 THR Chi-restraints excluded: chain B residue 1632 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 4.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 334 optimal weight: 0.9980 chunk 308 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25198 Z= 0.198 Angle : 0.520 6.879 34402 Z= 0.260 Chirality : 0.040 0.188 3868 Planarity : 0.005 0.049 4658 Dihedral : 4.904 59.019 3741 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.74 % Allowed : 10.79 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3370 helix: 1.28 (0.15), residues: 1290 sheet: 0.18 (0.21), residues: 574 loop : -0.87 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.008 0.001 HIS A1692 PHE 0.010 0.001 PHE B1238 TYR 0.008 0.001 TYR B1452 ARG 0.005 0.000 ARG B 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 GLU cc_start: 0.8363 (tp30) cc_final: 0.7915 (tm-30) REVERT: B 479 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7294 (tt) REVERT: B 573 ARG cc_start: 0.6920 (mtm-85) cc_final: 0.6539 (mtp180) REVERT: B 674 THR cc_start: 0.6912 (p) cc_final: 0.6590 (t) outliers start: 18 outliers final: 16 residues processed: 106 average time/residue: 0.8912 time to fit residues: 150.1856 Evaluate side-chains 106 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1580 THR Chi-restraints excluded: chain B residue 1632 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.6980 chunk 283 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 245 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081397 restraints weight = 183423.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082146 restraints weight = 158358.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.082923 restraints weight = 143074.099| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25198 Z= 0.131 Angle : 0.497 6.310 34402 Z= 0.245 Chirality : 0.040 0.160 3868 Planarity : 0.005 0.050 4658 Dihedral : 4.690 59.539 3740 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.66 % Allowed : 10.87 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3370 helix: 1.46 (0.15), residues: 1290 sheet: 0.39 (0.22), residues: 564 loop : -0.76 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1468 HIS 0.008 0.001 HIS A1692 PHE 0.013 0.001 PHE A 778 TYR 0.007 0.001 TYR A 659 ARG 0.006 0.000 ARG B 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7296.94 seconds wall clock time: 128 minutes 36.93 seconds (7716.93 seconds total)