Starting phenix.real_space_refine on Sat Sep 12 15:09:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9f_27260/09_2026/8d9f_27260.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 33 5.49 5 S 57 5.16 5 C 10177 2.51 5 N 2793 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5436 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 650} Chain breaks: 2 Chain: "B" Number of atoms: 10034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1242, 10034 Classifications: {'peptide': 1242} Link IDs: {'PTRANS': 59, 'TRANS': 1182} Chain breaks: 7 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 2, 'rna3p_pyr': 11} Link IDs: {'rna2p': 19, 'rna3p': 13} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6104 SG CYS B 83 38.936 26.446 26.156 1.00133.42 S ATOM 6375 SG CYS B 116 36.827 23.888 24.100 1.00155.67 S ATOM 6421 SG CYS B 122 37.693 23.283 27.769 1.00130.57 S ATOM 6445 SG CYS B 125 35.328 26.034 26.846 1.00125.50 S ATOM 9139 SG CYS B 486 50.070 47.433 49.719 1.00127.38 S ATOM 9207 SG CYS B 496 48.620 45.167 46.905 1.00118.87 S ATOM 9221 SG CYS B 498 52.348 45.172 48.258 1.00121.83 S ATOM 9243 SG CYS B 501 49.427 43.592 50.006 1.00119.03 S ATOM 11214 SG CYS B 745 54.251 67.386 72.428 1.00150.38 S ATOM 11227 SG CYS B 747 56.315 65.418 74.936 1.00140.80 S ATOM 11249 SG CYS B 750 53.200 63.747 73.492 1.00136.31 S ATOM 13200 SG CYS B1013 46.791 71.941 109.540 1.00179.40 S ATOM 13326 SG CYS B1401 46.249 73.597 106.140 1.00176.13 S ATOM 13377 SG CYS B1409 49.714 73.209 107.752 1.00162.63 S ATOM 13394 SG CYS B1412 48.089 70.245 106.283 1.00153.82 S Time building chain proxies: 3.65, per 1000 atoms: 0.23 Number of scatterers: 16163 At special positions: 0 Unit cell: (102.72, 104.86, 156.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 57 16.00 P 33 15.00 O 3099 8.00 N 2793 7.00 C 10177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 693.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 125 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 122 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 83 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 116 " pdb=" ZN B1702 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 498 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 486 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 496 " pdb=" ZN B1703 " pdb="ZN ZN B1703 " - pdb=" ND1 HIS B 742 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 747 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 745 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 750 " pdb=" ZN B1704 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1409 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1013 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1412 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1401 " Number of angles added : 21 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 25 sheets defined 42.0% alpha, 18.0% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 15 through 33 Processing helix chain 'A' and resid 37 through 59 removed outlier: 3.658A pdb=" N LYS A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 82 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.572A pdb=" N LYS A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 Processing helix chain 'A' and resid 141 through 155 Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.772A pdb=" N ILE A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 removed outlier: 4.372A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 230 through 246 removed outlier: 4.083A pdb=" N ASP A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 279 through 297 removed outlier: 4.737A pdb=" N VAL A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 322 Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.587A pdb=" N LYS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 362 removed outlier: 4.023A pdb=" N TYR A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.967A pdb=" N ASN A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.720A pdb=" N ALA A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.558A pdb=" N ASN A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 removed outlier: 3.763A pdb=" N TRP A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.579A pdb=" N PHE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 54 through 73 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.532A pdb=" N ASN B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 302 removed outlier: 3.694A pdb=" N ILE B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N HIS B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 369 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 466 through 483 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 681 through 688 Processing helix chain 'B' and resid 718 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 795 through 799 removed outlier: 3.664A pdb=" N LYS B 799 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 843 Processing helix chain 'B' and resid 868 through 878 removed outlier: 4.020A pdb=" N THR B 878 " --> pdb=" O MET B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1010 removed outlier: 3.613A pdb=" N LEU B 998 " --> pdb=" O PRO B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1395 through 1399 Processing helix chain 'B' and resid 1409 through 1415 Processing helix chain 'B' and resid 1458 through 1463 removed outlier: 4.355A pdb=" N SER B1462 " --> pdb=" O ARG B1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 1481 through 1488 removed