Starting phenix.real_space_refine on Sun May 18 06:04:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9f_27260/05_2025/8d9f_27260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9f_27260/05_2025/8d9f_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_27260/05_2025/8d9f_27260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9f_27260/05_2025/8d9f_27260.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9f_27260/05_2025/8d9f_27260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9f_27260/05_2025/8d9f_27260.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.23, per 1000 atoms: 0.57 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: 3.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 6.51 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: 7.23 Time building geometry restraints manager: 4.64 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: 9773 34.95 - 69.90: 210 69.90 - 104.85: 28 104.85 - 139.81: 1 139.81 - 174.76: 7 Dihedral angle restraints: 10019 sinusoidal: 4509 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 10016 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 45.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 15.696 174.757 6475 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (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 TRP 0.024 0.002 TRP B1625 HIS 0.006 0.001 HIS A 585 PHE 0.027 0.002 PHE B 825 TYR 0.029 0.002 TYR B 524 ARG 0.011 0.001 ARG B1583 Details of bonding type rmsd hydrogen bonds : bond 0.13523 ( 659) hydrogen bonds : angle 6.52559 ( 1923) metal coordination : bond 0.02095 ( 16) metal coordination : angle 4.60689 ( 21) covalent geometry : bond 0.00974 (16588) covalent geometry : angle 0.94341 (22511) *********************** 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 : 1.730 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: 0.8304 (m-80) cc_final: 0.8023 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 1.4580 time to fit residues: 310.2328 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 : 1.738 ------------------------------------------------------------------------------- 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 163 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 113 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.060563 restraints weight = 32576.129| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.26 r_work: 0.2607 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1362 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 : 0.589 8.764 22532 Z= 0.303 Chirality : 0.041 0.210 2432 Planarity : 0.004 0.068 2774 Dihedral : 14.842 179.821 2581 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 0.60 % Allowed : 7.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1890 helix: 1.86 (0.19), residues: 727 sheet: 0.27 (0.30), residues: 271 loop : -0.08 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1437 HIS 0.008 0.001 HIS A 585 PHE 0.017 0.001 PHE A 491 TYR 0.025 0.001 TYR B1585 ARG 0.010 0.001 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 659) hydrogen bonds : angle 4.57915 ( 1923) metal coordination : bond 0.00779 ( 16) metal coordination : angle 3.90673 ( 21) covalent geometry : bond 0.00279 (16588) covalent geometry : angle 0.57734 (22511) *********************** 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 183 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8347 (tp30) REVERT: A 111 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7921 (m-10) REVERT: A 117 ASP cc_start: 0.8785 (m-30) cc_final: 0.8463 (m-30) REVERT: A 138 GLU cc_start: 0.9549 (tp30) cc_final: 0.9102 (tm-30) REVERT: A 139 LYS cc_start: 0.9505 (mmpt) cc_final: 0.9158 (mmmm) REVERT: A 180 MET cc_start: 0.9280 (mmm) cc_final: 0.9025 (mmm) REVERT: A 411 GLU cc_start: 0.9176 (tp30) cc_final: 0.8976 (tp30) REVERT: A 467 GLU cc_start: 0.8885 (pp20) cc_final: 0.8354 (pp20) REVERT: A 504 LYS cc_start: 0.8943 (ptmm) cc_final: 0.8690 (pptt) REVERT: A 682 TYR cc_start: 0.8660 (m-10) cc_final: 0.8399 (m-10) REVERT: B 31 MET cc_start: 0.9135 (tpp) cc_final: 0.8651 (tpp) REVERT: B 119 GLU cc_start: 0.9188 (mp0) cc_final: 0.8956 (pm20) REVERT: B 273 GLU cc_start: 0.9245 (tp30) cc_final: 0.8998 (mm-30) REVERT: B 310 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8624 (mm-30) REVERT: B 