Starting phenix.real_space_refine on Mon Mar 18 12:11:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/03_2024/8eey_28065.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/03_2024/8eey_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/03_2024/8eey_28065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/03_2024/8eey_28065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/03_2024/8eey_28065.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eey_28065/03_2024/8eey_28065.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Residue "E GLU 418": "OE1" <-> "OE2" Residue "E GLU 493": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A GLU 1075": "OE1" <-> "OE2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A GLU 1135": "OE1" <-> "OE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A PHE 1277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1285": "OE1" <-> "OE2" Residue "A GLU 1437": "OE1" <-> "OE2" Residue "A GLU 1461": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 11.44, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 8.88 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 7.39 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: 9.07 Time building geometry restraints manager: 9.44 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: 77.69 - 89.02: 2 89.02 - 100.34: 16 100.34 - 111.67: 9699 111.67 - 122.99: 17457 122.99 - 134.32: 2109 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: 11926 19.97 - 39.95: 808 39.95 - 59.92: 264 59.92 - 79.89: 92 79.89 - 99.86: 19 Dihedral angle restraints: 13109 sinusoidal: 6166 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 13106 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 2.440 nonbonded pdb=" O GLU B 482 " pdb=" OG SER B 485 " model vdw 1.959 2.440 nonbonded pdb=" N GLU A 888 " pdb=" OE1 GLU A 888 " model vdw 2.253 2.520 nonbonded pdb=" N GLU A 491 " pdb=" OE1 GLU A 491 " model vdw 2.336 2.520 nonbonded pdb=" NZ LYS A 83 " pdb=" OE1 GLU A 213 " model vdw 2.388 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.020 Extract box with map and model: 8.350 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 66.390 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 21499 Z= 0.355 Angle : 0.876 25.506 29283 Z= 0.478 Chirality : 0.049 0.412 3115 Planarity : 0.009 0.186 3576 Dihedral : 16.420 99.863 8617 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (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 TRP 0.024 0.003 TRP B 555 HIS 0.008 0.002 HIS A1020 PHE 0.024 0.002 PHE B 17 TYR 0.025 0.002 TYR A1126 ARG 0.012 0.001 ARG A 896 *********************** 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 fitting. rotamer outliers: 3 poor density : 434 time to evaluate : 2.087 Fit side-chains REVERT: A 3 THR cc_start: 0.7623 (t) cc_final: 0.7305 (p) REVERT: A 25 ARG cc_start: 0.7275 (mmp80) cc_final: 0.6853 (mtm180) REVERT: A 47 LYS cc_start: 0.7861 (ptmm) cc_final: 0.7554 (ttpp) REVERT: A 79 LYS cc_start: 0.7765 (mptp) cc_final: 0.6981 (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: 0.7002 (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: 0.6155 (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: 0.7731 (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: 0.5777 (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: 0.7450 (tp) REVERT: B 263 TYR cc_start: 0.6444 (m-80) cc_final: 0.6178 (m-80) REVERT: B 388 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6836 (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: 1.7455 time to fit residues: 835.5247 Evaluate side-chains 219 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.587 ------------------------------------------------------------------------------- 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 205 optimal weight: 0.0170 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 482 ASN A 27 ASN A 43 HIS A 149 HIS A 208 ASN A 464 ASN A 531 GLN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 626 HIS A 640 ASN A 984 GLN A 985 ASN A1001 HIS A1020 HIS A1027 GLN A1168 ASN A1190 ASN A1195 ASN A1246 ASN B 36 GLN B 62 GLN B 716 ASN B 727 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21499 Z= 0.191 Angle : 0.603 11.200 29283 Z= 0.325 Chirality : 0.044 0.347 3115 Planarity : 0.005 0.055 3576 Dihedral : 13.651 99.172 3622 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.69 % Favored : 98.27 % Rotamer: Outliers : 2.86 % Allowed : 13.38 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2365 helix: 1.12 (0.18), residues: 832 sheet: 0.70 (0.24), residues: 424 loop : 0.03 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 474 HIS 0.006 0.001 HIS A1098 PHE 0.018 0.002 PHE B 17 TYR 0.018 0.002 TYR B 578 ARG 0.007 0.001 ARG A 780 *********************** 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 278 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 2.382 Fit side-chains REVERT: A 3 THR cc_start: 0.7567 (t) cc_final: 0.7320 (p) REVERT: A 22 GLU cc_start: 0.7174 (tp30) cc_final: 0.6813 (mt-10) REVERT: A 25 ARG cc_start: 0.7121 (mtp85) cc_final: 0.6802 (mtm180) REVERT: A 77 ASP cc_start: 0.7540 (t70) cc_final: 0.7282 (t70) REVERT: A 79 LYS cc_start: 0.7641 (mptp) cc_final: 0.7177 (mptp) REVERT: A 112 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7016 (mmmm) REVERT: A 538 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: A 554 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 601 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6811 (mtpt) REVERT: A 634 MET cc_start: 0.9008 (mtm) cc_final: 0.8688 (mtp) REVERT: A 650 LYS cc_start: 0.7897 (ptpt) cc_final: 