Starting phenix.real_space_refine on Fri Jul 3 22:24:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d9f_27260/07_2026/8d9f_27260.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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 33 5.49 5 S 57 5.16 5 C 10177 2.51 5 N 2793 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5436 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 650} Chain breaks: 2 Chain: "B" Number of atoms: 10034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1242, 10034 Classifications: {'peptide': 1242} Link IDs: {'PTRANS': 59, 'TRANS': 1182} Chain breaks: 7 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 2, 'rna3p_pyr': 11} Link IDs: {'rna2p': 19, 'rna3p': 13} Chain: "B" 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 6104 SG CYS B 83 38.936 26.446 26.156 1.00133.42 S ATOM 6375 SG CYS B 116 36.827 23.888 24.100 1.00155.67 S ATOM 6421 SG CYS B 122 37.693 23.283 27.769 1.00130.57 S ATOM 6445 SG CYS B 125 35.328 26.034 26.846 1.00125.50 S ATOM 9139 SG CYS B 486 50.070 47.433 49.719 1.00127.38 S ATOM 9207 SG CYS B 496 48.620 45.167 46.905 1.00118.87 S ATOM 9221 SG CYS B 498 52.348 45.172 48.258 1.00121.83 S ATOM 9243 SG CYS B 501 49.427 43.592 50.006 1.00119.03 S ATOM 11214 SG CYS B 745 54.251 67.386 72.428 1.00150.38 S ATOM 11227 SG CYS B 747 56.315 65.418 74.936 1.00140.80 S ATOM 11249 SG CYS B 750 53.200 63.747 73.492 1.00136.31 S ATOM 13200 SG CYS B1013 46.791 71.941 109.540 1.00179.40 S ATOM 13326 SG CYS B1401 46.249 73.597 106.140 1.00176.13 S ATOM 13377 SG CYS B1409 49.714 73.209 107.752 1.00162.63 S ATOM 13394 SG CYS B1412 48.089 70.245 106.283 1.00153.82 S Time building chain proxies: 3.30, per 1000 atoms: 0.20 Number of scatterers: 16163 At special positions: 0 Unit cell: (102.72, 104.86, 156.22, 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 57 16.00 P 33 15.00 O 3099 8.00 N 2793 7.00 C 10177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 587.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 125 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 122 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 83 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 116 " pdb=" ZN B1702 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 498 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 486 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 496 " pdb=" ZN B1703 " pdb="ZN ZN B1703 " - pdb=" ND1 HIS B 742 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 747 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 745 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 750 " pdb=" ZN B1704 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1409 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1013 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1412 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1401 " Number of angles added : 21 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 25 sheets defined 42.0% alpha, 18.0% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 15 through 33 Processing helix chain 'A' and resid 37 through 59 removed outlier: 3.658A pdb=" N LYS A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.572A pdb=" N LYS A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.772A pdb=" N ILE A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 removed outlier: 4.372A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 230 through 246 removed outlier: 4.083A pdb=" N ASP A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 279 through 297 removed outlier: 4.737A pdb=" N VAL A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 322 Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.587A pdb=" N LYS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 362 removed outlier: 4.023A pdb=" N TYR A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.967A pdb=" N ASN A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.720A pdb=" N ALA A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.558A pdb=" N ASN A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 removed outlier: 3.763A pdb=" N TRP A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.579A pdb=" N PHE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 54 through 73 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.532A pdb=" N ASN B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 302 removed outlier: 3.694A pdb=" N ILE B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 369 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 466 through 483 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 681 through 688 Processing helix chain 'B' and resid 718 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.664A pdb=" N LYS B 799 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 843 Processing helix chain 'B' and resid 868 through 878 removed outlier: 4.020A pdb=" N THR B 878 " --> pdb=" O MET B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1010 removed outlier: 3.613A pdb=" N LEU B 998 " --> pdb=" O PRO B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1395 through 1399 Processing helix chain 'B' and resid 1409 through 1415 Processing helix chain 'B' and resid 1458 through 1463 removed outlier: 4.355A pdb=" N SER B1462 " --> pdb=" O ARG B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1481 through 1488 removed outlier: 3.548A pdb=" N ILE B1485 " --> pdb=" O GLY B1481 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1496 removed outlier: 3.598A pdb=" N VAL B1496 " --> pdb=" O ILE B1492 " (cutoff:3.500A) Processing helix chain 'B' and resid 1523 through 1535 Processing helix chain 'B' and resid 1578 through 1597 Processing helix chain 'B' and resid 1610 through 1613 removed outlier: 3.573A pdb=" N VAL B1613 " --> pdb=" O GLN B1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1610 