Starting phenix.real_space_refine on Sat Jul 4 13:40:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eey_28065/07_2026/8eey_28065.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 64 5.49 5 S 88 5.16 5 C 12990 2.51 5 N 3675 2.21 5 O 4065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20886 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 4 Chain: "A" Number of atoms: 12493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 12493 Classifications: {'peptide': 1544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 84, 'TRANS': 1459} Chain breaks: 5 Chain: "B" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6102 Classifications: {'peptide': 735} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 705} Chain breaks: 2 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "D" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 591 Classifications: {'RNA': 28} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 7, 'rna3p': 20} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1591 SG CYS A 86 108.283 62.903 45.935 1.00 79.46 S ATOM 1837 SG CYS A 115 111.694 63.439 44.964 1.00101.35 S ATOM 1899 SG CYS A 123 108.801 65.997 43.831 1.00 88.24 S ATOM 1923 SG CYS A 126 110.019 65.755 47.465 1.00 78.35 S ATOM 4299 SG CYS A 463 79.698 64.258 64.553 1.00 66.28 S ATOM 4361 SG CYS A 472 82.442 62.327 62.644 1.00 48.27 S ATOM 4375 SG CYS A 474 79.015 63.190 60.941 1.00 49.36 S ATOM 4397 SG CYS A 477 81.478 65.783 61.571 1.00 49.30 S ATOM 6215 SG CYS A 706 59.947 66.538 85.373 1.00 58.72 S ATOM 6230 SG CYS A 708 57.091 68.269 83.636 1.00 52.24 S ATOM 6252 SG CYS A 711 60.665 69.312 82.801 1.00 57.35 S ATOM 8144 SG CYS A 965 44.728 95.059 107.529 1.00 44.16 S ATOM 11050 SG CYS A1312 46.774 91.811 107.994 1.00 40.55 S ATOM 11289 SG CYS A1342 43.041 91.677 107.236 1.00 24.45 S ATOM 11307 SG CYS A1345 45.570 92.658 104.584 1.00 40.75 S Time building chain proxies: 3.81, per 1000 atoms: 0.18 Number of scatterers: 20886 At special positions: 0 Unit cell: (131.274, 184.977, 165.087, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 88 16.00 P 64 15.00 O 4065 8.00 N 3675 7.00 C 12990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 948.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 86 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 126 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 115 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 123 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 477 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 474 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 463 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 472 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 708 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 706 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 711 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1345 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1312 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1342 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 965 " Number of angles added : 21 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4492 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 23 sheets defined 41.7% alpha, 13.8% beta 21 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'E' and resid 411 through 415 removed outlier: 3.717A pdb=" N ILE E 414 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 415 " --> pdb=" O PRO E 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 411 through 415' Processing helix chain 'E' and resid 467 through 479 Processing helix chain 'E' and resid 525 through 542 removed outlier: 3.684A pdb=" N LYS E 534 " --> pdb=" O ARG E 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.693A pdb=" N ARG A 26 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.603A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 123 through 129 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.925A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 302 removed outlier: 5.801A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 367 removed outlier: 3.631A pdb=" N MET A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.611A pdb=" N ILE A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 643 through 649 removed outlier: 3.572A pdb=" N VAL A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.540A pdb=" N LEU A 832 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.668A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1055 through 1059 removed outlier: 3.801A pdb=" N LYS A1058 " --> pdb=" O PRO A1055 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A1059 " --> pdb=" O GLN A1056 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1055 through 1059' Processing helix chain 'A' and resid 1060 through 1065 removed outlier: 4.074A pdb=" N ARG A1065 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1109 Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 3.849A pdb=" N ILE A1183 " --> pdb=" O TRP A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.553A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.837A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1326 Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 3.510A pdb=" N ARG A1332 " --> pdb=" O PRO A1329 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A1336 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 4.109A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1538 through 1549 removed outlier: 3.548A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1585 through 1594 removed outlier: 4.742A pdb=" N GLN A1590 " --> pdb=" O LYS A1586 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LYS A1591 " --> pdb=" O GLU A1587 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.675A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 64 Processing helix chain 'B' and resid 65 through 88 removed outlier: 3.780A pdb=" N GLY B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 Processing helix chain 'B' and resid 118 through 134 removed outlier: 3.754A pdb=" N LEU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.940A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 207 through 222 removed outlier: 4.022A pdb=" N ILE B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.604A pdb=" N ILE B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 296 through 314 removed outlier: 4.539A pdb=" N GLU B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.730A pdb=" N TYR B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.818A pdb=" N ARG B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 395 removed outlier: 3.506A pdb=" N ILE B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 452 through 455 Processing helix chain 'B' and resid 464 through 481 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.769A pdb=" N GLU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'B' and resid 527 through 531 Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.547A pdb=" N ASN B 585 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 603 Processing helix chain 'B' and resid 622 through 625 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 675 through 683 Processing helix chain 'B' and resid 696 through 710 removed outlier: 3.607A pdb=" N TYR B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.556A pdb=" N GLN B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing sheet with id=AA1, first strand: chain 'E' and resid 419 through 422 Processing sheet with id=AA2, first strand: chain 'E' and resid 444 