0.7478 (pttm) REVERT: A 669 LYS cc_start: 0.6799 (ttpt) cc_final: 0.6002 (mptt) REVERT: A 735 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6886 (pm20) REVERT: A 878 GLU cc_start: 0.7832 (mp0) cc_final: 0.7544 (mp0) REVERT: A 885 LYS cc_start: 0.8651 (pttt) cc_final: 0.8442 (ptmt) REVERT: A 896 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7246 (ttp-170) REVERT: A 1036 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7600 (ttm170) REVERT: A 1044 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7519 (mptt) REVERT: A 1145 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: A 1161 LYS cc_start: 0.8208 (ptmt) cc_final: 0.7913 (ptpp) REVERT: A 1187 ASP cc_start: 0.8181 (p0) cc_final: 0.7931 (p0) REVERT: A 1227 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 1264 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 1426 ASP cc_start: 0.7798 (m-30) cc_final: 0.7594 (m-30) REVERT: B 20 LYS cc_start: 0.6197 (mmtm) cc_final: 0.5658 (tppp) REVERT: B 94 LYS cc_start: 0.7147 (mmtp) cc_final: 0.6749 (tptp) REVERT: B 242 GLU cc_start: 0.7207 (tt0) cc_final: 0.6949 (tt0) REVERT: B 261 ARG cc_start: 0.6915 (ttm110) cc_final: 0.6402 (mtt90) REVERT: B 388 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6902 (mm-30) REVERT: B 611 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6994 (mp) REVERT: B 727 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.6681 (t0) outliers start: 60 outliers final: 15 residues processed: 262 average time/residue: 1.7244 time to fit residues: 501.2517 Evaluate side-chains 209 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 311 ASP Chi-restraints excluded: chain A residue 538 GLU 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 1044 LYS Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1202 GLU Chi-restraints excluded: chain A residue 1264 GLU Chi-restraints excluded: chain A residue 1306 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 469 HIS A 276 ASN A 464 ASN A 500 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS A 984 GLN A1089 ASN A1098 HIS A1190 ASN B 69 GLN B 362 GLN B 427 HIS B 632 ASN B 673 HIS B 727 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 21499 Z= 0.541 Angle : 0.834 13.057 29283 Z= 0.441 Chirality : 0.056 0.440 3115 Planarity : 0.008 0.142 3576 Dihedral : 13.717 99.199 3618 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 4.29 % Allowed : 13.43 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2365 helix: 0.80 (0.17), residues: 817 sheet: 0.63 (0.24), residues: 440 loop : -0.35 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 517 HIS 0.011 0.002 HIS B 556 PHE 0.027 0.003 PHE A1220 TYR 0.020 0.003 TYR B 84 ARG 0.007 0.001 ARG A 951 *********************** 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 285 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 195 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 3 THR cc_start: 0.7592 (t) cc_final: 0.7263 (p) REVERT: A 24 THR cc_start: 0.7796 (p) cc_final: 0.7584 (m) REVERT: A 25 ARG cc_start: 0.7209 (mtp85) cc_final: 0.6986 (mtm180) REVERT: A 77 ASP cc_start: 0.7801 (t70) cc_final: 0.7299 (t0) REVERT: A 79 LYS cc_start: 0.7756 (mptp) cc_final: 0.7185 (mptp) REVERT: A 112 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6968 (mmmm) REVERT: A 263 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6397 (mm-30) REVERT: A 601 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7150 (mtpt) REVERT: A 609 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7572 (ptm160) REVERT: A 634 MET cc_start: 0.9068 (mtm) cc_final: 0.8758 (mtp) REVERT: A 650 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7506 (pttm) REVERT: A 669 LYS cc_start: 0.6771 (ttpt) cc_final: 0.5993 (mptt) REVERT: A 735 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6786 (pm20) REVERT: A 878 GLU cc_start: 0.7815 (mp0) cc_final: 0.7504 (mp0) REVERT: A 885 LYS cc_start: 0.8657 (pttt) cc_final: 0.8435 (ptmt) REVERT: A 896 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7170 (ttm170) REVERT: A 1036 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7599 (ttt180) REVERT: A 1044 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7667 (mptt) REVERT: A 1145 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: A 1161 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7948 (mppt) REVERT: A 1191 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7390 (ttm170) REVERT: A 1264 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: A 1268 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8303 (mtmm) REVERT: A 1299 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: A 1390 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8123 (tt) REVERT: A 1403 SER cc_start: 0.8988 (p) cc_final: 0.8693 (t) REVERT: A 1426 ASP cc_start: 0.7879 (m-30) cc_final: 0.7658 (m-30) REVERT: A 1518 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: A 1537 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: A 1583 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: B 20 LYS cc_start: 0.6375 (mmtm) cc_final: 0.6008 (mptt) REVERT: B 94 LYS cc_start: 0.7498 (mmtp) cc_final: 0.6891 (tptp) REVERT: B 182 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7051 (tpp-160) REVERT: B 220 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7208 (mmm-85) REVERT: B 330 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7301 (ttp80) REVERT: B 388 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6839 (mm-30) outliers start: 90 outliers final: 33 residues processed: 262 average time/residue: 1.8024 time to fit residues: 519.5379 Evaluate side-chains 