through 1613' Processing helix chain 'B' and resid 1614 through 1624 Processing helix chain 'B' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 275 Processing sheet with id=AA2, first strand: chain 'A' and resid 425 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 540 removed outlier: 6.368A pdb=" N LEU A 580 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 622 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N THR A 660 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU A 624 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 586 through 587 Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 7.133A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG B 14 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TRP B 39 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 16 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TRP B 41 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP B 190 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N GLU B 17 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 13.189A pdb=" N ARG B 188 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 185 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.528A pdb=" N THR B 4 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 8 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.528A pdb=" N VAL B 80 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.136A pdb=" N THR B 105 " --> pdb=" O VAL B 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.519A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.519A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 426 through 427 removed outlier: 3.535A pdb=" N VAL B 427 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN B 454 " --> pdb=" O VAL B 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB5, first strand: chain 'B' and resid 521 through 525 Processing sheet with id=AB6, first strand: chain 'B' and resid 528 through 529 removed outlier: 3.679A pdb=" N THR B 534 " --> pdb=" O ASN B 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.788A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.788A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN B 668 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE B 863 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 670 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 861 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 672 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 694 through 695 removed outlier: 7.201A pdb=" N ALA B 694 " --> pdb=" O TYR B 803 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC2, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AC3, first strand: chain 'B' and resid 919 through 922 Processing sheet with id=AC4, first strand: chain 'B' and resid 986 through 987 removed outlier: 7.051A pdb=" N LEU B 991 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA B1429 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ASP B1516 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B1431 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER B1514 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B1433 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1424 through 1426 removed outlier: 7.134A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1416 through 1417 Processing sheet with id=AC7, first strand: chain 'B' and resid 1448 through 1450 691 hydrogen bonds defined for protein. 1923 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2654 1.32 - 1.44: 4650 1.44 - 1.56: 9169 1.56 - 1.69: 35 1.69 - 1.81: 80 Bond restraints: 16588 Sorted by residual: bond pdb=" O3' A C 28 " pdb=" P C C 29 " ideal model delta sigma weight residual 1.607 1.459 0.148 1.50e-02 4.44e+03 9.71e+01 bond pdb=" O3' U C 19 " pdb=" P G C 20 " ideal model delta sigma weight residual 1.607 1.460 0.147 1.50e-02 4.44e+03 9.64e+01 bond pdb=" O3' G C 20 " pdb=" P U C 21 " ideal model delta sigma weight residual 1.607 1.477 0.130 1.50e-02 4.44e+03 7.48e+01 bond pdb=" O3' U C 36 " pdb=" P U C 37 " ideal model delta sigma weight residual 1.607 1.490 0.117 1.50e-02 4.44e+03 6.05e+01 bond pdb=" O3' U C 27 " pdb=" P A C 28 " ideal model delta sigma weight residual 1.607 1.492 0.115 1.50e-02 4.44e+03 5.91e+01 ... (remaining 16583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.58: 22435 5.58 - 11.16: 56 11.16 - 16.75: 18 16.75 - 22.33: 1 22.33 - 27.91: 1 Bond angle restraints: 22511 Sorted by residual: angle pdb=" O2' U C 16 " pdb=" C2' U C 16 " pdb=" C1' U C 16 " ideal model delta sigma weight residual 108.40 80.49 27.91 1.50e+00 4.44e-01 3.46e+02 angle pdb=" O2' U C 35 " pdb=" C2' U C 35 " pdb=" C1' U C 35 " ideal model delta sigma weight residual 108.40 88.18 20.22 1.50e+00 4.44e-01 1.82e+02 angle pdb=" O2' A C 32 " pdb=" C2' A C 32 " pdb=" C1' A C 32 " ideal model delta sigma weight residual 111.80 96.72 15.08 1.50e+00 4.44e-01 1.01e+02 angle pdb=" O2' C C 30 " pdb=" C2' C C 30 " pdb=" C1' C C 30 " ideal model delta sigma weight residual 108.40 93.49 14.91 1.50e+00 4.44e-01 9.89e+01 angle pdb=" C4' C C 43 " pdb=" C3' C C 43 " pdb=" O3' C C 43 " ideal model delta sigma weight residual 109.40 94.49 14.91 1.50e+00 4.44e-01 9.88e+01 ... (remaining 22506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.95: 9703 34.95 - 69.90: 177 69.90 - 104.85: 17 104.85 - 139.81: 1 139.81 - 174.76: 7 Dihedral angle restraints: 9905 sinusoidal: 4395 harmonic: 5510 Sorted by residual: dihedral pdb=" O4' C C 31 " pdb=" C1' C C 31 " pdb=" N1 C C 31 " pdb=" C2 C C 31 " ideal model delta sinusoidal sigma weight residual 200.00 34.07 165.93 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' C C 30 " pdb=" C1' C C 30 " pdb=" N1 C C 30 " pdb=" C2 C C 30 " ideal model delta sinusoidal sigma weight residual 200.00 37.21 162.79 