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA4, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.664A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA6, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA7, first strand: chain 'A' and resid 106 through 107 removed outlier: 5.914A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 402 through 412 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 402 through 412 current: chain 'A' and resid 527 through 536 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 527 through 536 current: chain 'A' and resid 569 through 581 Processing sheet with id=AA9, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AB1, first strand: chain 'A' and resid 497 through 504 removed outlier: 5.874A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 625 through 634 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 625 through 634 current: chain 'A' and resid 667 through 674 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 667 through 674 current: chain 'A' and resid 770 through 779 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.729A pdb=" N VAL A 656 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB5, first strand: chain 'A' and resid 739 through 744 removed outlier: 11.639A pdb=" N PHE A 739 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N LYS A 756 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 10.421A pdb=" N HIS A 741 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 10.008A pdb=" N LYS A 754 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA A 743 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1558 through 1559 Processing sheet with id=AB7, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB8, first strand: chain 'A' and resid 891 through 901 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 891 through 901 current: chain 'A' and resid 942 through 945 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 942 through 945 current: chain 'A' and resid 1453 through 1463 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1453 through 1463 current: chain 'A' and resid 1495 through 1508 removed outlier: 6.692A pdb=" N GLN A1511 " --> pdb=" O LYS A1507 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.390A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 936 " --> pdb=" O GLU A1446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AC2, first strand: chain 'A' and resid 991 through 995 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1001 through 1012 current: chain 'A' and resid 1080 through 1087 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1093 through 1098 current: chain 'A' and resid 1215 through 1222 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1215 through 1222 current: chain 'A' and resid 1284 through 1288 Processing sheet with id=AC3, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 7.570A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 457 through 463 removed outlier: 6.604A pdb=" N ILE B 424 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 518 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 426 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 570 through 574 removed outlier: 6.555A pdb=" N LEU B 571 " --> pdb=" O TYR B 591 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 590 through 591 current: chain 'B' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 634 through 636 current: chain 'B' and resid 687 through 691 720 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 5.32 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 6703 1.34 - 1.50: 6402 1.50 - 1.66: 8263 1.66 - 1.82: 130 Bond restraints: 21499 Sorted by residual: bond pdb=" CG PRO A1570 " pdb=" CD PRO A1570 " ideal model delta sigma weight residual 1.503 1.022 0.481 3.40e-02 8.65e+02 2.00e+02 bond pdb=" CA ILE A1519 " pdb=" CB ILE A1519 " ideal model delta sigma weight residual 1.539 1.510 0.029 5.40e-03 3.43e+04 2.82e+01 bond pdb=" N PRO A1570 " pdb=" CD PRO A1570 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.57e+01 bond pdb=" N PRO A1570 " pdb=" CA PRO A1570 " ideal model delta sigma weight residual 1.470 1.513 -0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" N VAL A1275 " pdb=" CA VAL A1275 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.07e-02 8.73e+03 4.70e+00 ... (remaining 21494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.10: 29235 5.10 - 10.20: 45 10.20 - 15.30: 1 15.30 - 20.40: 0 20.40 - 25.51: 2 Bond angle restraints: 29283 Sorted by residual: angle pdb=" N PRO A1570 " pdb=" CD PRO A1570 " pdb=" CG PRO A1570 " ideal model delta sigma weight residual 103.20 77.69 25.51 1.50e+00 4.44e-01 2.89e+02 angle pdb=" CA PRO A1570 " pdb=" CB PRO A1570 " pdb=" CG PRO A1570 " ideal model delta sigma weight residual 104.50 82.22 22.28 1.90e+00 2.77e-01 1.37e+02 angle pdb=" C ASN B 481 " pdb=" N GLU B 482 " pdb=" CA GLU B 482 " ideal model delta sigma weight residual 121.70 134.32 -12.62 1.80e+00 3.09e-01 4.91e+01 angle pdb=" O4' G C 5 " pdb=" C1' G C 5 " pdb=" N9 G C 5 " ideal model delta sigma weight residual 108.20 117.10 -8.90 1.50e+00 4.44e-01 3.52e+01 angle pdb=" N PRO A1570 " pdb=" CA PRO A1570 " pdb=" CB PRO A1570 " ideal model delta sigma weight residual 103.19 97.77 5.42 1.00e+00 1.00e+00 2.94e+01 ... (remaining 29278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.97: 11854 19.97 - 39.95: 760 39.95 - 59.92: 212 59.92 - 79.89: 48 79.89 - 99.86: 19 Dihedral angle restraints: 12893 sinusoidal: 5950 harmonic: 6943 Sorted by residual: dihedral pdb=" CA ASN A 640 " pdb=" C ASN A 640 " pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta harmonic sigma weight residual 180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLN A1059 " pdb=" C GLN A1059 " pdb=" N ASP A1060 " pdb=" CA ASP A1060 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLN A1056 " pdb=" C GLN A1056 " pdb=" N LYS A1057 " pdb=" CA LYS A1057 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 12890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2833 0.083 - 0.165: 273 0.165 - 0.247: 6 0.247 - 0.330: 2 0.330 - 0.412: 1 Chirality restraints: 3115 Sorted by residual: chirality pdb=" C1' G C 5 " pdb=" O4' G C 5 " pdb=" C2' G C 5 " pdb=" N9 G C 5 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C1' U C 11 " pdb=" O4' U C 11 " pdb=" C2' U C 11 " pdb=" N1 U C 11 " both_signs ideal model delta sigma weight residual False 2.45 2.14 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1' A C -2 " pdb=" O4' A C -2 " pdb=" C2' A C -2 " pdb=" N9 A C -2 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 3112 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 876 " -0.414 9.50e-02 1.11e+02 1.86e-01 2.12e+01 pdb=" NE ARG A 876 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 876 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 876 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 876 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 5 " -0.060 2.00e-02 2.50e+03 2.62e-02 2.06e+01 pdb=" N9 G C 5 " 0.064 2.00e-02 2.50e+03 pdb=" C8 G C 5 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G C 5 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G C 5 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G C 5 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G C 5 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G C 5 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G C 5 " 0.009 2.00e-02 2.50e+03 pdb=" N3 G C 5 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G C 5 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 11 " -0.042 2.00e-02 2.50e+03 2.36e-02 1.26e+01 pdb=" N1 