outlier: 3.548A pdb=" N ILE B1485 " --> pdb=" O GLY B1481 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1496 removed outlier: 3.598A pdb=" N VAL B1496 " --> pdb=" O ILE B1492 " (cutoff:3.500A) Processing helix chain 'B' and resid 1523 through 1535 Processing helix chain 'B' and resid 1578 through 1597 Processing helix chain 'B' and resid 1610 through 1613 removed outlier: 3.573A pdb=" N VAL B1613 " --> pdb=" O GLN B1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1610 through 1613' Processing helix chain 'B' and resid 1614 through 1624 Processing helix chain 'B' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 275 Processing sheet with id=AA2, first strand: chain 'A' and resid 425 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 540 removed outlier: 6.368A pdb=" N LEU A 580 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 622 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N THR A 660 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU A 624 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 586 through 587 Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 7.133A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG B 14 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TRP B 39 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 16 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TRP B 41 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP B 190 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N GLU B 17 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 13.189A pdb=" N ARG B 188 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP B 185 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.528A pdb=" N THR B 4 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 8 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.528A pdb=" N VAL B 80 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.136A pdb=" N THR B 105 " --> pdb=" O VAL B 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AB1, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.519A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.519A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 426 through 427 removed outlier: 3.535A pdb=" N VAL B 427 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN B 454 " --> pdb=" O VAL B 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB5, first strand: chain 'B' and resid 521 through 525 Processing sheet with id=AB6, first strand: chain 'B' and resid 528 through 529 removed outlier: 3.679A pdb=" N THR B 534 " --> pdb=" O ASN B 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.788A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.788A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN B 668 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE B 863 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 670 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 861 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU B 672 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 694 through 695 removed outlier: 7.201A pdb=" N ALA B 694 " --> pdb=" O TYR B 803 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC2, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AC3, first strand: chain 'B' and resid 919 through 922 Processing sheet with id=AC4, first strand: chain 'B' and resid 986 through 987 removed outlier: 7.051A pdb=" N LEU B 991 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ALA B1429 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ASP B1516 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B1431 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER B1514 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B1433 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1424 through 1426 removed outlier: 7.134A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1416 through 1417 Processing sheet with id=AC7, first strand: chain 'B' and resid 1448 through 1450 691 hydrogen bonds defined for protein. 1923 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.93 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 1.20e-02 6.94e+03 1.52e+02 bond pdb=" O3' U C 19 " pdb=" P G C 20 " ideal model delta sigma weight residual 1.607 1.460 0.147 1.20e-02 6.94e+03 1.51e+02 bond pdb=" O3' G C 20 " pdb=" P U C 21 " ideal model delta sigma weight residual 1.607 1.477 0.130 1.20e-02 6.94e+03 1.17e+02 bond pdb=" O3' U C 36 " pdb=" P U C 37 " ideal model delta sigma weight residual 1.607 1.490 0.117 1.20e-02 6.94e+03 9.45e+01 bond pdb=" O3' U C 27 " pdb=" P A C 28 " ideal model delta sigma weight residual 1.607 1.492 0.115 1.20e-02 6.94e+03 9.23e+01 ... (remaining 16583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.54: 22428 5.54 - 11.08: 61 11.08 - 16.63: 17 16.63 - 22.17: 4 22.17 - 27.71: 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 108.20 80.49 27.71 3.00e+00 1.11e-01 8.53e+01 angle pdb=" C3' A C 33 " pdb=" C2' A C 33 " pdb=" O2' A C 33 " ideal model delta sigma weight residual 109.80 126.72 -16.92 2.00e+00 2.50e-01 7.16e+01 angle pdb=" O2' U C 35 " pdb=" C2' U C 35 " pdb=" C1' U C 35 " ideal model delta sigma weight residual 108.20 88.18 20.02 3.00e+00 1.11e-01 4.45e+01 angle pdb=" C4' A C 18 " pdb=" C3' A C 18 " pdb=" O3' A C 18 " ideal model delta sigma weight residual 112.50 100.23 12.27 2.00e+00 2.50e-01 3.76e+01 angle pdb=" C4' C C 43 " pdb=" C3' C C 43 " pdb=" O3' C C 43 " ideal model delta sigma weight residual 112.50 94.49 18.01 3.00e+00 1.11e-01 3.60e+01 ... (remaining 22506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8875 