548 GLU cc_start: 0.8993 (tt0) cc_final: 0.8331 (tp30) REVERT: B 672 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8435 (mt-10) REVERT: B 693 ASP cc_start: 0.8670 (m-30) cc_final: 0.8280 (m-30) REVERT: B 876 ASN cc_start: 0.9336 (m110) cc_final: 0.8985 (m-40) REVERT: B 929 TYR cc_start: 0.8604 (t80) cc_final: 0.8398 (t80) REVERT: B 942 GLU cc_start: 0.8557 (tp30) cc_final: 0.8263 (tp30) REVERT: B 1581 ASP cc_start: 0.9221 (m-30) cc_final: 0.8878 (m-30) REVERT: B 1583 ARG cc_start: 0.9096 (ptp90) cc_final: 0.8855 (ptt90) REVERT: B 1590 TYR cc_start: 0.9352 (t80) cc_final: 0.9133 (t80) outliers start: 10 outliers final: 2 residues processed: 179 average time/residue: 1.3985 time to fit residues: 277.0609 Evaluate side-chains 144 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 172 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 161 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 876 ASN B 919 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.060356 restraints weight = 32567.877| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.23 r_work: 0.2589 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16604 Z= 0.145 Angle : 0.553 8.102 22532 Z= 0.284 Chirality : 0.040 0.214 2432 Planarity : 0.004 0.056 2774 Dihedral : 14.657 179.878 2578 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.55 % Allowed : 9.17 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 1890 helix: 1.99 (0.19), residues: 729 sheet: 0.49 (0.31), residues: 259 loop : -0.08 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 607 HIS 0.004 0.001 HIS A 585 PHE 0.018 0.001 PHE A 491 TYR 0.016 0.001 TYR B 524 ARG 0.009 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 659) hydrogen bonds : angle 4.27546 ( 1923) metal coordination : bond 0.00950 ( 16) metal coordination : angle 3.55187 ( 21) covalent geometry : bond 0.00330 (16588) covalent geometry : angle 0.54279 (22511) *********************** 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 189 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8206 (tp30) REVERT: A 117 ASP cc_start: 0.8895 (m-30) cc_final: 0.8573 (m-30) REVERT: A 138 GLU cc_start: 0.9553 (tp30) cc_final: 0.9107 (tm-30) REVERT: A 139 LYS cc_start: 0.9523 (mmpt) cc_final: 0.9196 (mmmm) REVERT: A 180 MET cc_start: 0.9287 (mmm) cc_final: 0.8932 (mmm) REVERT: A 235 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8500 (mt-10) REVERT: A 411 GLU cc_start: 0.9189 (tp30) cc_final: 0.8907 (tp30) REVERT: A 504 LYS cc_start: 0.8827 (ptmm) cc_final: 0.8587 (pptt) REVERT: A 637 ASP cc_start: 0.8345 (p0) cc_final: 0.7898 (p0) REVERT: A 682 TYR cc_start: 0.8663 (m-10) cc_final: 0.8266 (m-10) REVERT: B 31 MET cc_start: 0.9109 (tpp) cc_final: 0.8789 (tpp) REVERT: B 118 LYS cc_start: 0.9338 (mtpp) cc_final: 0.9050 (tttm) REVERT: B 140 ARG cc_start: 0.8857 (mtp180) cc_final: 0.8490 (mtp85) REVERT: B 273 GLU cc_start: 0.9255 (tp30) cc_final: 0.9007 (mm-30) REVERT: B 548 GLU cc_start: 0.9044 (tt0) cc_final: 0.8324 (tp30) REVERT: B 583 MET cc_start: 0.9110 (tpp) cc_final: 0.8691 (mmm) REVERT: B 672 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 693 ASP cc_start: 0.8702 (m-30) cc_final: 0.8308 (m-30) REVERT: B 876 ASN cc_start: 0.9381 (m-40) cc_final: 0.8967 (m-40) REVERT: B 938 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: B 942 GLU cc_start: 0.8588 (tp30) cc_final: 0.8275 (tp30) REVERT: B 1476 TYR cc_start: 0.8564 (m-80) cc_final: 0.8303 (m-80) REVERT: B 1560 ASP cc_start: 0.9288 (t0) cc_final: 0.9015 (m-30) REVERT: B 1581 ASP cc_start: 0.9206 (m-30) cc_final: 0.8860 (m-30) REVERT: B 1583 ARG cc_start: 0.9085 (ptp90) cc_final: 0.8840 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9357 (t80) cc_final: 0.9032 (t80) outliers start: 26 outliers final: 5 residues processed: 178 average time/residue: 1.3549 time to fit residues: 267.3235 Evaluate side-chains 154 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.086132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.057690 restraints weight = 32975.891| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.25 r_work: 0.2521 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16604 Z= 0.244 Angle : 0.601 11.024 22532 Z= 0.307 Chirality : 0.042 0.206 2432 Planarity : 0.004 0.051 2774 Dihedral : 14.576 179.741 2578 