U C 11 " 0.056 2.00e-02 2.50e+03 pdb=" C2 U C 11 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U C 11 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U C 11 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U C 11 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U C 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U C 11 " 0.003 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 29 2.53 - 3.12: 15080 3.12 - 3.71: 31354 3.71 - 4.31: 47752 4.31 - 4.90: 77329 Nonbonded interactions: 171544 Sorted by model distance: nonbonded pdb=" O ASP A 753 " pdb=" O2' A D -11 " model vdw 1.937 3.040 nonbonded pdb=" O GLU B 482 " pdb=" OG SER B 485 " model vdw 1.959 3.040 nonbonded pdb=" N GLU A 888 " pdb=" OE1 GLU A 888 " model vdw 2.253 3.120 nonbonded pdb=" N GLU A 491 " pdb=" OE1 GLU A 491 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS A 83 " pdb=" OE1 GLU A 213 " model vdw 2.388 3.120 ... (remaining 171539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.481 21515 Z= 0.241 Angle : 0.882 25.506 29304 Z= 0.479 Chirality : 0.049 0.412 3115 Planarity : 0.009 0.186 3576 Dihedral : 15.164 99.863 8401 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.14 % Rotamer: Outliers : 0.14 % Allowed : 10.48 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.17), residues: 2365 helix: 0.02 (0.17), residues: 848 sheet: 0.56 (0.24), residues: 428 loop : -0.06 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 896 TYR 0.025 0.002 TYR A1126 PHE 0.024 0.002 PHE B 17 TRP 0.024 0.003 TRP B 555 HIS 0.008 0.002 HIS A1020 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.24 (21499) covalent geometry : angle 0.87588 / 0.48 (29283) hydrogen bonds : bond 0.17481 / 11.35 ( 771) hydrogen bonds : angle 6.13575 / 4.38 ( 2037) metal coordination : bond 0.00768 / 0.46 ( 16) metal coordination : angle 3.88422 / 2.41 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 434 time to evaluate : 1.039 Fit side-chains REVERT: A 3 THR cc_start: 0.7623 (t) cc_final: 0.7305 (p) REVERT: A 25 ARG cc_start: 0.7276 (mmp80) cc_final: 0.6853 (mtm180) REVERT: A 47 LYS cc_start: 0.7861 (ptmm) cc_final: 0.7555 (ttpp) REVERT: A 79 LYS cc_start: 0.7766 (mptp) cc_final: 0.6980 (mptp) REVERT: A 112 LYS cc_start: 0.7202 (mppt) cc_final: 0.6878 (mmmm) REVERT: A 340 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.6058 (ptmm) REVERT: A 554 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7878 (mt-10) REVERT: A 604 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7001 (tt0) REVERT: A 634 MET cc_start: 0.8965 (mtm) cc_final: 0.8632 (mtp) REVERT: A 650 LYS cc_start: 0.7894 (ptpt) cc_final: 0.7442 (pttm) REVERT: A 669 LYS cc_start: 0.6782 (ttpt) cc_final: 0.6157 (mptt) REVERT: A 735 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6914 (pm20) REVERT: A 878 GLU cc_start: 0.7800 (mp0) cc_final: 0.7507 (mp0) REVERT: A 885 LYS cc_start: 0.8574 (pttt) cc_final: 0.8352 (ptmt) REVERT: A 896 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7171 (ttm170) REVERT: A 1036 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7572 (ttm170) REVERT: A 1161 LYS cc_start: 0.8293 (ptmt) cc_final: 0.7917 (ptpp) REVERT: A 1227 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 1270 LYS cc_start: 0.8343 (mttp) cc_final: 0.8118 (ptmt) REVERT: A 1426 ASP cc_start: 0.7931 (m-30) cc_final: 0.7714 (m-30) REVERT: A 1434 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7483 (mtmm) REVERT: A 1501 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7345 (mm-30) REVERT: A 1518 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7347 (mm-30) REVERT: A 1587 GLU cc_start: 0.7749 (mp0) cc_final: 0.7045 (mp0) REVERT: B 20 LYS cc_start: 0.6247 (mmtm) cc_final: 0.5550 (tppp) REVERT: B 38 MET cc_start: 0.8296 (mmm) cc_final: 0.7700 (mmt) REVERT: B 89 ASN cc_start: 0.6205 (m110) cc_final: 0.5776 (t0) REVERT: B 94 LYS cc_start: 0.7342 (mmtp) cc_final: 0.6967 (tptp) REVERT: B 168 SER cc_start: 0.6510 (p) cc_final: 0.6171 (m) REVERT: B 240 LEU cc_start: 0.7721 (tp) cc_final: 0.7449 (tp) REVERT: B 263 TYR cc_start: 0.6444 (m-80) cc_final: 0.6179 (m-80) REVERT: B 388 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6839 (mm-30) REVERT: B 579 ASP cc_start: 0.5098 (t0) cc_final: 0.4825 (m-30) outliers start: 3 outliers final: 0 residues processed: 435 average time/residue: 0.8727 time to fit residues: 417.6531 Evaluate side-chains 219 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 43 HIS A 149 HIS A 208 ASN A 276 ASN A 464 ASN A 500 HIS A 531 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS A 640 ASN ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS A 985 ASN A1020 HIS A1027 GLN A1089 ASN A1190 ASN A1195 ASN A1246 ASN B 62 GLN B 69 GLN B 673 HIS B 716 ASN B 727 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105373 restraints weight = 24703.328| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.56 r_work: 0.2805 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21515 Z= 0.239 Angle : 0.738 10.936 29304 Z= 0.393 Chirality : 0.050 0.412 3115 Planarity : 0.006 0.112 3576 Dihedral : 9.356 99.072 3406 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % Rotamer: Outliers : 3.43 % Allowed : 13.10 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2365 helix: 0.82 (0.18), residues: 825 sheet: 0.54 (0.24), residues: 437 loop : -0.15 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 780 TYR 0.020 0.002 TYR B 578 PHE 0.023 0.002 PHE A1220 TRP 0.016 0.002 TRP B 517 HIS 0.008 0.002 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (21499) covalent geometry : angle 0.73200 / 0.39 (29283) hydrogen bonds : bond 0.06289 / 4.19 ( 771) hydrogen bonds : angle 4.76126 / 3.39 ( 2037) metal coordination : bond 0.01228 / 0.90 ( 16) metal coordination : angle 3.69988 / 2.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: E 445 LEU cc_start: 0.3403 (OUTLIER) cc_final: 0.3184 (mt) REVERT: A 3 THR cc_start: 0.8152 (t) cc_final: 0.7948 (p) REVERT: A 77 ASP cc_start: 0.8334 (t70) cc_final: 0.8093 (t70) REVERT: A 79 LYS cc_start: 0.8267 (mptp) cc_final: 0.7808 (mptp) REVERT: A 112 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7390 (mmmm) REVERT: A 113 ASN cc_start: 0.8356 (m-40) cc_final: 0.8109 (m110) REVERT: A 263 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: A 601 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7418 (mtpt) REVERT: A 604 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7695 (tt0) REVERT: A 634 MET cc_start: 0.9159 (mtm) cc_final: 0.8864 (mtp) REVERT: A 650 LYS cc_start: 0.8437 (ptpt) cc_final: 0.8113 (pttm) REVERT: A 669 LYS cc_start: 0.7184 (ttpt) cc_final: 0.6541 (mptt) REVERT: A 707 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 735 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7444 (pm20) REVERT: A 878 GLU cc_start: 0.8237 (mp0) cc_final: 0.8030 (mp0) REVERT: A 896 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8122 (ttp-170) REVERT: A 929 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5582 (pt0) REVERT: A 1036 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7853 (ttt180) REVERT: A 1044 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7347 (mptt) REVERT: A 1145 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: A 1161 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7924 (ptpt) REVERT: A 1264 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: A 1299 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7506 (mtp85) REVERT: A 1390 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8296 (tt) REVERT: B 20 LYS cc_start: 0.6342 (mmtm) cc_final: 