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' C C 14 " pdb=" C1' C C 14 " pdb=" N1 C C 14 " pdb=" C2 C C 14 " ideal model delta sinusoidal sigma weight residual 200.00 38.90 161.10 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 9902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 2370 0.154 - 0.308: 51 0.308 - 0.463: 8 0.463 - 0.617: 2 0.617 - 0.771: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" P G C 12 " pdb=" OP1 G C 12 " pdb=" OP2 G C 12 " pdb=" O5' G C 12 " both_signs ideal model delta sigma weight residual True 2.41 -1.64 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" P G C 20 " pdb=" OP1 G C 20 " pdb=" OP2 G C 20 " pdb=" O5' G C 20 " both_signs ideal model delta sigma weight residual True 2.41 -1.85 0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" C3' A C 23 " pdb=" C4' A C 23 " pdb=" O3' A C 23 " pdb=" C2' A C 23 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 2429 not shown) Planarity restraints: 2774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 28 " 0.102 2.00e-02 2.50e+03 4.58e-02 5.77e+01 pdb=" N9 A C 28 " -0.100 2.00e-02 2.50e+03 pdb=" C8 A C 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A C 28 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A C 28 " -0.021 2.00e-02 2.50e+03 pdb=" C6 A C 28 " 0.031 2.00e-02 2.50e+03 pdb=" N6 A C 28 " 0.023 2.00e-02 2.50e+03 pdb=" N1 A C 28 " 0.010 2.00e-02 2.50e+03 pdb=" C2 A C 28 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A C 28 " -0.022 2.00e-02 2.50e+03 pdb=" C4 A C 28 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 18 " -0.036 2.00e-02 2.50e+03 2.79e-02 2.13e+01 pdb=" N9 A C 18 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A C 18 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A C 18 " 0.033 2.00e-02 2.50e+03 pdb=" C5 A C 18 " 0.037 2.00e-02 2.50e+03 pdb=" C6 A C 18 " -0.023 2.00e-02 2.50e+03 pdb=" N6 A C 18 " -0.032 2.00e-02 2.50e+03 pdb=" N1 A C 18 " -0.016 2.00e-02 2.50e+03 pdb=" C2 A C 18 " 0.012 2.00e-02 2.50e+03 pdb=" N3 A C 18 " 0.031 2.00e-02 2.50e+03 pdb=" C4 A C 18 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1497 " 0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B1498 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO B1498 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B1498 " 0.061 5.00e-02 4.00e+02 ... (remaining 2771 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.17: 14332 3.17 - 3.75: 25318 3.75 - 4.32: 36539 4.32 - 4.90: 60032 Nonbonded interactions: 136385 Sorted by model distance: nonbonded pdb=" O GLU B1455 " pdb=" O2' C C 42 " model vdw 2.015 3.040 nonbonded pdb=" OG SER B 849 " pdb=" OP2 U C 35 " model vdw 2.059 3.040 nonbonded pdb=" O ILE B1594 " pdb=" OG SER B1597 " model vdw 2.172 3.040 nonbonded pdb=" O GLN B 904 " pdb=" NZ LYS B1622 " model vdw 2.172 3.120 nonbonded pdb=" CE1 PHE A 542 " pdb=" CE1 HIS A 585 " model vdw 2.195 3.560 ... (remaining 136380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.010 0.148 16604 Z= 0.509 Angle : 0.953 27.911 22532 Z= 0.568 Chirality : 0.063 0.771 2432 Planarity : 0.005 0.113 2774 Dihedral : 14.919 174.757 6361 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 0.06 % Allowed : 0.00 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1890 helix: 1.23 (0.19), residues: 731 sheet: 0.03 (0.31), residues: 263 loop : -0.23 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1583 TYR 0.029 0.002 TYR B 524 PHE 0.027 0.002 PHE B 825 TRP 0.024 0.002 TRP B1625 HIS 0.006 0.001 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.51 (16588) covalent geometry : angle 0.94341 / 0.57 (22511) hydrogen bonds : bond 0.13523 / 8.92 ( 659) hydrogen bonds : angle 6.52559 / 4.70 ( 1923) metal coordination : bond 0.02095 / 1.52 ( 16) metal coordination : angle 4.60689 / 2.88 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8756 (m-30) cc_final: 0.8331 (m-30) REVERT: A 138 GLU cc_start: 0.9294 (tp30) cc_final: 0.8941 (tm-30) REVERT: A 139 LYS cc_start: 0.9488 (mmpt) cc_final: 0.9183 (mmmm) REVERT: A 180 MET cc_start: 0.9260 (mmm) cc_final: 0.9049 (mmm) REVERT: A 287 MET cc_start: 0.8990 (mtm) cc_final: 0.8772 (mtm) REVERT: A 682 TYR cc_start: 0.8509 (m-10) cc_final: 0.8206 (m-10) REVERT: B 273 GLU cc_start: 0.9138 (tp30) cc_final: 0.8819 (mm-30) REVERT: B 283 ASP cc_start: 0.9232 (t70) cc_final: 0.9006 (t0) REVERT: B 310 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8541 (mm-30) REVERT: B 672 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 876 ASN cc_start: 0.9236 (m110) cc_final: 0.8897 (m-40) REVERT: B 956 LEU cc_start: 0.9014 (mm) cc_final: 0.8771 (mm) REVERT: B 1581 ASP cc_start: 0.9253 (m-30) cc_final: 0.8957 (m-30) REVERT: B 1583 ARG cc_start: 0.8950 (ptp90) cc_final: 0.8647 (mtm-85) REVERT: B 1590 TYR cc_start: 0.9256 (t80) cc_final: 0.8933 (t80) REVERT: B 1621 TYR cc_start: 0.8305 (m-80) cc_final: 0.8024 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.7078 time to fit residues: 150.2428 Evaluate side-chains 144 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1507 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 ASN B 147 HIS B 323 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1687 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.060601 restraints weight = 32546.738| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.28 r_work: 0.2606 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16604 Z= 0.124 Angle : 0.588 8.104 22532 Z= 0.302 Chirality : 0.040 0.234 2432 Planarity : 0.004 0.069 2774 Dihedral : 12.351 179.832 2467 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 0.71 % Allowed : 7.86 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1890 helix: 1.86 (0.19), residues: 727 sheet: 0.28 (0.30), residues: 271 loop : -0.08 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 35 TYR 0.025 0.001 TYR B1585 PHE 0.018 0.001 PHE A 491 TRP 0.015 0.001 TRP B1437 HIS 0.004 0.001 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16588) covalent geometry : angle 0.57601 / 0.30 (22511) hydrogen bonds : bond 0.04018 / 2.64 ( 659) hydrogen bonds : angle 4.58351 / 3.26 ( 1923) metal coordination : bond 0.00750 / 0.52 ( 16) metal coordination : angle 3.88589 / 2.