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.37 % Allowed : 10.89 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1890 helix: 1.94 (0.19), residues: 730 sheet: 0.38 (0.32), residues: 256 loop : -0.12 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1596 HIS 0.003 0.001 HIS B1616 PHE 0.018 0.001 PHE A 491 TYR 0.016 0.001 TYR B 524 ARG 0.009 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 659) hydrogen bonds : angle 4.32975 ( 1923) metal coordination : bond 0.01777 ( 16) metal coordination : angle 3.91305 ( 21) covalent geometry : bond 0.00555 (16588) covalent geometry : angle 0.58915 (22511) *********************** 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 184 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8359 (tp30) REVERT: A 117 ASP cc_start: 0.8910 (m-30) cc_final: 0.8576 (m-30) REVERT: A 138 GLU cc_start: 0.9591 (tp30) cc_final: 0.9163 (tm-30) REVERT: A 139 LYS cc_start: 0.9512 (mmpt) cc_final: 0.9211 (mmmm) REVERT: A 180 MET cc_start: 0.9381 (mmm) cc_final: 0.9024 (mmm) REVERT: A 235 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: A 392 GLU cc_start: 0.8622 (mp0) cc_final: 0.8379 (pm20) REVERT: A 411 GLU cc_start: 0.9188 (tp30) cc_final: 0.8889 (tp30) REVERT: A 512 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8686 (mt-10) REVERT: A 637 ASP cc_start: 0.8400 (p0) cc_final: 0.7922 (p0) REVERT: A 690 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8413 (mm-30) REVERT: B 31 MET cc_start: 0.9131 (tpp) cc_final: 0.8765 (tpp) REVERT: B 273 GLU cc_start: 0.9288 (tp30) cc_final: 0.9039 (mm-30) REVERT: B 628 GLU cc_start: 0.9007 (mp0) cc_final: 0.8804 (mp0) REVERT: B 672 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8359 (mt-10) REVERT: B 876 ASN cc_start: 0.9410 (m-40) cc_final: 0.9025 (m110) REVERT: B 938 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: B 942 GLU cc_start: 0.8599 (tp30) cc_final: 0.8305 (tp30) REVERT: B 1488 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7675 (pttp) REVERT: B 1560 ASP cc_start: 0.9339 (t0) cc_final: 0.9052 (m-30) REVERT: B 1581 ASP cc_start: 0.9234 (m-30) cc_final: 0.8900 (m-30) REVERT: B 1583 ARG cc_start: 0.9104 (ptp90) cc_final: 0.8852 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9336 (t80) cc_final: 0.9072 (t80) REVERT: B 1591 GLN cc_start: 0.9113 (mm110) cc_final: 0.8878 (mp10) REVERT: B 1635 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7635 (mp0) outliers start: 23 outliers final: 10 residues processed: 176 average time/residue: 1.4015 time to fit residues: 272.0457 Evaluate side-chains 155 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 929 TYR Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1507 MET 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 81 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 54 optimal weight: 0.0050 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.059379 restraints weight = 33064.828| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.22 r_work: 0.2554 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16604 Z= 0.165 Angle : 0.571 9.066 22532 Z= 0.291 Chirality : 0.040 0.206 2432 Planarity : 0.004 0.050 2774 Dihedral : 14.465 179.351 2578 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.19 % Allowed : 12.38 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.19), residues: 1890 helix: 2.01 (0.19), residues: 730 sheet: 0.52 (0.32), residues: 252 loop : -0.12 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 PHE 0.018 0.001 PHE A 491 TYR 0.022 0.001 TYR B1640 ARG 0.011 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 659) hydrogen bonds : angle 4.17625 ( 1923) metal coordination : bond 0.01145 ( 16) metal coordination : angle 3.38673 ( 21) covalent geometry : bond 0.00377 (16588) covalent geometry : angle 0.56162 (22511) *********************** 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 181 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8227 (tp30) REVERT: A 117 ASP cc_start: 0.8925 (m-30) cc_final: 0.8586 (m-30) REVERT: A 138 GLU cc_start: 0.9566 (tp30) cc_final: 0.9171 (tm-30) REVERT: A 139 LYS cc_start: 0.9512 (mmpt) cc_final: 0.9181 (mmmm) REVERT: A 180 MET cc_start: 0.9288 (mmm) cc_final: 0.8936 (mmm) REVERT: A 235 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: A 411 GLU cc_start: 0.9155 (tp30) cc_final: 0.8836 (tp30) REVERT: A 637 ASP cc_start: 0.8334 (p0) cc_final: 0.7845 (p0) REVERT: A 690 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8515 (mm-30) REVERT: B 31 MET cc_start: 0.9088 (tpp) cc_final: 0.8722 (tpp) REVERT: B 273 GLU cc_start: 0.9280 (tp30) cc_final: 0.8992 (mm-30) REVERT: B 277 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 583 MET cc_start: 0.9018 (tpp) cc_final: 0.8673 (mmm) REVERT: B 628 GLU cc_start: 0.8981 (mp0) cc_final: 0.8768 (mp0) REVERT: B 672 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8358 (mt-10) REVERT: B 876 ASN cc_start: 0.9426 (m-40) cc_final: 0.9038 (m110) REVERT: B 938 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: B 942 GLU cc_start: 0.8586 (tp30) cc_final: 0.8257 (tp30) REVERT: B 1488 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7592 (pttp) REVERT: B 1506 VAL cc_start: 0.8877 (t) cc_final: 0.8580 (p) REVERT: B 1560 ASP cc_start: 0.9299 (t0) cc_final: 0.9041 (m-30) REVERT: B 1581 ASP cc_start: 0.9247 (m-30) cc_final: 0.8874 (m-30) REVERT: B 1583 ARG cc_start: 0.9093 (ptp90) cc_final: 0.8838 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9327 (t80) cc_final: 0.8979 (t80) REVERT: B 1591 GLN cc_start: 0.9123 (mm110) cc_final: 0.8893 (mp10) REVERT: B 1635 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7707 (mp0) outliers start: 20 outliers final: 10 residues processed: 174 average time/residue: 1.3782 time to fit residues: 264.8551 Evaluate side-chains 159 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 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 1484 ILE 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 96 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 159 optimal weight: 0.0010 chunk 188 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.087933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.059487 restraints weight = 32912.467| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.29 r_work: 0.2557 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16604 Z= 0.163 Angle : 0.571 8.842 22532 Z= 0.292 Chirality : 0.041 0.200 2432 Planarity : 0.004 0.046 2774 Dihedral : 14.409 179.521 2578 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.19 % Allowed : 13.21 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1890 helix: 2.04 (0.19), residues: 729 sheet: 0.45 (0.32), residues: 251 loop : -0.13 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B1596 HIS 0.007 0.001 HIS B1616 PHE 0.017 0.001 PHE A 491 TYR 0.013 0.001 TYR B 385 ARG 0.011 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 659) hydrogen bonds : angle 4.14884 ( 1923) metal coordination : bond 0.01206 ( 16) metal coordination : angle 3.17623 ( 21) covalent geometry : bond 0.00374 (16588) covalent geometry : angle 0.56292 (22511) *********************** 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 183 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8285 (tmm-80) cc_final: 0.7862 (tmt170) REVERT: A 95 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8252 (tp30) REVERT: A 117 ASP cc_start: 0.8930 (m-30) cc_final: 0.8604 (m-30) REVERT: A 138 GLU cc_start: 0.9572 (tp30) cc_final: 0.9174 (tm-30) REVERT: A 139 LYS cc_start: 0.9501 (mmpt) cc_final: 0.9171 (mmmm) REVERT: A 180 MET cc_start: 0.9298 (mmm) cc_final: 0.9076 (mmm) REVERT: A 235 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: A 411 GLU cc_start: 0.9185 (tp30) cc_final: 0.8840 (tp30) REVERT: A 637 ASP cc_start: 0.8360 (p0) cc_final: 0.7812 (p0) REVERT: A 639 MET cc_start: 0.8872 (mpp) cc_final: 0.8366 (mmp) REVERT: A 682 TYR cc_start: 0.8824 (m-10) cc_final: 0.8510 (m-10) REVERT: A 690 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8632 (mm-30) REVERT: B 31 MET cc_start: 0.9107 (tpp) cc_final: 0.8873 (tpp) REVERT: B 273 GLU cc_start: 0.9271 (tp30) cc_final: 0.8988 (mm-30) REVERT: B 277 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 583 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8772 (mmm) REVERT: B 628 GLU cc_start: 0.8997 (mp0) cc_final: 0.8779 (mp0) REVERT: B 672 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 876 ASN cc_start: 0.9432 (m-40) cc_final: 0.9035 (m110) REVERT: B 938 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: B 942 GLU cc_start: 0.8581 (tp30) cc_final: 0.8284 (tp30) REVERT: B 1396 