0.5853 (tppp) REVERT: B 22 ASP cc_start: 0.7054 (m-30) cc_final: 0.6789 (m-30) REVERT: B 38 MET cc_start: 0.8911 (mmm) cc_final: 0.8664 (mmt) REVERT: B 182 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7058 (tpp-160) REVERT: B 330 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7342 (ttp80) REVERT: B 388 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6890 (mm-30) REVERT: B 432 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6522 (pt0) REVERT: B 566 GLU cc_start: 0.4977 (mp0) cc_final: 0.4730 (mm-30) REVERT: B 579 ASP cc_start: 0.5080 (t0) cc_final: 0.4810 (m-30) REVERT: B 611 LEU cc_start: 0.7429 (mp) cc_final: 0.7020 (mp) REVERT: B 640 LEU cc_start: 0.7892 (mt) cc_final: 0.7470 (tp) REVERT: B 727 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.7047 (t0) REVERT: B 736 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7638 (tm) outliers start: 72 outliers final: 23 residues processed: 275 average time/residue: 0.8740 time to fit residues: 265.6581 Evaluate side-chains 223 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 61 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS A 887 HIS A1084 ASN A1098 HIS B 427 HIS B 632 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106114 restraints weight = 24932.386| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.86 r_work: 0.2794 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21515 Z= 0.199 Angle : 0.663 12.245 29304 Z= 0.352 Chirality : 0.047 0.394 3115 Planarity : 0.006 0.067 3576 Dihedral : 9.184 99.782 3402 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 3.81 % Allowed : 14.10 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2365 helix: 1.10 (0.18), residues: 824 sheet: 0.62 (0.24), residues: 442 loop : -0.23 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 780 TYR 0.016 0.002 TYR A1126 PHE 0.020 0.002 PHE A1220 TRP 0.015 0.002 TRP B 517 HIS 0.006 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (21499) covalent geometry : angle 0.65798 / 0.35 (29283) hydrogen bonds : bond 0.05597 / 3.71 ( 771) hydrogen bonds : angle 4.55411 / 3.26 ( 2037) metal coordination : bond 0.00878 / 0.61 ( 16) metal coordination : angle 3.07325 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 24 THR cc_start: 0.8036 (p) cc_final: 0.7823 (m) REVERT: A 77 ASP cc_start: 0.8332 (t70) cc_final: 0.7994 (t0) REVERT: A 79 LYS cc_start: 0.8302 (mptp) cc_final: 0.7874 (mptp) REVERT: A 112 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7389 (mmmm) REVERT: A 587 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7293 (tp-100) REVERT: A 601 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7389 (mtpt) REVERT: A 604 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7736 (tt0) REVERT: A 634 MET cc_start: 0.9143 (mtm) cc_final: 0.8837 (mtp) REVERT: A 650 LYS cc_start: 0.8421 (ptpt) cc_final: 0.8090 (pttm) REVERT: A 669 LYS cc_start: 0.7173 (ttpt) cc_final: 0.6497 (mptt) REVERT: A 707 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8394 (mt-10) REVERT: A 735 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7436 (pm20) REVERT: A 738 THR cc_start: 0.9223 (t) cc_final: 0.8864 (m) REVERT: A 855 ARG cc_start: 0.8110 (mpt-90) cc_final: 0.7907 (mtp-110) REVERT: A 896 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8132 (ttp-170) REVERT: A 929 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5611 (pt0) REVERT: A 1036 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7909 (ttt180) REVERT: A 1044 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7354 (mptt) REVERT: A 1065 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5916 (mtt-85) REVERT: A 1145 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: A 1161 LYS cc_start: 0.8354 (ptmt) cc_final: 0.7960 (mppt) REVERT: A 1187 ASP cc_start: 0.8394 (p0) cc_final: 0.8173 (t70) REVERT: A 1264 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: A 1268 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8315 (mtmm) REVERT: A 1299 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7503 (mtp85) REVERT: A 1390 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 1518 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: A 1537 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: A 1585 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7517 (ptmt) REVERT: B 20 LYS cc_start: 0.6466 (mmtm) cc_final: 0.6253 (mmtm) REVERT: B 220 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6777 (mmm160) REVERT: B 234 ASN cc_start: 0.5748 (t0) cc_final: 0.4907 (p0) REVERT: B 261 ARG cc_start: 0.6683 (ttm110) cc_final: 0.5731 (mtm110) REVERT: B 322 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8473 (tp) REVERT: B 330 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7348 (ttp80) REVERT: B 388 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6925 (mm-30) REVERT: B 432 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6502 (pt0) REVERT: B 451 LYS cc_start: 0.6330 (OUTLIER) cc_final: 0.6102 (mptt) REVERT: B 579 ASP cc_start: 0.5269 (t0) cc_final: 0.4942 (m-30) REVERT: B 611 LEU cc_start: 0.7320 (mp) cc_final: 0.6950 (mp) REVERT: B 619 ASP cc_start: 0.8348 (t70) cc_final: 0.7639 (t70) REVERT: B 640 LEU cc_start: 0.7838 (mt) cc_final: 0.7372 (tp) REVERT: B 719 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6876 (pt0) REVERT: B 727 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6805 (t0) REVERT: B 731 GLU cc_start: 0.5661 (pm20) cc_final: 0.5378 (pm20) REVERT: B 736 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7563 (tm) outliers start: 80 outliers final: 32 residues processed: 256 average time/residue: 0.8829 time to fit residues: 248.8960 Evaluate side-chains 237 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1065 ARG Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain A residue 1585 LYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 525 ARG Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 212 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS A1001 HIS A1061 ASN A1084 ASN A1098 HIS A1376 ASN B 362 GLN B 547 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103565 restraints weight = 24838.107| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.65 r_work: 0.2777 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 21515 Z= 0.302 Angle : 0.773 13.260 29304 Z= 0.407 Chirality : 0.053 0.432 3115 Planarity : 0.007 0.133 3576 Dihedral : 9.293 98.152 3402 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 4.71 % Allowed : 14.29 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2365 helix: 0.81 (0.18), residues: 825 sheet: 0.54 (0.24), residues: 440 loop : -0.47 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 680 TYR 0.019 0.003 TYR B 84 PHE 0.024 0.003 PHE A1220 TRP 0.018 0.002 TRP B 517 HIS 0.008 0.002 HIS B 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.30 (21499) covalent geometry : angle 0.76803 / 0.41 (29283) hydrogen bonds : bond 0.06674 / 4.42 ( 771) hydrogen bonds : angle 4.77303 / 3.42 ( 2037) metal coordination : bond 0.01529 / 1.16 ( 16) metal coordination : angle 3.39761 / 2.