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8347 (tp30) REVERT: A 111 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7905 (m-10) REVERT: A 117 ASP cc_start: 0.8857 (m-30) cc_final: 0.8532 (m-30) REVERT: A 138 GLU cc_start: 0.9550 (tp30) cc_final: 0.9095 (tm-30) REVERT: A 139 LYS cc_start: 0.9503 (mmpt) cc_final: 0.9157 (mmmm) REVERT: A 180 MET cc_start: 0.9259 (mmm) cc_final: 0.9001 (mmm) REVERT: A 467 GLU cc_start: 0.8887 (pp20) cc_final: 0.8355 (pp20) REVERT: A 504 LYS cc_start: 0.8942 (ptmm) cc_final: 0.8701 (pptt) REVERT: A 682 TYR cc_start: 0.8643 (m-10) cc_final: 0.8141 (m-10) REVERT: B 31 MET cc_start: 0.9120 (tpp) cc_final: 0.8634 (tpp) REVERT: B 119 GLU cc_start: 0.9215 (mp0) cc_final: 0.9001 (pm20) REVERT: B 273 GLU cc_start: 0.9247 (tp30) cc_final: 0.8998 (mm-30) REVERT: B 310 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8629 (mm-30) REVERT: B 548 GLU cc_start: 0.8995 (tt0) cc_final: 0.8312 (tp30) REVERT: B 672 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8446 (mt-10) REVERT: B 693 ASP cc_start: 0.8672 (m-30) cc_final: 0.8283 (m-30) REVERT: B 876 ASN cc_start: 0.9338 (m110) cc_final: 0.8985 (m-40) REVERT: B 942 GLU cc_start: 0.8565 (tp30) cc_final: 0.8279 (tp30) REVERT: B 1476 TYR cc_start: 0.8586 (m-80) cc_final: 0.8253 (m-80) REVERT: B 1581 ASP cc_start: 0.9221 (m-30) cc_final: 0.8880 (m-30) REVERT: B 1583 ARG cc_start: 0.9090 (ptp90) cc_final: 0.8846 (ptt90) REVERT: B 1590 TYR cc_start: 0.9351 (t80) cc_final: 0.9108 (t80) outliers start: 12 outliers final: 2 residues processed: 182 average time/residue: 0.6270 time to fit residues: 125.9717 Evaluate side-chains 146 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1624 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 42 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 131 optimal weight: 0.0770 chunk 54 optimal weight: 10.0000 chunk 83 optimal weight: 0.0570 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS B 876 ASN B 908 GLN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.061980 restraints weight = 32936.173| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.24 r_work: 0.2630 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16604 Z= 0.109 Angle : 0.547 8.434 22532 Z= 0.279 Chirality : 0.039 0.221 2432 Planarity : 0.004 0.056 2774 Dihedral : 12.152 179.649 2464 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.49 % Allowed : 9.40 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1890 helix: 2.00 (0.19), residues: 728 sheet: 0.45 (0.30), residues: 269 loop : -0.06 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1639 TYR 0.014 0.001 TYR B1640 PHE 0.018 0.001 PHE A 491 TRP 0.027 0.001 TRP B1596 HIS 0.003 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16588) covalent geometry : angle 0.53533 / 0.28 (22511) hydrogen bonds : bond 0.03599 / 2.38 ( 659) hydrogen bonds : angle 4.20300 / 3.00 ( 1923) metal coordination : bond 0.00524 / 0.35 ( 16) metal coordination : angle 3.66120 / 2.21 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8280 (tp30) REVERT: A 117 ASP cc_start: 0.8892 (m-30) cc_final: 0.8566 (m-30) REVERT: A 138 GLU cc_start: 0.9552 (tp30) cc_final: 0.9107 (tm-30) REVERT: A 139 LYS cc_start: 0.9522 (mmpt) cc_final: 0.9191 (mmmm) REVERT: A 180 MET cc_start: 0.9225 (mmm) cc_final: 0.8881 (mmm) REVERT: A 411 GLU cc_start: 0.9098 (tp30) cc_final: 0.8893 (tp30) REVERT: A 467 GLU cc_start: 0.8939 (pp20) cc_final: 0.8388 (pp20) REVERT: A 637 ASP cc_start: 0.8326 (p0) cc_final: 0.7898 (p0) REVERT: A 682 TYR cc_start: 0.8718 (m-10) cc_final: 0.8366 (m-10) REVERT: B 31 MET cc_start: 0.9087 (tpp) cc_final: 0.8820 (tpp) REVERT: B 140 ARG cc_start: 0.8862 (mtp180) cc_final: 0.8521 (mtp85) REVERT: B 273 GLU cc_start: 0.9256 (tp30) cc_final: 0.8996 (mm-30) REVERT: B 384 TYR cc_start: 0.8993 (t80) cc_final: 0.8742 (t80) REVERT: B 548 GLU cc_start: 0.9006 (tt0) cc_final: 0.8438 (tp30) REVERT: B 672 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 693 ASP cc_start: 0.8651 (m-30) cc_final: 0.8268 (m-30) REVERT: B 748 ASP cc_start: 0.8836 (m-30) cc_final: 0.8420 (t0) REVERT: B 876 ASN cc_start: 0.9380 (m-40) cc_final: 0.8965 (m-40) REVERT: B 938 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: B 942 GLU cc_start: 0.8569 (tp30) cc_final: 0.8252 (tp30) REVERT: B 1560 ASP cc_start: 0.9261 (t0) cc_final: 0.9041 (m-30) REVERT: B 1581 ASP cc_start: 0.9206 (m-30) cc_final: 0.8850 (m-30) REVERT: B 1583 ARG cc_start: 0.9086 (ptp90) cc_final: 0.8829 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9339 (t80) cc_final: 0.8913 (t80) REVERT: B 1640 TYR cc_start: 0.7734 (m-80) cc_final: 0.7390 (m-80) outliers start: 25 outliers final: 7 residues processed: 191 average time/residue: 0.6908 time to fit residues: 145.2646 Evaluate side-chains 163 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 929 TYR Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 131 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.057873 restraints weight = 33198.057| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.23 r_work: 0.2517 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 16604 Z= 0.296 Angle : 0.630 12.244 22532 Z= 0.321 Chirality : 0.043 0.203 2432 Planarity : 0.004 0.051 2774 Dihedral : 12.121 178.145 2464 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.49 % Allowed : 11.07 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 1890 helix: 1.93 (0.19), residues: 730 sheet: 0.41 (0.32), residues: 252 loop : -0.17 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1639 TYR 0.018 0.001 TYR B 524 PHE 0.020 0.001 PHE A 491 TRP 0.019 0.001 TRP B1596 HIS 0.003 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.30 (16588) covalent geometry : angle 0.61837 / 0.32 (22511) hydrogen bonds : bond 0.04351 / 2.84 ( 659) hydrogen bonds : angle 4.40927 / 3.15 ( 1923) metal coordination : bond 0.02114 / 1.56 ( 16) metal coordination : angle 3.98681 / 2.