234 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 184 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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 263 GLU 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 401 LEU Chi-restraints excluded: chain A residue 538 GLU 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 787 GLU Chi-restraints excluded: chain A residue 1044 LYS 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 1191 ARG 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 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 B residue 171 LEU 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 330 ARG Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 469 HIS A 464 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN A1084 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21499 Z= 0.269 Angle : 0.623 12.061 29283 Z= 0.333 Chirality : 0.046 0.387 3115 Planarity : 0.005 0.063 3576 Dihedral : 13.654 99.446 3618 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 3.43 % Allowed : 15.52 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2365 helix: 1.17 (0.18), residues: 825 sheet: 0.73 (0.24), residues: 429 loop : -0.33 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 517 HIS 0.005 0.001 HIS A 865 PHE 0.019 0.002 PHE A1220 TYR 0.015 0.002 TYR B 738 ARG 0.008 0.001 ARG A 780 *********************** 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 269 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 197 time to evaluate : 2.469 Fit side-chains revert: symmetry clash REVERT: A 3 THR cc_start: 0.7546 (t) cc_final: 0.7305 (p) REVERT: A 77 ASP cc_start: 0.7829 (t70) cc_final: 0.7358 (t70) REVERT: A 79 LYS cc_start: 0.7799 (mptp) cc_final: 0.7237 (mptp) REVERT: A 86 CYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7162 (p) REVERT: A 111 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: A 112 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6997 (mmmm) REVERT: A 263 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6408 (mm-30) REVERT: A 497 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6977 (pt0) REVERT: A 538 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: A 587 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6758 (tp-100) REVERT: A 634 MET cc_start: 0.9057 (mtm) cc_final: 0.8737 (mtp) REVERT: A 650 LYS cc_start: 0.7936 (ptpt) cc_final: 0.7501 (pttm) REVERT: A 669 LYS cc_start: 0.6777 (ttpt) cc_final: 0.5980 (mptt) REVERT: A 735 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6768 (pm20) REVERT: A 738 THR cc_start: 0.9045 (t) cc_final: 0.8729 (m) REVERT: A 849 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8150 (tttt) REVERT: A 878 GLU cc_start: 0.7799 (mp0) cc_final: 0.7474 (mp0) REVERT: A 896 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7192 (ttp-170) REVERT: A 1036 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7627 (ttt180) REVERT: A 1044 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7626 (mptt) REVERT: A 1131 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: A 1145 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: A 1161 LYS cc_start: 0.8139 (ptmt) cc_final: 0.7903 (mppt) REVERT: A 1264 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: A 1268 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8275 (mtmm) REVERT: A 1299 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7369 (mtp85) REVERT: A 1334 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8415 (mt) REVERT: A 1390 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 1403 SER cc_start: 0.9015 (p) cc_final: 0.8728 (t) REVERT: A 1426 ASP cc_start: 0.7835 (m-30) cc_final: 0.7614 (m-30) REVERT: A 1518 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: A 1537 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: B 20 LYS cc_start: 0.6427 (mmtm) cc_final: 0.6169 (mmtm) REVERT: B 94 LYS cc_start: 0.7429 (mmtp) cc_final: 0.6836 (tptp) REVERT: B 181 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7351 (mp) REVERT: B 182 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6910 (tpp-160) REVERT: B 234 ASN cc_start: 0.5783 (t0) cc_final: 0.5266 (p0) REVERT: B 258 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7128 (m-40) REVERT: B 388 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6887 (mm-30) outliers start: 72 outliers final: 27 residues processed: 248 average time/residue: 1.7118 time to fit residues: 469.5586 Evaluate side-chains 229 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 86 CYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 111 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 367 SER Chi-restraints excluded: chain A residue 397 ILE 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 605 GLU Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1062 LYS Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1164 ASP 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 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 B residue 78 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 ARG 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 390 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 735 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 HIS A 887 HIS A1084 ASN A1098 HIS A1376 ASN B 130 HIS B 225 ASN B 547 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21499 Z= 0.390 Angle : 0.712 12.324 29283 Z= 0.378 Chirality : 0.050 0.421 3115 Planarity : 0.006 0.083 3576 Dihedral : 13.677 98.243 3618 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 4.14 % Allowed : 15.43 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2365 