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 195 time to evaluate : 0.790 Fit side-chains REVERT: A 77 ASP cc_start: 0.8373 (t70) cc_final: 0.8000 (t70) REVERT: A 79 LYS cc_start: 0.8452 (mptp) cc_final: 0.8099 (mptp) REVERT: A 112 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7447 (mmmm) REVERT: A 497 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7344 (pt0) REVERT: A 587 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7344 (tp-100) REVERT: A 601 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7544 (mtpt) REVERT: A 604 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7851 (tt0) REVERT: A 650 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8074 (pttm) REVERT: A 669 LYS cc_start: 0.7171 (ttpt) cc_final: 0.6493 (mptt) REVERT: A 735 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7387 (pm20) REVERT: A 896 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8127 (ttp-170) REVERT: A 1036 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7815 (ttt180) REVERT: A 1044 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7454 (mptt) REVERT: A 1131 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: A 1145 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: A 1161 LYS cc_start: 0.8347 (ptmt) cc_final: 0.8008 (mppt) REVERT: A 1187 ASP cc_start: 0.8362 (p0) cc_final: 0.8131 (t70) REVERT: A 1264 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: A 1268 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8437 (mtmm) REVERT: A 1299 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7474 (mtp85) REVERT: A 1390 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 1518 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7930 (mm-30) REVERT: A 1537 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: A 1583 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: A 1585 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7602 (ptmt) REVERT: B 20 LYS cc_start: 0.6547 (mmtm) cc_final: 0.6286 (mmtm) REVERT: B 182 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6996 (tpp-160) REVERT: B 220 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6668 (mmm160) REVERT: B 234 ASN cc_start: 0.5983 (t0) cc_final: 0.5289 (p0) REVERT: B 258 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6894 (m-40) REVERT: B 322 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8471 (tp) REVERT: B 388 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6893 (mm-30) REVERT: B 432 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: B 579 ASP cc_start: 0.5397 (t0) cc_final: 0.5019 (m-30) REVERT: B 611 LEU cc_start: 0.7165 (mp) cc_final: 0.6823 (mp) REVERT: B 640 LEU cc_start: 0.7827 (mt) cc_final: 0.7336 (tp) REVERT: B 727 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6836 (t0) REVERT: B 736 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7549 (tm) outliers start: 99 outliers final: 41 residues processed: 271 average time/residue: 0.8619 time to fit residues: 257.2871 Evaluate side-chains 246 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1232 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain A residue 1585 LYS Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 525 ARG Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 482 ASN A 464 ASN A 587 GLN A 626 HIS A1084 ASN A1326 ASN A1376 ASN B 225 ASN B 727 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.145974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107199 restraints weight = 25018.825| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.84 r_work: 0.2869 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21515 Z= 0.104 Angle : 0.536 11.267 29304 Z= 0.284 Chirality : 0.042 0.339 3115 Planarity : 0.004 0.053 3576 Dihedral : 9.193 102.062 3402 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.22 % Rotamer: Outliers : 2.57 % Allowed : 16.52 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2365 helix: 1.46 (0.18), residues: 829 sheet: 0.77 (0.24), residues: 427 loop : -0.22 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 780 TYR 0.014 0.001 TYR B 738 PHE 0.014 0.001 PHE B 17 TRP 0.016 0.001 TRP B 474 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (21499) covalent geometry : angle 0.53136 / 0.28 (29283) hydrogen bonds : bond 0.03901 / 2.61 ( 771) hydrogen bonds : angle 4.23888 / 3.03 ( 2037) metal coordination : bond 0.00395 / 0.22 ( 16) metal coordination : angle 2.77638 / 1.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.816 Fit side-chains REVERT: A 77 ASP cc_start: 0.8345 (t70) cc_final: 0.7966 (t70) REVERT: A 79 LYS cc_start: 0.8263 (mptp) cc_final: 0.8010 (mptp) REVERT: A 86 CYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7775 (p) REVERT: A 111 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7838 (p0) REVERT: A 112 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7284 (mmmm) REVERT: A 497 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7440 (pt0) REVERT: A 538 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: A 587 GLN cc_start: 0.7996 (tp40) cc_final: 0.7433 (tp-100) REVERT: A 634 MET cc_start: 0.9112 (mtm) cc_final: 0.8822 (mtp) REVERT: A 650 LYS cc_start: 0.8362 (ptpt) cc_final: 0.8048 (pttm) REVERT: A 735 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7351 (pm20) REVERT: A 738 THR cc_start: 0.9151 (t) cc_final: 0.8865 (m) REVERT: A 1036 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7760 (ttt90) REVERT: A 1044 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7427 (mptt) REVERT: A 1161 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7923 (mppt) REVERT: A 1264 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 1268 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8292 (mtmm) REVERT: A 1282 LYS cc_start: 0.8022 (tptm) cc_final: 0.7654 (tptm) REVERT: A 1390 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 1437 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 1518 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: A 1583 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: B 20 LYS cc_start: 0.6390 (mmtm) cc_final: 0.5868 (mmtm) REVERT: B 24 MET cc_start: 0.7510 (mtp) cc_final: 0.6961 (mtm) REVERT: B 98 GLU cc_start: 0.7712 (pt0) cc_final: 0.7328 (tp30) REVERT: B 234 ASN cc_start: 0.5970 (t0) cc_final: 0.5247 (p0) REVERT: B 238 GLU cc_start: 0.6007 (pm20) cc_final: 0.5726 (tp30) REVERT: B 258 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6948 (m-40) REVERT: B 388 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6773 (mm-30) REVERT: B 601 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6517 (mt-10) REVERT: B 611 LEU cc_start: 0.7158 (mp) cc_final: 0.6796 (mp) REVERT: B 619 ASP cc_start: 0.8324 (t70) cc_final: 0.7594 (t70) REVERT: B 633 LYS cc_start: 0.6106 (tttp) cc_final: 0.5445 (mppt) REVERT: B 640 LEU cc_start: 0.7893 (mt) cc_final: 0.7415 (tp) REVERT: B 715 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6909 (ttp-110) REVERT: B 719 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7011 (pt0) REVERT: B 727 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6923 (t0) REVERT: B 736 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7541 (tm) outliers start: 54 outliers final: 12 residues processed: 241 average time/residue: 0.8189 time to fit residues: 219.1205 Evaluate side-chains 202 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 67 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 187 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN A 626 HIS A1084 ASN A1326 ASN B 727 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106225 restraints weight = 24909.053| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.72 r_work: 0.2870 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21515 Z= 0.109 Angle : 0.530 11.265 29304 Z= 0.280 Chirality : 0.042 0.353 3115 Planarity : 0.004 0.051 3576 Dihedral : 9.080 101.182 3402 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Rotamer: Outliers : 2.52 % Allowed : 16.95 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2365 helix: 1.64 (0.18), residues: 829 sheet: 0.84 (0.24), residues: 429 loop : -0.15 