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8756 (mmpt) REVERT: B 1488 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7591 (pttp) REVERT: B 1560 ASP cc_start: 0.9304 (t0) cc_final: 0.9058 (m-30) REVERT: B 1581 ASP cc_start: 0.9257 (m-30) cc_final: 0.8882 (m-30) REVERT: B 1583 ARG cc_start: 0.9076 (ptp90) cc_final: 0.8801 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9393 (t80) cc_final: 0.9129 (t80) REVERT: B 1591 GLN cc_start: 0.9170 (mm110) cc_final: 0.8904 (mp10) outliers start: 20 outliers final: 11 residues processed: 176 average time/residue: 1.3675 time to fit residues: 265.9399 Evaluate side-chains 167 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 A residue 542 PHE Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 583 MET 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 1484 ILE Chi-restraints excluded: chain B residue 1624 LEU 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 163 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.059739 restraints weight = 32776.724| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.30 r_work: 0.2583 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 16604 Z= 0.136 Angle : 0.584 8.303 22532 Z= 0.301 Chirality : 0.040 0.198 2432 Planarity : 0.004 0.048 2774 Dihedral : 14.355 178.829 2578 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.01 % Allowed : 14.29 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1890 helix: 2.01 (0.19), residues: 730 sheet: 0.37 (0.31), residues: 254 loop : -0.12 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 PHE 0.016 0.001 PHE A 491 TYR 0.012 0.001 TYR B 385 ARG 0.012 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 659) hydrogen bonds : angle 4.10545 ( 1923) metal coordination : bond 0.00844 ( 16) metal coordination : angle 2.93986 ( 21) covalent geometry : bond 0.00325 (16588) covalent geometry : angle 0.57763 (22511) *********************** 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 185 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8251 (tp30) REVERT: A 102 GLU cc_start: 0.8888 (tp30) cc_final: 0.8224 (tp30) REVERT: A 111 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: A 117 ASP cc_start: 0.8908 (m-30) cc_final: 0.8592 (m-30) REVERT: A 138 GLU cc_start: 0.9572 (tp30) cc_final: 0.9190 (tm-30) REVERT: A 139 LYS cc_start: 0.9507 (mmpt) cc_final: 0.9179 (mmmm) REVERT: A 180 MET cc_start: 0.9271 (mmm) cc_final: 0.9054 (mmm) REVERT: A 235 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: A 332 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8456 (mp0) REVERT: A 411 GLU cc_start: 0.9178 (tp30) cc_final: 0.8829 (tp30) REVERT: A 637 ASP cc_start: 0.8356 (p0) cc_final: 0.7799 (p0) REVERT: A 639 MET cc_start: 0.8826 (mpp) cc_final: 0.8342 (mmp) REVERT: A 682 TYR cc_start: 0.8855 (m-10) cc_final: 0.8614 (m-10) REVERT: A 690 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8748 (mm-30) REVERT: B 31 MET cc_start: 0.9077 (tpp) cc_final: 0.8847 (tpp) REVERT: B 273 GLU cc_start: 0.9290 (tp30) cc_final: 0.8998 (mm-30) REVERT: B 277 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 384 TYR cc_start: 0.9040 (t80) cc_final: 0.8733 (t80) REVERT: B 524 TYR cc_start: 0.8512 (m-80) cc_final: 0.8264 (m-80) REVERT: B 583 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8733 (mmm) REVERT: B 628 GLU cc_start: 0.8973 (mp0) cc_final: 0.8771 (mp0) REVERT: B 672 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 876 ASN cc_start: 0.9443 (m-40) cc_final: 0.9038 (m110) REVERT: B 938 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: B 942 GLU cc_start: 0.8568 (tp30) cc_final: 0.8266 (tp30) REVERT: B 1396 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8759 (mmpt) REVERT: B 1488 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7713 (pttp) REVERT: B 1505 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8321 (mt-10) REVERT: B 1506 VAL cc_start: 0.8936 (t) cc_final: 0.8671 (p) REVERT: B 1560 ASP cc_start: 0.9290 (t0) cc_final: 0.9058 (m-30) REVERT: B 1581 ASP cc_start: 0.9253 (m-30) cc_final: 0.8870 (m-30) REVERT: B 1583 ARG cc_start: 0.9077 (ptp90) cc_final: 0.8795 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9405 (t80) cc_final: 0.9073 (t80) outliers start: 17 outliers final: 9 residues processed: 177 average time/residue: 1.3649 time to fit residues: 268.2916 