helix: 1.03 (0.18), residues: 824 sheet: 0.67 (0.24), residues: 431 loop : -0.46 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 517 HIS 0.008 0.002 HIS B 556 PHE 0.022 0.002 PHE A1220 TYR 0.017 0.002 TYR B 84 ARG 0.007 0.001 ARG B 261 *********************** 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 286 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 199 time to evaluate : 2.477 Fit side-chains REVERT: A 3 THR cc_start: 0.7552 (t) cc_final: 0.7272 (p) REVERT: A 77 ASP cc_start: 0.7854 (t70) cc_final: 0.7347 (t70) REVERT: A 79 LYS cc_start: 0.7793 (mptp) cc_final: 0.7352 (mptp) REVERT: A 86 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7344 (p) REVERT: A 112 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7053 (mmmm) REVERT: A 263 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6396 (mm-30) REVERT: A 309 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6963 (mtpt) REVERT: A 497 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7062 (pt0) REVERT: A 587 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.6774 (tp-100) REVERT: A 650 LYS cc_start: 0.7920 (ptpt) cc_final: 0.7471 (pttm) REVERT: A 669 LYS cc_start: 0.6766 (ttpt) cc_final: 0.5986 (mptt) REVERT: A 717 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: A 735 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6784 (pm20) REVERT: A 738 THR cc_start: 0.9012 (t) cc_final: 0.8649 (m) REVERT: A 849 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8129 (tttt) REVERT: A 878 GLU cc_start: 0.7796 (mp0) cc_final: 0.7477 (mp0) REVERT: A 896 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7192 (ttp-170) REVERT: A 1036 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7567 (ttt180) REVERT: A 1044 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7595 (mptt) REVERT: A 1121 VAL cc_start: 0.7112 (OUTLIER) cc_final: 0.6907 (t) REVERT: A 1131 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: A 1145 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: A 1161 LYS cc_start: 0.8145 (ptmt) cc_final: 0.7930 (mppt) REVERT: A 1191 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7522 (ttm170) REVERT: A 1264 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: A 1268 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8322 (mtmm) REVERT: A 1299 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7367 (mtp85) REVERT: A 1390 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 1403 SER cc_start: 0.8998 (p) cc_final: 0.8721 (t) REVERT: A 1426 ASP cc_start: 0.7855 (m-30) cc_final: 0.7589 (m-30) REVERT: A 1518 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: A 1537 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: A 1583 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: B 20 LYS cc_start: 0.6382 (mmtm) cc_final: 0.6176 (mmtm) REVERT: B 94 LYS cc_start: 0.7499 (mmtp) cc_final: 0.6968 (tptp) REVERT: B 182 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6973 (tpp-160) REVERT: B 220 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6798 (ttp-170) REVERT: B 234 ASN cc_start: 0.5937 (t0) cc_final: 0.5422 (p0) REVERT: B 256 GLN cc_start: 0.6402 (mt0) cc_final: 0.6047 (mt0) REVERT: B 258 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7107 (m-40) REVERT: B 261 ARG cc_start: 0.7291 (ttm110) cc_final: 0.7045 (ttm110) REVERT: B 330 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7392 (ttp80) REVERT: B 388 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6891 (mm-30) REVERT: B 432 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6848 (pt0) REVERT: B 465 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8405 (mtmm) outliers start: 87 outliers final: 42 residues processed: 266 average time/residue: 1.7446 time to fit residues: 512.7821 Evaluate side-chains 257 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 190 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 96 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 309 LYS 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 401 LEU Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 451 LEU 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 605 GLU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1062 LYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1191 ARG 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 B residue 182 ARG 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 330 ARG Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 465 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 735 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 587 GLN A 626 HIS A1084 ASN A1207 ASN A1326 ASN A1376 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21499 Z= 0.177 Angle : 0.543 11.009 29283 Z= 0.291 Chirality : 0.043 0.349 3115 Planarity : 0.004 0.058 3576 Dihedral : 13.642 100.952 3618 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.82 % Favored : 98.14 % Rotamer: Outliers : 3.52 % Allowed : 16.33 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2365 helix: 1.51 (0.18), residues: 824 sheet: 0.79 (0.25), residues: 431 loop : -0.29 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 474 HIS 0.005 0.001 HIS A 865 PHE 0.013 0.001 PHE A1220 TYR 0.014 0.001 TYR B 738 ARG 0.009 0.000 ARG A 780 *********************** 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 266 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 192 time to evaluate : 2.420 Fit side-chains REVERT: A 3 THR cc_start: 0.7459 (t) cc_final: 0.7254 (p) REVERT: A 77 ASP cc_start: 0.7876 (t70) cc_final: 0.7394 (t70) REVERT: A 79 LYS cc_start: 0.7812 (mptp) cc_final: 0.7389 (mptp) REVERT: A 86 CYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7134 (p) REVERT: A 111 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: A 112 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7013 (mmmm) REVERT: A 263 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6484 (mm-30) REVERT: A 309 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6981 (mtpt) REVERT: A 497 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7071 (pt0) REVERT: A 538 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: A 587 GLN cc_start: 0.7640 (tp40) cc_final: 0.6802 (tp-100) REVERT: A 609 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7841 (ptm160) REVERT: A 650 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7453 (pttm) REVERT: A 735 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6755 (pm20) REVERT: A 738 THR cc_start: 0.8962 (t) cc_final: 0.8683 (m) REVERT: A 849 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8143 (tttm) REVERT: A 878 GLU cc_start: 0.7819 (mp0) cc_final: 0.7495 (mp0) REVERT: A 896 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7169 (ttp-170) REVERT: A 1044 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7607 (mptt) REVERT: A 1191 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7477 (ttm170) REVERT: A 1264 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: A 1268 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: A 1282 LYS cc_start: 0.8162 (tptm) cc_final: 0.7847 (tptm) REVERT: A 1299 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7807 (mtp85) REVERT: A 1334 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 1403 SER cc_start: 0.8997 (p) cc_final: 0.8718 (t) REVERT: A 1426 ASP cc_start: 0.7846 (m-30) cc_final: 0.7618 (m-30) REVERT: A 1437 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6940 (mm-30) REVERT: A 1518 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: A 1583 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: B 20 LYS cc_start: 0.6317 (mmtm) cc_final: 0.5907 (mmtm) REVERT: B 24 MET cc_start: 0.7004 (mtp) cc_final: 0.6594 (mtm) REVERT: B 94 LYS cc_start: 0.7426 (mmtp) cc_final: 0.6844 (tptp) REVERT: B 258 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.7136 (m-40) REVERT: B 330 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7160 (ttp80) REVERT: B 388 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6873 (mm-30) outliers start: 74 outliers final: 27 residues processed: 249 average time/residue: 1.7591 time to fit residues: 483.5503 Evaluate side-chains 227 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 183 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 111 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 309 LYS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 451 LEU 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 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1033 LYS Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1191 ARG 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 1583 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 330 ARG Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 570 THR 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 226 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 146 optimal weight: 0.0670 chunk 142 optimal weight: 6.9990 chunk 108 optimal weight: 0.0980 chunk 144 optimal weight: 5.9990 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A1084 ASN A1225 ASN A1326 ASN A1376 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21499 Z= 0.206 Angle : 0.565 11.479 29283 Z= 0.300 Chirality : 0.043 0.356 3115 Planarity : 0.005 0.056 3576 Dihedral : 13.608 100.560 3618 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.24 % Favored : 97.72 % Rotamer: Outliers : 3.24 % Allowed : 17.00 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2365 helix: 1.54 (0.18), residues: 829 sheet: 0.85 (0.25), residues: 432 loop : -0.27 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 474 HIS 0.006 0.001 HIS A 887 PHE 0.014 0.001 PHE A1220 TYR 0.014 0.001 TYR B 738 ARG 0.009 0.000 ARG B 261 *********************** 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 257 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 189 time to evaluate : 2.391 Fit side-chains REVERT: A 77 ASP cc_start: 0.7889 (t70) cc_final: 0.7405 (t70) REVERT: A 79 LYS cc_start: 0.7753 (mptp) cc_final: 0.7340 (mptp) REVERT: A 86 CYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7179 (p) REVERT: A 111 ASP cc_start: 0.7948 (m-30) cc_final: 0.7612 (m-30) REVERT: A 112 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7024 (mmmm) REVERT: A 263 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6457 (mm-30) REVERT: A 497 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7226 (pt0) REVERT: A 538 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: A 587 GLN cc_start: 0.7616 (tp40) cc_final: 0.6805 (tp-100) REVERT: A 609 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7830 (ptm160) REVERT: A 650 LYS cc_start: 0.7892 (ptpt) cc_final: 0.7457 (pttm) REVERT: A 735 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6766 (pm20) REVERT: A 738 THR cc_start: 0.8977 (t) cc_final: 0.8664 (m) REVERT: A 849 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8151 (tttt) REVERT: A 878 GLU cc_start: 0.7816 (mp0) cc_final: 0.7526 (mp0) REVERT: A 896 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.7160 (ttp-170) REVERT: A 1044 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7600 (mptt) REVERT: A 1191 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7535 (ttm170) REVERT: A 1264 