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 261 TYR 0.013 0.001 TYR B 738 PHE 0.011 0.001 PHE A1220 TRP 0.014 0.001 TRP B 474 HIS 0.004 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (21499) covalent geometry : angle 0.52558 / 0.28 (29283) hydrogen bonds : bond 0.03911 / 2.60 ( 771) hydrogen bonds : angle 4.18948 / 3.00 ( 2037) metal coordination : bond 0.00367 / 0.20 ( 16) metal coordination : angle 2.51134 / 1.53 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.725 Fit side-chains REVERT: A 77 ASP cc_start: 0.8350 (t70) cc_final: 0.7938 (t70) REVERT: A 79 LYS cc_start: 0.8279 (mptp) cc_final: 0.8021 (mptp) REVERT: A 86 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7816 (p) REVERT: A 111 ASP cc_start: 0.8113 (m-30) cc_final: 0.7853 (p0) REVERT: A 112 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7342 (mmmm) REVERT: A 497 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7431 (pt0) REVERT: A 538 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: A 587 GLN cc_start: 0.7951 (tp40) cc_final: 0.7478 (tp-100) REVERT: A 634 MET cc_start: 0.9110 (mtm) cc_final: 0.8805 (mtp) REVERT: A 650 LYS cc_start: 0.8341 (ptpt) cc_final: 0.8041 (pttm) REVERT: A 735 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7353 (pm20) REVERT: A 738 THR cc_start: 0.9160 (t) cc_final: 0.8850 (m) REVERT: A 898 LYS cc_start: 0.8712 (tptm) cc_final: 0.8429 (tptt) REVERT: A 1036 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7750 (ttt90) REVERT: A 1044 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7436 (mptt) REVERT: A 1145 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: A 1161 LYS cc_start: 0.8219 (ptmt) cc_final: 0.7947 (mppt) REVERT: A 1264 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: A 1268 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8188 (mtmm) REVERT: A 1437 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 1518 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: A 1537 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: A 1583 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: B 20 LYS cc_start: 0.6298 (mmtm) cc_final: 0.5904 (mmtm) REVERT: B 24 MET cc_start: 0.7465 (mtp) cc_final: 0.7014 (mtm) REVERT: B 98 GLU cc_start: 0.7715 (pt0) cc_final: 0.7290 (tp30) REVERT: B 182 ARG cc_start: 0.7033 (tpp80) cc_final: 0.6810 (tpp-160) REVERT: B 207 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.6063 (pt0) REVERT: B 234 ASN cc_start: 0.6224 (t0) cc_final: 0.5481 (p0) REVERT: B 238 GLU cc_start: 0.5983 (pm20) cc_final: 0.5759 (tp30) REVERT: B 258 ASN cc_start: 0.7233 (OUTLIER) cc_final: 0.6671 (m-40) REVERT: B 261 ARG cc_start: 0.6563 (ttm110) cc_final: 0.6084 (ptp-110) REVERT: B 322 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 388 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6893 (mm-30) REVERT: B 601 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6502 (mt-10) REVERT: B 611 LEU cc_start: 0.7223 (mp) cc_final: 0.6868 (mp) REVERT: B 619 ASP cc_start: 0.8330 (t70) cc_final: 0.7587 (t70) REVERT: B 620 MET cc_start: 0.8711 (mmp) cc_final: 0.8469 (mmp) REVERT: B 633 LYS cc_start: 0.6109 (tttp) cc_final: 0.5500 (mppt) REVERT: B 640 LEU cc_start: 0.7839 (mt) cc_final: 0.7379 (tp) REVERT: B 715 ARG cc_start: 0.7184 (mtm110) cc_final: 0.6844 (ttp-110) REVERT: B 719 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6937 (pt0) REVERT: B 727 ASN cc_start: 0.7290 (OUTLIER) cc_final: 0.7017 (t0) outliers start: 53 outliers final: 21 residues processed: 225 average time/residue: 0.8444 time to fit residues: 210.5285 Evaluate side-chains 216 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 146 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 234 optimal weight: 9.9990 chunk 204 optimal weight: 0.4980 chunk 25 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN A1084 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106271 restraints weight = 25015.097| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.81 r_work: 0.2861 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21515 Z= 0.115 Angle : 0.532 10.744 29304 Z= 0.281 Chirality : 0.042 0.358 3115 Planarity : 0.004 0.050 3576 Dihedral : 9.044 101.142 3402 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % Rotamer: Outliers : 2.90 % Allowed : 16.81 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.17), residues: 2365 helix: 1.68 (0.18), residues: 830 sheet: 0.87 (0.24), residues: 428 loop : -0.12 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 261 TYR 0.013 0.001 TYR A1126 PHE 0.011 0.001 PHE A1220 TRP 0.013 0.001 TRP B 474 HIS 0.005 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21499) covalent geometry : angle 0.52800 / 0.28 (29283) hydrogen bonds : bond 0.03963 / 2.62 ( 771) hydrogen bonds : angle 4.17217 / 2.98 ( 2037) metal coordination : bond 0.00386 / 0.22 ( 16) metal coordination : angle 2.47287 / 1.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 0.786 Fit side-chains REVERT: A 77 ASP cc_start: 0.8357 (t70) cc_final: 0.7920 (t70) REVERT: A 79 LYS cc_start: 0.8276 (mptp) cc_final: 0.7968 (mptp) REVERT: A 86 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7811 (p) REVERT: A 111 ASP cc_start: 0.8131 (m-30) cc_final: 0.7870 (p0) REVERT: A 112 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7363 (mmmm) REVERT: A 260 ASN cc_start: 0.5804 (t0) cc_final: 0.4938 (p0) REVERT: A 497 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7451 (pt0) REVERT: A 538 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: A 587 GLN cc_start: 0.7971 (tp40) cc_final: 0.7481 (tp-100) REVERT: A 634 MET cc_start: 0.9102 (mtm) cc_final: 0.8794 (mtp) REVERT: A 650 LYS cc_start: 0.8337 (ptpt) cc_final: 0.8032 (pttm) REVERT: A 735 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7366 (pm20) REVERT: A 738 THR cc_start: 0.9136 (t) cc_final: 0.8818 (m) REVERT: A 898 LYS cc_start: 0.8734 (tptm) cc_final: 0.8437 (tptt) REVERT: A 989 ASP cc_start: 0.8181 (m-30) cc_final: 0.7811 (m-30) REVERT: A 1036 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7753 (ttt90) REVERT: A 1145 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: A 1161 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7941 (mppt) REVERT: A 1264 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: A 1268 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8127 (mtmm) REVERT: A 1334 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8674 (mt) REVERT: A 1403 SER cc_start: 0.8907 (p) cc_final: 0.8530 (t) REVERT: A 1437 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 1518 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: A 1537 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: A 1583 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: B 24 MET cc_start: 0.7445 (mtp) cc_final: 0.7040 (mtm) REVERT: B 98 GLU cc_start: 0.7713 (pt0) cc_final: 0.7277 (tp30) REVERT: B 182 ARG cc_start: 0.7040 (tpp80) cc_final: 0.6824 (tpp-160) REVERT: B 220 ARG cc_start: 0.6996 (mmm160) cc_final: 0.6749 (ttp-170) REVERT: B 234 ASN cc_start: 0.6222 (t0) cc_final: 0.5415 (p0) REVERT: B 238 GLU cc_start: 0.6008 (pm20) cc_final: 0.5797 (tp30) REVERT: B 258 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.7001 (m-40) REVERT: B 340 GLN cc_start: 0.6905 (tp-100) cc_final: 0.6646 (tp40) REVERT: B 388 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6881 (mm-30) REVERT: B 465 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8105 (mtmm) REVERT: B 601 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6452 (mt-10) REVERT: B 611 LEU cc_start: 0.7208 (mp) cc_final: 0.6868 (mp) REVERT: B 619 