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 : 1.857 ------------------------------------------------------------------------------- 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 A residue 542 PHE Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 583 MET 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 1624 LEU 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 36 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 133 optimal weight: 0.0030 chunk 161 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.089500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.060924 restraints weight = 32621.797| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.29 r_work: 0.2590 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.169 16604 Z= 0.126 Angle : 0.591 11.462 22532 Z= 0.300 Chirality : 0.040 0.197 2432 Planarity : 0.004 0.051 2774 Dihedral : 14.317 178.547 2578 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.13 % Allowed : 14.82 % Favored : 84.05 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 1890 helix: 2.02 (0.19), residues: 730 sheet: 0.43 (0.31), residues: 254 loop : -0.08 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 PHE 0.015 0.001 PHE A 491 TYR 0.015 0.001 TYR B 385 ARG 0.014 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 659) hydrogen bonds : angle 4.06254 ( 1923) metal coordination : bond 0.00714 ( 16) metal coordination : angle 2.67456 ( 21) covalent geometry : bond 0.00315 (16588) covalent geometry : angle 0.58546 (22511) *********************** 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 182 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8214 (tp30) REVERT: A 102 GLU cc_start: 0.8867 (tp30) cc_final: 0.8243 (tp30) REVERT: A 111 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: A 117 ASP cc_start: 0.8938 (m-30) cc_final: 0.8637 (m-30) REVERT: A 138 GLU cc_start: 0.9563 (tp30) cc_final: 0.9189 (tm-30) REVERT: A 139 LYS cc_start: 0.9501 (mmpt) cc_final: 0.9157 (mmmm) REVERT: A 180 MET cc_start: 0.9222 (mmm) cc_final: 0.9011 (mmm) REVERT: A 235 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: A 328 LEU cc_start: 0.8595 (tp) cc_final: 0.8219 (tp) REVERT: A 332 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8548 (mt-10) REVERT: A 411 GLU cc_start: 0.9172 (tp30) cc_final: 0.8810 (tp30) REVERT: A 637 ASP cc_start: 0.8356 (p0) cc_final: 0.7792 (p0) REVERT: A 639 MET cc_start: 0.8842 (mpp) cc_final: 0.8375 (mmp) REVERT: A 682 TYR cc_start: 0.8857 (m-10) cc_final: 0.8636 (m-10) REVERT: A 690 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8753 (mm-30) REVERT: B 31 MET cc_start: 0.9042 (tpp) cc_final: 0.8693 (tpp) REVERT: B 140 ARG cc_start: 0.8872 (mtp180) cc_final: 0.8564 (mtp85) REVERT: B 273 GLU cc_start: 0.9293 (tp30) cc_final: 0.9003 (mm-30) REVERT: B 277 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 384 TYR cc_start: 0.9011 (t80) cc_final: 0.8767 (t80) REVERT: B 524 TYR cc_start: 0.8404 (m-80) cc_final: 0.8203 (m-80) REVERT: B 536 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8779 (tp30) REVERT: B 583 MET cc_start: 0.9005 (tpp) cc_final: 0.8714 (mmm) REVERT: B 628 GLU cc_start: 0.8965 (mp0) cc_final: 0.8729 (mp0) REVERT: B 672 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 693 ASP cc_start: 0.8672 (m-30) cc_final: 0.8282 (m-30) REVERT: B 748 ASP cc_start: 0.8883 (m-30) cc_final: 0.8577 (m-30) REVERT: B 876 ASN cc_start: 0.9436 (m-40) cc_final: 0.9029 (m110) REVERT: B 938 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8343 (pm20) REVERT: B 942 GLU cc_start: 0.8576 (tp30) cc_final: 0.8271 (tp30) REVERT: B 1488 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7697 (pttp) REVERT: B 1506 VAL cc_start: 0.8985 (t) cc_final: 0.8729 (p) REVERT: B 1560 ASP cc_start: 0.9270 (t0) cc_final: 0.9057 (m-30) REVERT: B 1581 ASP cc_start: 0.9225 (m-30) cc_final: 0.8827 (m-30) REVERT: B 1583 ARG cc_start: 0.9071 (ptp90) cc_final: 0.8799 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9342 (t80) cc_final: 0.8983 (t80) outliers start: 19 outliers final: 9 residues processed: 177 average time/residue: 1.3278 time to fit residues: 260.4502 Evaluate side-chains 169 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 A residue 542 PHE Chi-restraints excluded: chain B residue 28 HIS 