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8365 (tp30) REVERT: A 102 GLU cc_start: 0.8912 (tp30) cc_final: 0.8243 (tp30) REVERT: A 117 ASP cc_start: 0.8910 (m-30) cc_final: 0.8581 (m-30) REVERT: A 138 GLU cc_start: 0.9587 (tp30) cc_final: 0.9155 (tm-30) REVERT: A 139 LYS cc_start: 0.9511 (mmpt) cc_final: 0.9211 (mmmm) REVERT: A 180 MET cc_start: 0.9398 (mmm) cc_final: 0.9004 (mmm) REVERT: A 235 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: A 411 GLU cc_start: 0.9188 (tp30) cc_final: 0.8863 (tm-30) REVERT: A 512 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8713 (mt-10) REVERT: A 637 ASP cc_start: 0.8382 (p0) cc_final: 0.7877 (p0) REVERT: B 31 MET cc_start: 0.9141 (tpp) cc_final: 0.8656 (tpp) REVERT: B 273 GLU cc_start: 0.9291 (tp30) cc_final: 0.9043 (mm-30) REVERT: B 277 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 876 ASN cc_start: 0.9406 (m-40) cc_final: 0.9020 (m110) REVERT: B 938 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: B 942 GLU cc_start: 0.8597 (tp30) cc_final: 0.8308 (tp30) REVERT: B 948 LYS cc_start: 0.9113 (ptmt) cc_final: 0.8909 (ptpp) REVERT: B 1488 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7607 (pttm) REVERT: B 1560 ASP cc_start: 0.9316 (t0) cc_final: 0.9015 (m-30) REVERT: B 1575 LYS cc_start: 0.6542 (mmtt) cc_final: 0.6304 (mppt) REVERT: B 1581 ASP cc_start: 0.9241 (m-30) cc_final: 0.8915 (m-30) REVERT: B 1583 ARG cc_start: 0.9098 (ptp90) cc_final: 0.8849 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9376 (t80) cc_final: 0.9068 (t80) REVERT: B 1591 GLN cc_start: 0.9166 (mm110) cc_final: 0.8908 (mp10) REVERT: B 1640 TYR cc_start: 0.7866 (m-80) cc_final: 0.7542 (m-80) outliers start: 25 outliers final: 8 residues processed: 171 average time/residue: 0.6518 time to fit residues: 123.1972 Evaluate side-chains 148 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1623 LEU Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 171 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 165 optimal weight: 0.0670 chunk 158 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 190 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.059981 restraints weight = 32975.557| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.27 r_work: 0.2576 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16604 Z= 0.127 Angle : 0.562 8.159 22532 Z= 0.287 Chirality : 0.040 0.207 2432 Planarity : 0.004 0.053 2774 Dihedral : 12.020 178.765 2464 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.31 % Allowed : 12.56 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1890 helix: 2.06 (0.19), residues: 729 sheet: 0.39 (0.31), residues: 260 loop : -0.11 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1639 TYR 0.014 0.001 TYR B 385 PHE 0.019 0.001 PHE A 491 TRP 0.024 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16588) covalent geometry : angle 0.55458 / 0.29 (22511) hydrogen bonds : bond 0.03578 / 2.37 ( 659) hydrogen bonds : angle 4.12479 / 2.95 ( 1923) metal coordination : bond 0.00743 / 0.53 ( 16) metal coordination : angle 3.05860 / 1.68 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8192 (tp30) REVERT: A 117 ASP cc_start: 0.8919 (m-30) cc_final: 0.8587 (m-30) REVERT: A 138 GLU cc_start: 0.9561 (tp30) cc_final: 0.9162 (tm-30) REVERT: A 139 LYS cc_start: 0.9527 (mmpt) cc_final: 0.9187 (mmmm) REVERT: A 180 MET cc_start: 0.9263 (mmm) cc_final: 0.8988 (mmm) REVERT: A 235 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8520 (mp0) REVERT: A 411 GLU cc_start: 0.9171 (tp30) cc_final: 0.8857 (tp30) REVERT: A 637 ASP cc_start: 0.8330 (p0) cc_final: 0.7843 (p0) REVERT: A 682 TYR cc_start: 0.8838 (m-10) cc_final: 0.8632 (m-10) REVERT: B 31 MET cc_start: 0.9060 (tpp) cc_final: 0.8707 (tpp) REVERT: B 140 ARG cc_start: 0.8865 (mtp180) cc_final: 0.8519 (mtp85) REVERT: B 273 GLU cc_start: 0.9260 (tp30) cc_final: 0.8977 (mm-30) REVERT: B 277 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8511 (tm-30) REVERT: B 384 TYR cc_start: 0.9028 (t80) cc_final: 0.8773 (t80) REVERT: B 876 ASN cc_start: 0.9427 (m-40) cc_final: 0.9036 (m110) REVERT: B 938 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: B 942 GLU cc_start: 0.8566 (tp30) cc_final: 0.8238 (tp30) REVERT: B 1488 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7662 (pttm) REVERT: B 1560 ASP cc_start: 0.9293 (t0) cc_final: 0.9064 (m-30) REVERT: B 1581 ASP cc_start: 0.9244 (m-30) cc_final: 0.8868 (m-30) REVERT: B 1583 ARG cc_start: 0.9097 (ptp90) cc_final: 0.8854 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9344 (t80) cc_final: 0.8988 (t80) REVERT: B 1640 TYR cc_start: 0.7774 (m-80) cc_final: 0.7380 (m-80) outliers start: 22 outliers final: 8 residues processed: 186 average time/residue: 0.6852 time to fit residues: 140.2729 Evaluate side-chains 165 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 986 ASN ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1487 GLN ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.060769 restraints weight = 32520.499| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.22 r_work: 0.2582 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16604 Z= 0.143 Angle : 0.571 8.166 22532 Z= 0.292 Chirality : 0.040 0.202 2432 Planarity : 0.004 0.047 2774 Dihedral : 11.899 179.374 2464 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.37 % Allowed : 13.63 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1890 helix: 2.09 (0.19), residues: 730 sheet: 0.38 (0.32), residues: 254 loop : -0.10 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1639 TYR 0.011 0.001 TYR B 385 PHE 0.017 0.001 PHE A 491 TRP 0.029 0.001 TRP B1596 HIS 0.005 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16588) covalent geometry : angle 0.56377 / 0.29 (22511) hydrogen bonds : bond 0.03563 / 2.36 ( 659) hydrogen bonds : angle 4.08637 / 2.92 ( 1923) metal coordination : bond 0.01022 / 0.75 ( 16) metal coordination : angle 2.94423 / 1.