ASP cc_start: 0.8327 (t70) cc_final: 0.7607 (t70) REVERT: B 620 MET cc_start: 0.8643 (mmp) cc_final: 0.8369 (mmp) REVERT: B 640 LEU cc_start: 0.7798 (mt) cc_final: 0.7318 (tp) REVERT: B 715 ARG cc_start: 0.7176 (mtm110) cc_final: 0.6851 (ttp-110) REVERT: B 719 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6923 (pt0) REVERT: B 727 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.7036 (t0) outliers start: 61 outliers final: 24 residues processed: 230 average time/residue: 0.8388 time to fit residues: 214.1758 Evaluate side-chains 221 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 163 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 166 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 219 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN A 626 HIS A1003 GLN A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 ASN B 727 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104697 restraints weight = 24744.708| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.73 r_work: 0.2839 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21515 Z= 0.147 Angle : 0.576 11.707 29304 Z= 0.303 Chirality : 0.044 0.370 3115 Planarity : 0.005 0.054 3576 Dihedral : 9.039 100.709 3402 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 2.62 % Allowed : 17.29 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2365 helix: 1.60 (0.18), residues: 831 sheet: 0.85 (0.24), residues: 428 loop : -0.17 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 261 TYR 0.014 0.001 TYR A1126 PHE 0.013 0.002 PHE A1220 TRP 0.013 0.001 TRP B 474 HIS 0.007 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21499) covalent geometry : angle 0.57174 / 0.30 (29283) hydrogen bonds : bond 0.04493 / 2.97 ( 771) hydrogen bonds : angle 4.26401 / 3.05 ( 2037) metal coordination : bond 0.00570 / 0.38 ( 16) metal coordination : angle 2.54849 / 1.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.844 Fit side-chains REVERT: A 77 ASP cc_start: 0.8383 (t70) cc_final: 0.7928 (t70) REVERT: A 79 LYS cc_start: 0.8285 (mptp) cc_final: 0.7974 (mptp) REVERT: A 86 CYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7890 (p) REVERT: A 111 ASP cc_start: 0.8112 (m-30) cc_final: 0.7850 (p0) REVERT: A 112 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7416 (mmmm) REVERT: A 497 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7479 (pt0) REVERT: A 587 GLN cc_start: 0.8015 (tp40) cc_final: 0.7499 (tp-100) REVERT: A 634 MET cc_start: 0.9110 (mtm) cc_final: 0.8794 (mtp) REVERT: A 650 LYS cc_start: 0.8333 (ptpt) cc_final: 0.8025 (pttm) REVERT: A 735 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7358 (pm20) REVERT: A 738 THR cc_start: 0.9174 (t) cc_final: 0.8834 (m) REVERT: A 898 LYS cc_start: 0.8743 (tptm) cc_final: 0.8456 (tptt) REVERT: A 989 ASP cc_start: 0.8161 (m-30) cc_final: 0.7869 (m-30) REVERT: A 1036 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7768 (ttt180) REVERT: A 1145 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: A 1161 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7963 (mppt) REVERT: A 1264 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: A 1268 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8145 (mtmm) REVERT: A 1334 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8630 (mt) REVERT: A 1403 SER cc_start: 0.8875 (p) cc_final: 0.8499 (t) REVERT: A 1437 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 1518 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: A 1537 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: A 1583 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: B 24 MET cc_start: 0.7483 (mtp) cc_final: 0.7086 (mtm) REVERT: B 98 GLU cc_start: 0.7742 (pt0) cc_final: 0.7321 (tp30) REVERT: B 182 ARG cc_start: 0.6980 (tpp80) cc_final: 0.6752 (tpp-160) REVERT: B 220 ARG cc_start: 0.7043 (mmm160) cc_final: 0.6788 (ttp-170) REVERT: B 234 ASN cc_start: 0.6125 (t0) cc_final: 0.5360 (p0) REVERT: B 258 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6774 (m-40) REVERT: B 261 ARG cc_start: 0.6827 (ttm110) cc_final: 0.6093 (ptp-110) REVERT: B 289 MET cc_start: 0.7357 (tpp) cc_final: 0.7153 (tmm) REVERT: B 388 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6912 (mm-30) REVERT: B 465 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: B 601 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6540 (mt-10) REVERT: B 605 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6046 (mm-30) REVERT: B 611 LEU cc_start: 0.7312 (mp) cc_final: 0.6995 (mp) REVERT: B 640 LEU cc_start: 0.7804 (mt) cc_final: 0.7339 (tp) REVERT: B 668 PHE cc_start: 0.6915 (t80) cc_final: 0.6581 (m-80) REVERT: B 715 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6829 (ttp-110) REVERT: B 719 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6967 (pt0) REVERT: B 727 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6881 (t0) outliers start: 55 outliers final: 30 residues processed: 225 average time/residue: 0.8219 time to fit residues: 205.3982 Evaluate side-chains 221 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 39 optimal weight: 10.0000 chunk 88 optimal weight: 0.4980 chunk 227 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 ASN B 520 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105214 restraints weight = 24812.531| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.81 r_work: 0.2832 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21515 Z= 0.140 Angle : 0.569 11.521 29304 Z= 0.298 Chirality : 0.043 0.367 3115 Planarity : 0.005 0.053 3576 Dihedral : 8.968 100.965 3402 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 2.62 % Allowed : 17.52 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2365 helix: 1.62 (0.18), residues: 830 sheet: 0.87 (0.24), residues: 428 loop : -0.16 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 261 TYR 0.013 0.001 TYR A1126 PHE 0.013 0.001 PHE A1220 TRP 0.014 0.001 TRP B 474 HIS 0.006 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21499) covalent geometry : angle 0.56509 / 0.30 (29283) hydrogen bonds : bond 0.04385 / 2.90 ( 771) hydrogen bonds : angle 4.24008 / 3.03 ( 2037) metal coordination : bond 0.00514 / 0.33 ( 16) metal coordination : angle 2.55146 / 1.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.586 Fit side-chains REVERT: A 77 ASP cc_start: 0.8380 (t70) cc_final: 0.7962 (t70) REVERT: A 79 LYS cc_start: 0.8274 (mptp) cc_final: 0.8033 (mptp) REVERT: A 86 CYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7815 (p) REVERT: A 111 ASP cc_start: 0.8113 (m-30) cc_final: 0.7840 (p0) REVERT: A 112 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7373 (mmmm) REVERT: A 497 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7476 (pt0) REVERT: A 587 GLN cc_start: 0.8014 (tp40) cc_final: 0.7449 (tp-100) REVERT: A 634 MET cc_start: 0.9113 (mtm) cc_final: 0.8797 (mtp) REVERT: A 650 LYS cc_start: 0.8330 (ptpt) cc_final: 0.8019 (pttm) REVERT: A 735 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7347 (pm20) REVERT: A 738 THR cc_start: 0.9173 (t) cc_final: 0.8833 (m) REVERT: A 896 ARG cc_start: 0.8656 (ttp-170) cc_final: 0.8171 (mtp85) REVERT: A 898 LYS cc_start: 0.8739 (tptm) cc_final: 0.8437 (tptt) REVERT: A 989 ASP cc_start: 0.8153 (m-30) cc_final: 0.7857 (m-30) REVERT: A 1036 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7809 (ttt180) REVERT: A 1044 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7708 (mptp) REVERT: A 1161 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7957 (mppt) REVERT: A 1264 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: A 1268 