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 1624 LEU 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 5 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.061131 restraints weight = 32657.747| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.31 r_work: 0.2601 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 16604 Z= 0.126 Angle : 0.615 12.034 22532 Z= 0.309 Chirality : 0.040 0.195 2432 Planarity : 0.004 0.055 2774 Dihedral : 14.308 178.475 2578 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.07 % Allowed : 15.36 % Favored : 83.57 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1890 helix: 2.06 (0.19), residues: 730 sheet: 0.51 (0.31), residues: 255 loop : -0.09 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 PHE 0.023 0.001 PHE A 491 TYR 0.011 0.001 TYR A 607 ARG 0.013 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 659) hydrogen bonds : angle 4.01858 ( 1923) metal coordination : bond 0.00660 ( 16) metal coordination : angle 2.82917 ( 21) covalent geometry : bond 0.00321 (16588) covalent geometry : angle 0.60919 (22511) *********************** 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 180 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8155 (tp30) REVERT: A 102 GLU cc_start: 0.8866 (tp30) cc_final: 0.8174 (tp30) REVERT: A 105 ASP cc_start: 0.9173 (t70) cc_final: 0.8762 (t0) REVERT: A 111 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: A 117 ASP cc_start: 0.8944 (m-30) cc_final: 0.8655 (m-30) REVERT: A 138 GLU cc_start: 0.9560 (tp30) cc_final: 0.9178 (tm-30) REVERT: A 139 LYS cc_start: 0.9498 (mmpt) cc_final: 0.9208 (mmmm) REVERT: A 180 MET cc_start: 0.9205 (mmm) cc_final: 0.8917 (mmm) REVERT: A 235 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: A 327 ARG cc_start: 0.7999 (mpp80) cc_final: 0.7668 (mpt-90) REVERT: A 328 LEU cc_start: 0.8587 (tp) cc_final: 0.7821 (tt) REVERT: A 332 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 411 GLU cc_start: 0.9177 (tp30) cc_final: 0.8804 (tp30) REVERT: A 637 ASP cc_start: 0.8344 (p0) cc_final: 0.7781 (p0) REVERT: A 639 MET cc_start: 0.8858 (mpp) cc_final: 0.8384 (mmp) REVERT: A 682 TYR cc_start: 0.8862 (m-10) cc_final: 0.8656 (m-10) REVERT: A 690 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8790 (mm-30) REVERT: B 273 GLU cc_start: 0.9283 (tp30) cc_final: 0.8991 (mm-30) REVERT: B 277 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 310 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8610 (mm-30) REVERT: B 378 ILE cc_start: 0.9376 (pp) cc_final: 0.9095 (pt) REVERT: B 384 TYR cc_start: 0.9037 (t80) cc_final: 0.8832 (t80) REVERT: B 536 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8811 (tp30) REVERT: B 583 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8681 (mmm) REVERT: B 628 GLU cc_start: 0.8959 (mp0) cc_final: 0.8720 (mp0) REVERT: B 672 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 693 ASP cc_start: 0.8676 (m-30) cc_final: 0.8287 (m-30) REVERT: B 748 ASP cc_start: 0.8861 (m-30) cc_final: 0.8558 (m-30) REVERT: B 876 ASN cc_start: 0.9438 (m-40) cc_final: 0.9017 (m-40) REVERT: B 938 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: B 942 GLU cc_start: 0.8619 (tp30) cc_final: 0.8321 (tp30) REVERT: B 1488 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7710 (pttp) REVERT: B 1506 VAL cc_start: 0.9019 (t) cc_final: 0.8768 (p) REVERT: B 1581 ASP cc_start: 0.9221 (m-30) cc_final: 0.8818 (m-30) REVERT: B 1583 ARG cc_start: 0.9079 (ptp90) cc_final: 0.8806 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9338 (t80) cc_final: 0.8950 (t80) outliers start: 18 outliers final: 10 residues processed: 173 average time/residue: 1.3389 time to fit residues: 255.6120 Evaluate side-chains 165 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 A residue 491 PHE Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 583 MET 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 1624 LEU 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 123 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.061429 restraints weight = 32819.772| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.23 r_work: 0.2588 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 16604 Z= 0.150 Angle : 0.630 15.243 22532 Z= 0.314 Chirality : 0.041 0.329 2432 Planarity : 0.004 0.057 2774 Dihedral : 14.333 179.248 2578 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.89 % Allowed : 15.89 % Favored : 83.