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8243 (tp30) REVERT: A 102 GLU cc_start: 0.8887 (tp30) cc_final: 0.8203 (tp30) REVERT: A 111 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: A 117 ASP cc_start: 0.8916 (m-30) cc_final: 0.8592 (m-30) REVERT: A 138 GLU cc_start: 0.9567 (tp30) cc_final: 0.9175 (tm-30) REVERT: A 139 LYS cc_start: 0.9504 (mmpt) cc_final: 0.9173 (mmmm) REVERT: A 180 MET cc_start: 0.9286 (mmm) cc_final: 0.9045 (mmm) REVERT: A 235 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: A 392 GLU cc_start: 0.8603 (mp0) cc_final: 0.8321 (pm20) REVERT: A 411 GLU cc_start: 0.9157 (tp30) cc_final: 0.8807 (tp30) REVERT: A 637 ASP cc_start: 0.8350 (p0) cc_final: 0.7795 (p0) REVERT: A 639 MET cc_start: 0.8875 (mpp) cc_final: 0.8356 (mmp) REVERT: A 682 TYR cc_start: 0.8816 (m-10) cc_final: 0.8608 (m-10) REVERT: B 31 MET cc_start: 0.9084 (tpp) cc_final: 0.8725 (tpp) REVERT: B 140 ARG cc_start: 0.8894 (mtp180) cc_final: 0.8524 (mtp85) REVERT: B 273 GLU cc_start: 0.9261 (tp30) cc_final: 0.8966 (mm-30) REVERT: B 277 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8512 (tm-30) REVERT: B 384 TYR cc_start: 0.9037 (t80) cc_final: 0.8750 (t80) REVERT: B 672 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7974 (mp0) REVERT: B 693 ASP cc_start: 0.8681 (m-30) cc_final: 0.8284 (m-30) REVERT: B 876 ASN cc_start: 0.9429 (m-40) cc_final: 0.9011 (m-40) REVERT: B 938 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: B 942 GLU cc_start: 0.8563 (tp30) cc_final: 0.8268 (tp30) REVERT: B 1488 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7798 (pttm) REVERT: B 1560 ASP cc_start: 0.9291 (t0) cc_final: 0.9067 (m-30) REVERT: B 1581 ASP cc_start: 0.9260 (m-30) cc_final: 0.8878 (m-30) REVERT: B 1583 ARG cc_start: 0.9083 (ptp90) cc_final: 0.8818 (ptt90) REVERT: B 1590 TYR cc_start: 0.9355 (t80) cc_final: 0.8957 (t80) REVERT: B 1591 GLN cc_start: 0.9161 (mm110) cc_final: 0.8905 (mp10) outliers start: 23 outliers final: 7 residues processed: 179 average time/residue: 0.7203 time to fit residues: 141.6964 Evaluate side-chains 159 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1473 ARG Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 37 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 185 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 HIS ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.058490 restraints weight = 33029.895| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.24 r_work: 0.2527 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 16604 Z= 0.238 Angle : 0.623 11.037 22532 Z= 0.319 Chirality : 0.042 0.188 2432 Planarity : 0.004 0.046 2774 Dihedral : 11.871 178.938 2464 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.25 % Allowed : 14.82 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1890 helix: 1.99 (0.19), residues: 730 sheet: 0.27 (0.31), residues: 256 loop : -0.09 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.024 0.001 TYR B1640 PHE 0.017 0.001 PHE A 491 TRP 0.026 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (16588) covalent geometry : angle 0.61443 / 0.32 (22511) hydrogen bonds : bond 0.04014 / 2.64 ( 659) hydrogen bonds : angle 4.25885 / 3.05 ( 1923) metal coordination : bond 0.01712 / 1.27 ( 16) metal coordination : angle 3.42545 / 1.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8299 (tmm-80) cc_final: 0.7885 (tmt170) REVERT: A 95 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8313 (tp30) REVERT: A 102 GLU cc_start: 0.8908 (tp30) cc_final: 0.8220 (tp30) REVERT: A 117 ASP cc_start: 0.8922 (m-30) cc_final: 0.8582 (m-30) REVERT: A 138 GLU cc_start: 0.9590 (tp30) cc_final: 0.9191 (tm-30) REVERT: A 139 LYS cc_start: 0.9500 (mmpt) cc_final: 0.9171 (mmmm) REVERT: A 180 MET cc_start: 0.9359 (mmm) cc_final: 0.9083 (mmm) REVERT: A 235 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: A 392 GLU cc_start: 0.8633 (mp0) cc_final: 0.8370 (pm20) REVERT: A 411 GLU cc_start: 0.9158 (tp30) cc_final: 0.8816 (tp30) REVERT: A 637 ASP cc_start: 0.8352 (p0) cc_final: 0.7850 (p0) REVERT: B 31 MET cc_start: 0.9112 (tpp) cc_final: 0.8836 (tpp) REVERT: B 273 GLU cc_start: 0.9293 (tp30) cc_final: 0.9008 (mm-30) REVERT: B 277 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8517 (tm-30) REVERT: B 672 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7976 (mp0) REVERT: B 876 ASN cc_start: 0.9441 (m-40) cc_final: 0.9031 (m-40) REVERT: B 938 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: B 942 GLU cc_start: 0.8596 (tp30) cc_final: 0.8273 (tp30) REVERT: B 1488 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7746 (pttm) REVERT: B 1554 SER cc_start: 0.9467 (m) cc_final: 0.9266 (p) REVERT: B 1560 ASP cc_start: 0.9323 (t0) cc_final: 0.9059 (m-30) REVERT: B 1581 ASP cc_start: 0.9267 (m-30) cc_final: 0.8907 (m-30) REVERT: B 1583 ARG cc_start: 0.9070 (ptp90) cc_final: 0.8805 (ptt90) REVERT: B 1590 TYR cc_start: 0.9385 (t80) cc_final: 0.9068 (t80) REVERT: B 1639 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.8002 (ttp-110) outliers start: 21 outliers final: 7 residues processed: 170 average time/residue: 0.6899 time to fit residues: 129.2903 Evaluate side-chains 160 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN B1444 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.060751 restraints