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8139 (mtmm) REVERT: A 1334 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8632 (mt) REVERT: A 1403 SER cc_start: 0.8876 (p) cc_final: 0.8500 (t) REVERT: A 1437 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 1518 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: A 1537 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: A 1583 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: B 24 MET cc_start: 0.7461 (mtp) cc_final: 0.7057 (mtm) REVERT: B 98 GLU cc_start: 0.7746 (pt0) cc_final: 0.7310 (tp30) REVERT: B 182 ARG cc_start: 0.6973 (tpp80) cc_final: 0.6742 (tpp-160) REVERT: B 220 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6767 (ttp-170) REVERT: B 234 ASN cc_start: 0.6072 (t0) cc_final: 0.5314 (p0) REVERT: B 258 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6681 (m-40) REVERT: B 261 ARG cc_start: 0.6810 (ttm110) cc_final: 0.6060 (ptp-110) REVERT: B 289 MET cc_start: 0.7373 (tpp) cc_final: 0.7164 (tmm) REVERT: B 388 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6900 (mm-30) REVERT: B 465 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: B 601 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6553 (mt-10) REVERT: B 605 GLU cc_start: 0.6338 (mm-30) cc_final: 0.6034 (mm-30) REVERT: B 611 LEU cc_start: 0.7295 (mp) cc_final: 0.6972 (mp) REVERT: B 640 LEU cc_start: 0.7758 (mt) cc_final: 0.7247 (tp) REVERT: B 668 PHE cc_start: 0.6976 (t80) cc_final: 0.6640 (m-80) REVERT: B 715 ARG cc_start: 0.7211 (mtm110) cc_final: 0.6876 (ttp-110) REVERT: B 719 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6910 (pt0) REVERT: B 727 ASN cc_start: 0.7212 (OUTLIER) cc_final: 0.6944 (t0) outliers start: 55 outliers final: 32 residues processed: 221 average time/residue: 0.7960 time to fit residues: 194.6656 Evaluate side-chains 218 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 89 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 148 optimal weight: 4.9990 chunk 226 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 177 optimal weight: 0.0000 chunk 97 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN A 626 HIS A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1326 ASN B 582 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101540 restraints weight = 24202.455| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.86 r_work: 0.2772 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21515 Z= 0.206 Angle : 0.647 12.391 29304 Z= 0.340 Chirality : 0.047 0.396 3115 Planarity : 0.005 0.074 3576 Dihedral : 8.981 99.241 3402 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 2.48 % Allowed : 17.81 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2365 helix: 1.42 (0.18), residues: 831 sheet: 0.85 (0.25), residues: 426 loop : -0.27 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 261 TYR 0.016 0.002 TYR B 84 PHE 0.017 0.002 PHE A1454 TRP 0.013 0.002 TRP E 558 HIS 0.008 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (21499) covalent geometry : angle 0.64259 / 0.34 (29283) hydrogen bonds : bond 0.05276 / 3.48 ( 771) hydrogen bonds : angle 4.41889 / 3.15 ( 2037) metal coordination : bond 0.00877 / 0.63 ( 16) metal coordination : angle 2.79528 / 1.72 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.769 Fit side-chains REVERT: A 77 ASP cc_start: 0.8406 (t70) cc_final: 0.7982 (t70) REVERT: A 79 LYS cc_start: 0.8307 (mptp) cc_final: 0.8002 (mptp) REVERT: A 86 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 111 ASP cc_start: 0.8215 (m-30) cc_final: 0.7869 (m-30) REVERT: A 112 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7323 (mmmm) REVERT: A 497 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7491 (pt0) REVERT: A 587 GLN cc_start: 0.8058 (tp40) cc_final: 0.7422 (tp-100) REVERT: A 634 MET cc_start: 0.9121 (mtm) cc_final: 0.8794 (mtp) REVERT: A 650 LYS cc_start: 0.8365 (ptpt) cc_final: 0.8038 (pttm) REVERT: A 735 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7327 (pm20) REVERT: A 738 THR cc_start: 0.9195 (t) cc_final: 0.8833 (m) REVERT: A 898 LYS cc_start: 0.8763 (tptm) cc_final: 0.8466 (tptt) REVERT: A 989 ASP cc_start: 0.8160 (m-30) cc_final: 0.7865 (m-30) REVERT: A 1036 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7887 (ttt180) REVERT: A 1044 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7666 (mptp) REVERT: A 1161 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7974 (mppt) REVERT: A 1264 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: A 1268 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8254 (mtmm) REVERT: A 1403 SER cc_start: 0.8917 (p) cc_final: 0.8510 (t) REVERT: A 1437 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7340 (mm-30) REVERT: A 1518 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: A 1537 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: A 1583 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: B 24 MET cc_start: 0.7531 (mtp) cc_final: 0.7096 (mtm) REVERT: B 98 GLU cc_start: 0.7754 (pt0) cc_final: 0.7306 (tp30) REVERT: B 182 ARG cc_start: 0.7026 (tpp80) cc_final: 0.6787 (tpp-160) REVERT: B 220 ARG cc_start: 0.6940 (mmm160) cc_final: 0.6683 (ttp-170) REVERT: B 234 ASN cc_start: 0.6081 (t0) cc_final: 0.5503 (p0) REVERT: B 258 ASN cc_start: 0.7197 (OUTLIER) cc_final: 0.6676 (m-40) REVERT: B 261 ARG cc_start: 0.6802 (ttm110) cc_final: 0.6043 (ptp-110) REVERT: B 289 MET cc_start: 0.7443 (tpp) cc_final: 0.7233 (tmm) REVERT: B 388 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6912 (mm-30) REVERT: B 465 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8146 (mtmm) REVERT: B 525 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7816 (mpt180) REVERT: B 611 LEU cc_start: 0.7112 (mp) cc_final: 0.6825 (tt) REVERT: B 640 LEU cc_start: 0.7692 (mt) cc_final: 0.7265 (tp) REVERT: B 668 PHE cc_start: 0.6891 (t80) cc_final: 0.6595 (m-80) REVERT: B 715 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6785 (ttp-110) REVERT: B 719 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7125 (mt-10) outliers start: 52 outliers final: 31 residues processed: 214 average time/residue: 0.7600 time to fit residues: 180.6343 Evaluate side-chains 217 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1518 GLU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 525 ARG Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 81 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 ASN A 626 HIS A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.101439 restraints weight = 24124.651| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.01 r_work: 0.2815 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21515 Z= 0.130 Angle : 0.566 11.562 29304 Z= 0.298 Chirality : 0.043 0.364 3115 Planarity : 0.004 0.055 3576 Dihedral : 8.960 100.621 3402 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 2.48 % Allowed : 17.81 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2365 helix: 1.63 (0.18), residues: 829 sheet: 0.86 (0.25), residues: 428 loop : -0.20 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 261 TYR 0.014 0.001 TYR B 738 PHE 0.012 0.001 PHE A1220 TRP 0.015 0.001 TRP B 474 HIS 0.006 0.001 HIS A 887 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (21499) covalent geometry : angle 0.56139 / 0.30 (29283) hydrogen bonds : bond 0.04308 / 2.84 ( 771) hydrogen bonds : angle 4.26356 / 3.04 ( 2037) metal coordination : bond 0.00495 / 0.30 ( 16) metal coordination : angle 2.62662 / 1.60 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10048.65 seconds wall clock time: 171 minutes 4.94 seconds (10264.94 seconds total)