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: A 1268 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8183 (mtmm) REVERT: A 1282 LYS cc_start: 0.8218 (tptm) cc_final: 0.7914 (tptm) REVERT: A 1334 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8418 (mt) REVERT: A 1403 SER cc_start: 0.9029 (p) cc_final: 0.8739 (t) REVERT: A 1518 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.6877 (mm-30) REVERT: A 1537 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: A 1583 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: B 16 LYS cc_start: 0.5867 (tppt) cc_final: 0.5171 (ttmm) REVERT: B 20 LYS cc_start: 0.6135 (mmtm) cc_final: 0.5761 (mmtm) REVERT: B 24 MET cc_start: 0.6974 (mtp) cc_final: 0.6552 (mtm) REVERT: B 94 LYS cc_start: 0.7390 (mmtp) cc_final: 0.6848 (tptp) REVERT: B 258 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7145 (m-40) REVERT: B 330 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7167 (ttp80) REVERT: B 388 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6945 (mm-30) REVERT: B 525 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7051 (mpp-170) outliers start: 68 outliers final: 33 residues processed: 240 average time/residue: 1.8078 time to fit residues: 479.5589 Evaluate side-chains 230 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 180 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 96 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 373 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 451 LEU 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 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1033 LYS Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1191 ARG 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 1317 VAL 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 213 LEU Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 525 ARG Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 695 VAL 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 93 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A 626 HIS A1084 ASN A1225 ASN A1376 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21499 Z= 0.238 Angle : 0.592 11.896 29283 Z= 0.313 Chirality : 0.044 0.360 3115 Planarity : 0.005 0.059 3576 Dihedral : 13.524 100.632 3618 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 3.29 % Allowed : 17.05 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2365 helix: 1.52 (0.18), residues: 820 sheet: 0.84 (0.25), residues: 432 loop : -0.27 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 474 HIS 0.005 0.001 HIS A 887 PHE 0.016 0.002 PHE A1220 TYR 0.014 0.002 TYR B 738 ARG 0.015 0.000 ARG B 261 *********************** 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 253 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 184 time to evaluate : 2.245 Fit side-chains REVERT: A 77 ASP cc_start: 0.7894 (t70) cc_final: 0.7410 (t70) REVERT: A 79 LYS cc_start: 0.7752 (mptp) cc_final: 0.7359 (mptp) REVERT: A 86 CYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7186 (p) REVERT: A 111 ASP cc_start: 0.7920 (m-30) cc_final: 0.7602 (m-30) REVERT: A 112 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7033 (mmmm) REVERT: A 263 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6450 (mm-30) REVERT: A 309 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.7003 (mtpt) REVERT: A 497 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7154 (pt0) REVERT: A 538 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 587 GLN cc_start: 0.7609 (tp40) cc_final: 0.6794 (tp-100) REVERT: A 609 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7824 (ptm160) REVERT: A 650 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7457 (pttm) REVERT: A 735 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6791 (pm20) REVERT: A 738 THR cc_start: 0.8976 (t) cc_final: 0.8651 (m) REVERT: A 849 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8163 (tttt) REVERT: A 878 GLU cc_start: 0.7840 (mp0) cc_final: 0.7546 (mp0) REVERT: A 896 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7160 (ttp-170) REVERT: A 989 ASP cc_start: 0.7962 (m-30) cc_final: 0.7551 (m-30) REVERT: A 1044 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7617 (mptt) REVERT: A 1145 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: A 1191 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7520 (ttm170) REVERT: A 1264 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: A 1268 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8183 (mtmm) REVERT: A 1282 LYS cc_start: 0.8238 (tptm) cc_final: 0.7924 (tptm) REVERT: A 1334 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 1403 SER cc_start: 0.8995 (p) cc_final: 0.8717 (t) REVERT: A 1537 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: A 1583 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: B 24 MET cc_start: 0.6970 (mtp) cc_final: 0.6548 (mtm) REVERT: B 94 LYS cc_start: 0.7457 (mmtp) cc_final: 0.6898 (tptp) REVERT: B 258 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7187 (m-40) REVERT: B 330 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7180 (ttp80) REVERT: B 388 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6973 (mm-30) outliers start: 69 outliers final: 37 residues processed: 235 average time/residue: 1.7447 time to fit residues: 453.4601 Evaluate side-chains 235 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 2.352 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 96 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 309 LYS Chi-restraints excluded: chain A residue 311 ASP 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 444 ARG