weight = 32547.373| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.22 r_work: 0.2586 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 16604 Z= 0.132 Angle : 0.599 10.526 22532 Z= 0.303 Chirality : 0.040 0.193 2432 Planarity : 0.004 0.045 2774 Dihedral : 11.863 178.304 2464 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.95 % Allowed : 15.36 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1890 helix: 2.06 (0.19), residues: 730 sheet: 0.34 (0.31), residues: 260 loop : -0.06 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.014 0.001 TYR B1640 PHE 0.016 0.001 PHE A 491 TRP 0.012 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (16588) covalent geometry : angle 0.59215 / 0.30 (22511) hydrogen bonds : bond 0.03452 / 2.28 ( 659) hydrogen bonds : angle 4.06687 / 2.91 ( 1923) metal coordination : bond 0.00843 / 0.60 ( 16) metal coordination : angle 3.00780 / 1.80 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8333 (tmm-80) cc_final: 0.7893 (tmt170) REVERT: A 95 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8245 (tp30) REVERT: A 102 GLU cc_start: 0.8886 (tp30) cc_final: 0.8225 (tp30) REVERT: A 117 ASP cc_start: 0.8914 (m-30) cc_final: 0.8594 (m-30) REVERT: A 138 GLU cc_start: 0.9564 (tp30) cc_final: 0.9175 (tm-30) REVERT: A 139 LYS cc_start: 0.9500 (mmpt) cc_final: 0.9206 (mmmm) REVERT: A 180 MET cc_start: 0.9280 (mmm) cc_final: 0.9039 (mmm) REVERT: A 235 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: A 328 LEU cc_start: 0.8606 (tp) cc_final: 0.7877 (tt) REVERT: A 332 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 392 GLU cc_start: 0.8586 (mp0) cc_final: 0.8295 (pm20) REVERT: A 411 GLU cc_start: 0.9132 (tp30) cc_final: 0.8797 (tp30) REVERT: A 637 ASP cc_start: 0.8348 (p0) cc_final: 0.7777 (p0) REVERT: A 639 MET cc_start: 0.8869 (mpp) cc_final: 0.8341 (mmp) REVERT: A 682 TYR cc_start: 0.8897 (m-10) cc_final: 0.8641 (m-10) REVERT: B 31 MET cc_start: 0.9071 (tpp) cc_final: 0.8840 (tpp) REVERT: B 140 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8516 (mtp85) REVERT: B 273 GLU cc_start: 0.9280 (tp30) cc_final: 0.8997 (mm-30) REVERT: B 277 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 384 TYR cc_start: 0.9033 (t80) cc_final: 0.8739 (t80) REVERT: B 536 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8712 (tp30) REVERT: B 672 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7982 (mp0) REVERT: B 693 ASP cc_start: 0.8664 (m-30) cc_final: 0.8275 (m-30) REVERT: B 748 ASP cc_start: 0.8865 (m-30) cc_final: 0.8545 (m-30) REVERT: B 876 ASN cc_start: 0.9441 (m-40) cc_final: 0.9043 (m110) REVERT: B 938 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: B 942 GLU cc_start: 0.8573 (tp30) cc_final: 0.8269 (tp30) REVERT: B 1488 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7689 (pttm) REVERT: B 1560 ASP cc_start: 0.9284 (t0) cc_final: 0.9052 (m-30) REVERT: B 1581 ASP cc_start: 0.9254 (m-30) cc_final: 0.8857 (m-30) REVERT: B 1583 ARG cc_start: 0.9072 (ptp90) cc_final: 0.8798 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9335 (t80) cc_final: 0.8909 (t80) REVERT: B 1639 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7846 (ttp-110) outliers start: 16 outliers final: 6 residues processed: 174 average time/residue: 0.6956 time to fit residues: 133.6768 Evaluate side-chains 160 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 34 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 114 optimal weight: 0.0670 chunk 146 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.087979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.059458 restraints weight = 32748.040| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.25 r_work: 0.2563 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 16604 Z= 0.173 Angle : 0.626 12.390 22532 Z= 0.317 Chirality : 0.041 0.190 2432 Planarity : 0.004 0.044 2774 Dihedral : 11.860 179.896 2464 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.07 % Allowed : 15.60 % Favored : 83.33 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1890 helix: 2.04 (0.19), residues: 730 sheet: 0.36 (0.31), residues: 250 loop : -0.08 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.017 0.001 TYR B 385 PHE 0.016 0.001 PHE A 491 TRP 0.014 0.001 TRP B1625 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (16588) covalent geometry : angle 0.61941 / 0.32 (22511) hydrogen bonds : bond 0.03682 / 2.44 ( 659) hydrogen bonds : angle 4.15663 / 2.98 ( 1923) metal coordination : bond 0.01063 / 0.77 ( 16) metal coordination : angle 3.09034 / 1.80 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8362 (tmm-80) cc_final: 0.7909 (tmt170) REVERT: A 95 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8220 (tp30) REVERT: A 102 GLU cc_start: 0.8877 (tp30) cc_final: 0.8231 (tp30) REVERT: A 117 ASP cc_start: 0.8916 (m-30) cc_final: 0.8578 (m-30) REVERT: A 138 GLU cc_start: 0.9577 (tp30) cc_final: 0.9181 (tm-30) REVERT: A 139 LYS cc_start: 0.9490 (mmpt) cc_final: 0.9198 (mmmm) REVERT: A 180 MET cc_start: 0.9310 (mmm) cc_final: 0.9045 (mmm) REVERT: A 235 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8555 (mt-10) REVERT: A 328 LEU cc_start: 0.8625 (tp) cc_final: 0.7906 (tt) REVERT: A 332 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8171 (mt-10) REVERT: A 392 GLU cc_start: 0.8604 (mp0) cc_final: 0.8315 (pm20) REVERT: A 411 GLU cc_start: 0.9154 (tp30) cc_final: 0.8805 (tp30) REVERT: A 637 ASP cc_start: 0.8352 (p0) cc_final: 0.7790 (p0) REVERT: A 639 MET cc_start: 0.8863 (mpp) cc_final: 0.8360 (mmp) REVERT: B 31 MET cc_start: 0.9090 (tpp) cc_final: 0.8846 (tpp) REVERT: B 140 ARG cc_start: 0.8925 (mtp180) cc_final: 0.8578 (mtp85) REVERT: B 273 GLU cc_start: 0.9323 (tp30) cc_final: 0.9023 (mm-30) REVERT: B 277 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 293 ASP cc_start: 0.8111 (m-30) cc_final: 