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1890 helix: 2.05 (0.20), residues: 730 sheet: 0.55 (0.32), residues: 249 loop : -0.10 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 PHE 0.023 0.001 PHE A 491 TYR 0.019 0.001 TYR B 385 ARG 0.014 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 659) hydrogen bonds : angle 4.05829 ( 1923) metal coordination : bond 0.00875 ( 16) metal coordination : angle 2.75109 ( 21) covalent geometry : bond 0.00370 (16588) covalent geometry : angle 0.62498 (22511) ********************** 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 168 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8208 (tp30) REVERT: A 102 GLU cc_start: 0.8867 (tp30) cc_final: 0.8174 (tp30) REVERT: A 105 ASP cc_start: 0.9176 (t70) cc_final: 0.8782 (t0) REVERT: A 111 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: A 117 ASP cc_start: 0.8945 (m-30) cc_final: 0.8644 (m-30) REVERT: A 138 GLU cc_start: 0.9563 (tp30) cc_final: 0.9202 (tm-30) REVERT: A 139 LYS cc_start: 0.9494 (mmpt) cc_final: 0.9223 (mmmm) REVERT: A 180 MET cc_start: 0.9252 (mmm) cc_final: 0.9046 (mmm) REVERT: A 235 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: A 328 LEU cc_start: 0.8625 (tp) cc_final: 0.7873 (tt) REVERT: A 332 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8319 (mt-10) REVERT: A 411 GLU cc_start: 0.9171 (tp30) cc_final: 0.8795 (tp30) REVERT: A 637 ASP cc_start: 0.8348 (p0) cc_final: 0.7786 (p0) REVERT: A 639 MET cc_start: 0.8864 (mpp) cc_final: 0.8388 (mmp) REVERT: A 690 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8804 (mm-30) REVERT: B 273 GLU cc_start: 0.9320 (tp30) cc_final: 0.9017 (mm-30) REVERT: B 277 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8496 (tm-30) REVERT: B 536 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8802 (tp30) REVERT: B 583 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8690 (mmm) REVERT: B 628 GLU cc_start: 0.8971 (mp0) cc_final: 0.8730 (mp0) REVERT: B 672 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 693 ASP cc_start: 0.8691 (m-30) cc_final: 0.8301 (m-30) REVERT: B 748 ASP cc_start: 0.8878 (m-30) cc_final: 0.8580 (m-30) REVERT: B 876 ASN cc_start: 0.9446 (m-40) cc_final: 0.9045 (m110) REVERT: B 938 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: B 942 GLU cc_start: 0.8612 (tp30) cc_final: 0.8315 (tp30) REVERT: B 1488 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7730 (pttp) REVERT: B 1506 VAL cc_start: 0.9065 (t) cc_final: 0.8488 (m) REVERT: B 1581 ASP cc_start: 0.9225 (m-30) cc_final: 0.8820 (m-30) REVERT: B 1583 ARG cc_start: 0.9068 (ptp90) cc_final: 0.8796 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9344 (t80) cc_final: 0.8951 (t80) outliers start: 15 outliers final: 9 residues processed: 162 average time/residue: 1.3356 time to fit residues: 239.7969 Evaluate side-chains 161 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 A residue 542 PHE Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 583 MET 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 1624 LEU 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 117 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.062583 restraints weight = 32659.424| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.23 r_work: 0.2655 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 16604 Z= 0.126 Angle : 0.617 12.566 22532 Z= 0.308 Chirality : 0.040 0.238 2432 Planarity : 0.004 0.061 2774 Dihedral : 14.346 178.474 2578 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.83 % Allowed : 16.37 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1890 helix: 2.10 (0.19), residues: 730 sheet: 0.53 (0.31), residues: 265 loop : -0.05 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 PHE 0.025 0.001 PHE A 491 TYR 0.018 0.001 TYR B 385 ARG 0.014 0.000 ARG B1639 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 659) hydrogen bonds : angle 3.99083 ( 1923) metal coordination : bond 0.00577 ( 16) metal coordination : angle 2.47266 ( 21) covalent geometry : bond 0.00314 (16588) covalent geometry : angle 0.61232 (22511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10691.32 seconds wall clock time: 185 minutes 23.24 seconds (11123.24 seconds total)