Chi-restraints excluded: chain A residue 451 LEU 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 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1191 ARG 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 1317 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1583 GLU 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 330 ARG Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 695 VAL 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 224 optimal weight: 0.0070 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A1084 ASN A1225 ASN A1376 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21499 Z= 0.238 Angle : 0.589 11.717 29283 Z= 0.311 Chirality : 0.044 0.364 3115 Planarity : 0.005 0.059 3576 Dihedral : 13.480 100.293 3618 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 3.29 % Allowed : 17.24 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.17), residues: 2365 helix: 1.47 (0.18), residues: 830 sheet: 0.83 (0.25), residues: 432 loop : -0.28 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 474 HIS 0.005 0.001 HIS A1483 PHE 0.016 0.002 PHE A1220 TYR 0.014 0.001 TYR B 738 ARG 0.014 0.000 ARG B 261 *********************** 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 252 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 183 time to evaluate : 2.446 Fit side-chains REVERT: A 77 ASP cc_start: 0.7890 (t70) cc_final: 0.7397 (t70) REVERT: A 79 LYS cc_start: 0.7777 (mptp) cc_final: 0.7374 (mptp) REVERT: A 86 CYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7188 (p) REVERT: A 111 ASP cc_start: 0.7944 (m-30) cc_final: 0.7642 (m-30) REVERT: A 112 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7078 (mmmm) REVERT: A 263 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6455 (mm-30) REVERT: A 309 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.7009 (mtpt) REVERT: A 497 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7236 (pt0) REVERT: A 538 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 587 GLN cc_start: 0.7607 (tp40) cc_final: 0.6800 (tp-100) REVERT: A 609 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7835 (ptm160) REVERT: A 650 LYS cc_start: 0.7893 (ptpt) cc_final: 0.7457 (pttm) REVERT: A 735 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6780 (pm20) REVERT: A 738 THR cc_start: 0.8969 (t) cc_final: 0.8652 (m) REVERT: A 849 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8167 (tttt) REVERT: A 878 GLU cc_start: 0.7840 (mp0) cc_final: 0.7546 (mp0) REVERT: A 896 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.7161 (ttp-170) REVERT: A 898 LYS cc_start: 0.8200 (tptm) cc_final: 0.7808 (tptt) REVERT: A 989 ASP cc_start: 0.7973 (m-30) cc_final: 0.7583 (m-30) REVERT: A 1044 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7609 (mptt) REVERT: A 1145 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: A 1191 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7534 (ttm170) REVERT: A 1264 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: A 1268 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8182 (mtmm) REVERT: A 1282 LYS cc_start: 0.8237 (tptm) cc_final: 0.7925 (tptm) REVERT: A 1299 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7735 (mtp85) REVERT: A 1334 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8429 (mt) REVERT: A 1403 SER cc_start: 0.8953 (p) cc_final: 0.8674 (t) REVERT: A 1518 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: A 1537 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: A 1583 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: B 16 LYS cc_start: 0.6050 (tppt) cc_final: 0.5435 (ttmm) REVERT: B 24 MET cc_start: 0.6968 (mtp) cc_final: 0.6554 (mtm) REVERT: B 94 LYS cc_start: 0.7391 (mmtp) cc_final: 0.6853 (tptp) REVERT: B 258 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6894 (m-40) REVERT: B 261 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6689 (ptp-110) REVERT: B 330 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7185 (ttp80) REVERT: B 388 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6962 (mm-30) REVERT: B 525 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7016 (mpp-170) outliers start: 69 outliers final: 38 residues processed: 235 average time/residue: 1.7809 time to fit residues: 463.7372 Evaluate side-chains 236 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 179 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 96 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 309 LYS Chi-restraints excluded: chain A residue 311 ASP 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 444 ARG Chi-restraints excluded: chain A residue 451 LEU 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 605 GLU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1164 ASP Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1191 ARG 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 1317 VAL 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 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 330 ARG Chi-restraints excluded: chain B residue 375 GLN 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 695 VAL 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 230 optimal weight: 0.3980 chunk 140 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A1003 GLN A1084 ASN A1225 ASN A1376 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21499 Z= 0.195 Angle : 0.559 11.246 29283 Z= 0.294 Chirality : 0.043 0.348 3115 Planarity : 0.005 0.056 3576 Dihedral : 13.475 100.658 3618 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 17.52 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2365 helix: 1.59 (0.18), residues: 830 sheet: 0.90 (0.25), residues: 430 loop : -0.23 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 474 HIS 0.004 0.001 HIS A 865 PHE 0.013 0.001 PHE A1220 TYR 0.014 0.001 TYR B 738 ARG 0.013 0.000 ARG B 261 ********************** 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 248 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 185 time to evaluate : 2.470 Fit side-chains REVERT: A 77 ASP cc_start: 0.7882 (t70) cc_final: 0.7483 (t70) REVERT: A 86 CYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7146 (p) REVERT: A 111 ASP cc_start: 0.7898 (m-30) cc_final: 0.7620 (m-30) REVERT: A 112 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7009 (mmmm) REVERT: A 263 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6490 (mm-30) REVERT: A 309 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.7019 (mtpt) REVERT: A 497 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7229 (pt0) REVERT: A 538 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: A 587 GLN cc_start: 0.7617 (tp40) cc_final: 0.6825 (tp-100) REVERT: A 650 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7455 (pttm) REVERT: A 735 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6751 (pm20) REVERT: A 738 THR cc_start: 0.8961 (t) cc_final: 0.8650 (m) REVERT: A 849 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8161 (tttt) REVERT: A 878 GLU cc_start: 0.7821 (mp0) cc_final: 0.7524 (mp0) REVERT: A 896 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.7149 (ttp-170) REVERT: A 898 LYS cc_start: 0.8186 (tptm) cc_final: 0.7788 (tptt) REVERT: A 989 ASP cc_start: 0.7923 (m-30) cc_final: 0.7571 (m-30) REVERT: A 1036 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7608 (ttt180) REVERT: A 1044 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7595 (mptt) REVERT: A 1131 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: A 1142 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: A 1145 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 1191 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7529 (ttm170) REVERT: A 1264 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: A 1268 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8135 (mtmm) REVERT: A 1282 LYS cc_start: 0.8148 (tptm) cc_final: 0.7872 (tptm) REVERT: A 1299 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7732 (mtp85) REVERT: A 1334 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 1376 ASN cc_start: 0.6966 (t0) cc_final: 0.6753 (t0) REVERT: A 1403 SER cc_start: 0.8956 (p) cc_final: 0.8707 (t) REVERT: A 1437 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6914 (mm-30) REVERT: A 1518 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: A 1537 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: A 1583 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: B 16 LYS cc_start: 0.6055 (tppt) cc_final: 0.5442 (ttmm) REVERT: B 24 MET cc_start: 0.6927 (mtp) cc_final: 0.6589 (mtm) REVERT: B 94 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6837 (tptp) REVERT: B 207 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6234 (pt0) REVERT: B 220 ARG cc_start: 0.6992 (mmm160) cc_final: 0.6688 (ttp-170) REVERT: B 258 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7109 (m-40) REVERT: B 330 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7177 (ttp80) REVERT: B 388 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6935 (mm-30) outliers start: 63 outliers final: 33 residues processed: 232 average time/residue: 1.7778 time to fit residues: 455.9953 Evaluate side-chains 232 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 179 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 96 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 309 LYS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 451 LEU 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 699 THR Chi-restraints excluded: chain A residue 787 GLU Chi-restraints excluded: chain A residue 849 LYS Chi-restraints excluded: chain A residue 1044 LYS Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1086 VAL 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 1164 ASP Chi-restraints excluded: chain A residue 1168 ASN Chi-restraints excluded: chain A residue 1191 ARG 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 1317 VAL 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 207 GLU 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 330 ARG Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 511 GLU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 695 VAL 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 205 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 198 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 ASN A1225 ASN B 340 GLN B 582 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105174 restraints weight = 24641.579| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.63 r_work: 0.2802 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21499 Z= 0.323 Angle : 0.650 12.140 29283 Z= 0.342 Chirality : 0.047 0.392 3115 Planarity : 0.006 0.063 3576 Dihedral : 13.495 99.050 3618 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 3.00 % Allowed : 17.43 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2365 helix: 1.36 (0.18), residues: 829 sheet: 0.82 (0.25), residues: 430 loop : -0.34 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 474 HIS 0.006 0.001 HIS B 556 PHE 0.018 0.002 PHE A1220 TYR 0.016 0.002 TYR B 84 ARG 0.015 0.001 ARG B 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8651.05 seconds wall clock time: 152 minutes 36.18 seconds (9156.18 seconds total)