0.7906 (m-30) REVERT: B 384 TYR cc_start: 0.9069 (t80) cc_final: 0.8813 (t80) REVERT: B 536 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8741 (tp30) REVERT: B 672 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7996 (mp0) REVERT: B 876 ASN cc_start: 0.9448 (m-40) cc_final: 0.9054 (m110) REVERT: B 938 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: B 942 GLU cc_start: 0.8628 (tp30) cc_final: 0.8334 (tp30) REVERT: B 954 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7683 (tp30) REVERT: B 1488 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7729 (pttm) REVERT: B 1560 ASP cc_start: 0.9298 (t0) cc_final: 0.9035 (m-30) REVERT: B 1581 ASP cc_start: 0.9241 (m-30) cc_final: 0.8804 (m-30) REVERT: B 1590 TYR cc_start: 0.9318 (t80) cc_final: 0.9073 (t80) REVERT: B 1591 GLN cc_start: 0.9134 (mm110) cc_final: 0.8894 (mp10) REVERT: B 1639 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7774 (ttp-110) outliers start: 18 outliers final: 8 residues processed: 167 average time/residue: 0.6650 time to fit residues: 122.3224 Evaluate side-chains 155 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1473 ARG Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 141 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.060626 restraints weight = 32760.854| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.32 r_work: 0.2591 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 16604 Z= 0.142 Angle : 0.636 12.490 22532 Z= 0.320 Chirality : 0.040 0.192 2432 Planarity : 0.004 0.044 2774 Dihedral : 11.866 178.932 2464 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.77 % Allowed : 15.89 % Favored : 83.33 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1890 helix: 2.02 (0.19), residues: 730 sheet: 0.36 (0.31), residues: 260 loop : -0.05 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.012 0.001 TYR A 682 PHE 0.024 0.001 PHE A 491 TRP 0.014 0.001 TRP B1625 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.14 (16588) covalent geometry : angle 0.63028 / 0.32 (22511) hydrogen bonds : bond 0.03493 / 2.32 ( 659) hydrogen bonds : angle 4.13338 / 2.97 ( 1923) metal coordination : bond 0.00772 / 0.55 ( 16) metal coordination : angle 2.79192 / 1.63 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8347 (tmm-80) cc_final: 0.8121 (tmm-80) REVERT: A 95 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8215 (tp30) REVERT: A 102 GLU cc_start: 0.8865 (tp30) cc_final: 0.8175 (tp30) REVERT: A 105 ASP cc_start: 0.9205 (t70) cc_final: 0.8792 (t0) REVERT: A 117 ASP cc_start: 0.8914 (m-30) cc_final: 0.8588 (m-30) REVERT: A 138 GLU cc_start: 0.9581 (tp30) cc_final: 0.9197 (tm-30) REVERT: A 139 LYS cc_start: 0.9489 (mmpt) cc_final: 0.9199 (mmmm) REVERT: A 180 MET cc_start: 0.9255 (mmm) cc_final: 0.9015 (mmm) REVERT: A 235 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: A 328 LEU cc_start: 0.8626 (tp) cc_final: 0.7908 (tt) REVERT: A 332 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8334 (mt-10) REVERT: A 392 GLU cc_start: 0.8589 (mp0) cc_final: 0.8285 (pm20) REVERT: A 411 GLU cc_start: 0.9145 (tp30) cc_final: 0.8793 (tp30) REVERT: A 637 ASP cc_start: 0.8348 (p0) cc_final: 0.7791 (p0) REVERT: A 639 MET cc_start: 0.8840 (mpp) cc_final: 0.8355 (mmp) REVERT: B 140 ARG cc_start: 0.8914 (mtp180) cc_final: 0.8539 (mtp85) REVERT: B 273 GLU cc_start: 0.9309 (tp30) cc_final: 0.9010 (mm-30) REVERT: B 277 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 384 TYR cc_start: 0.9049 (t80) cc_final: 0.8821 (t80) REVERT: B 524 TYR cc_start: 0.8498 (m-80) cc_final: 0.8265 (m-80) REVERT: B 536 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8754 (tp30) REVERT: B 672 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8001 (mp0) REVERT: B 693 ASP cc_start: 0.8674 (m-30) cc_final: 0.8289 (m-30) REVERT: B 748 ASP cc_start: 0.8870 (m-30) cc_final: 0.8556 (m-30) REVERT: B 876 ASN cc_start: 0.9453 (m-40) cc_final: 0.9046 (m-40) REVERT: B 938 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: B 942 GLU cc_start: 0.8626 (tp30) cc_final: 0.8327 (tp30) REVERT: B 1488 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7709 (pttm) REVERT: B 1560 ASP cc_start: 0.9291 (t0) cc_final: 0.9058 (m-30) REVERT: B 1581 ASP cc_start: 0.9150 (m-30) cc_final: 0.8757 (m-30) REVERT: B 1590 TYR cc_start: 0.9380 (t80) cc_final: 0.9042 (t80) REVERT: B 1639 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7772 (ttp-110) outliers start: 13 outliers final: 9 residues processed: 161 average time/residue: 0.6442 time to fit residues: 114.0433 Evaluate side-chains 161 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1473 ARG Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 158 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.059768 restraints weight = 32603.945| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.23 r_work: 0.2566 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 16604 Z= 0.197 Angle : 0.654 13.823 22532 Z= 0.328 Chirality : 0.041 0.193 2432 Planarity : 0.004 0.045 2774 Dihedral : 11.890 179.693 2464 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.89 % Allowed : 15.77 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1890 helix: 2.02 (0.20), residues: 730 sheet: 0.34 (0.31), residues: 250 loop : -0.09 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1583 TYR 0.015 0.001 TYR A 682 PHE 0.023 0.001 PHE A 491 TRP 0.017 0.001 TRP B1625 HIS 0.005 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (16588) covalent geometry : angle 0.64675 / 0.33 (22511) hydrogen bonds : bond 0.03768 / 2.49 ( 659) hydrogen bonds : angle 4.19097 / 3.02 ( 1923) metal coordination : bond 0.01248 / 0.91 ( 16) metal coordination : angle 3.17092 / 1.81 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5137.19 seconds wall clock time: 88 minutes 37.12 seconds (5317.12 seconds total)