17.86 - 35.73: 764 35.73 - 53.59: 159 53.59 - 71.46: 77 71.46 - 89.32: 30 Dihedral angle restraints: 9905 sinusoidal: 4395 harmonic: 5510 Sorted by residual: dihedral pdb=" C4' C C 43 " pdb=" C3' C C 43 " pdb=" C2' C C 43 " pdb=" C1' C C 43 " ideal model delta sinusoidal sigma weight residual 36.34 -44.84 81.18 1 3.10e+00 1.04e-01 8.46e+02 dihedral pdb=" C4' A C 33 " pdb=" C3' A C 33 " pdb=" C2' A C 33 " pdb=" C1' A C 33 " ideal model delta sinusoidal sigma weight residual 36.34 -43.57 79.92 1 3.10e+00 1.04e-01 8.24e+02 dihedral pdb=" C4' U C 34 " pdb=" C3' U C 34 " pdb=" C2' U C 34 " pdb=" C1' U C 34 " ideal model delta sinusoidal sigma weight residual 36.35 -43.45 79.79 1 3.10e+00 1.04e-01 8.22e+02 ... (remaining 9902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2306 0.107 - 0.214: 93 0.214 - 0.321: 24 0.321 - 0.427: 5 0.427 - 0.534: 4 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 2.17 -1.64 0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" C2' C C 43 " pdb=" C3' C C 43 " pdb=" O2' C C 43 " pdb=" C1' C C 43 " both_signs ideal model delta sigma weight residual False -2.79 -2.31 -0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" C3' C C 43 " pdb=" C4' C C 43 " pdb=" O3' C C 43 " pdb=" C2' C C 43 " both_signs ideal model delta sigma weight residual False -2.50 -2.95 0.45 2.00e-01 2.50e+01 5.13e+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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.148 16604 Z= 0.525 Angle : 0.982 27.711 22532 Z= 0.480 Chirality : 0.060 0.534 2432 Planarity : 0.005 0.113 2774 Dihedral : 15.507 89.322 6361 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Rotamer: Outliers : 0.06 % Allowed : 0.00 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1890 helix: 1.23 (0.19), residues: 731 sheet: 0.03 (0.31), residues: 263 loop : -0.23 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1583 TYR 0.029 0.002 TYR B 524 PHE 0.027 0.002 PHE B 825 TRP 0.024 0.002 TRP B1625 HIS 0.006 0.001 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00976 / 0.53 (16588) covalent geometry : angle 0.97223 / 0.48 (22511) hydrogen bonds : bond 0.13523 / 8.92 ( 659) hydrogen bonds : angle 6.52559 / 4.70 ( 1923) metal coordination : bond 0.02095 / 1.52 ( 16) metal coordination : angle 4.60689 / 2.88 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8756 (m-30) cc_final: 0.8331 (m-30) REVERT: A 138 GLU cc_start: 0.9294 (tp30) cc_final: 0.8941 (tm-30) REVERT: A 139 LYS cc_start: 0.9488 (mmpt) cc_final: 0.9183 (mmmm) REVERT: A 180 MET cc_start: 0.9260 (mmm) cc_final: 0.9049 (mmm) REVERT: A 287 MET cc_start: 0.8990 (mtm) cc_final: 0.8772 (mtm) REVERT: A 682 TYR cc_start: 0.8509 (m-10) cc_final: 0.8206 (m-10) REVERT: B 273 GLU cc_start: 0.9138 (tp30) cc_final: 0.8819 (mm-30) REVERT: B 283 ASP cc_start: 0.9232 (t70) cc_final: 0.9006 (t0) REVERT: B 310 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8541 (mm-30) REVERT: B 672 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 876 ASN cc_start: 0.9236 (m110) cc_final: 0.8897 (m-40) REVERT: B 956 LEU cc_start: 0.9014 (mm) cc_final: 0.8771 (mm) REVERT: B 1581 ASP cc_start: 0.9253 (m-30) cc_final: 0.8957 (m-30) REVERT: B 1583 ARG cc_start: 0.8950 (ptp90) cc_final: 0.8647 (mtm-85) REVERT: B 1590 TYR cc_start: 0.9256 (t80) cc_final: 0.8933 (t80) REVERT: B 1621 TYR cc_start: 0.8305 (m-80) cc_final: 0.8024 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.7258 time to fit residues: 154.0949 Evaluate side-chains 144 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1507 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 ASN B 147 HIS ** B 919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1687 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.062582 restraints weight = 32502.517| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.24 r_work: 0.2657 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16604 Z= 0.154 Angle : 0.896 19.770 22532 Z= 0.394 Chirality : 0.088 1.274 2432 Planarity : 0.004 0.070 2774 Dihedral : 10.992 145.406 2467 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1890 helix: 1.82 (0.19), residues: 727 sheet: 0.25 (0.30), residues: 269 loop : -0.11 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 35 TYR 0.024 0.001 TYR B1585 PHE 0.017 0.001 PHE A 491 TRP 0.015 0.001 TRP B1437 HIS 0.008 0.001 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16588) covalent geometry : angle 0.88862 / 0.39 (22511) hydrogen bonds : bond 0.04239 / 2.78 ( 659) hydrogen bonds : angle 4.67683 / 3.32 ( 1923) metal coordination : bond 0.00948 / 0.68 ( 16) metal coordination : angle 3.96602 / 2.30 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8358 (tp30) REVERT: A 117 ASP cc_start: 0.8781 (m-30) cc_final: 0.8451 (m-30) REVERT: A 138 GLU cc_start: 0.9540 (tp30) cc_final: 0.9089 (tm-30) REVERT: A 139 LYS cc_start: 0.9506 (mmpt) cc_final: 0.9165 (mmmm) REVERT: A 180 MET cc_start: 0.9276 (mmm) cc_final: 0.8987 (mmm) REVERT: A 467 GLU cc_start: 0.8910 (pp20) cc_final: 0.8394 (pp20) REVERT: A 504 LYS cc_start: 0.8960 (ptmm) cc_final: 0.8705 (pptt) REVERT: A 682 TYR cc_start: 0.8692 (m-10) cc_final: 0.8393 (m-10) REVERT: B 31 MET cc_start: 0.9150 (tpp) cc_final: 0.8571 (tpp) REVERT: B 119 GLU cc_start: 0.9200 (mp0) cc_final: 0.8992 (pm20) REVERT: B 273 GLU cc_start: 0.9254 (tp30) cc_final: 0.9011 (mm-30) REVERT: B 283 ASP cc_start: 0.9526 (t70) cc_final: 0.9319 (t0) REVERT: B 310 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8632 (mm-30) REVERT: B 548 GLU cc_start: 0.8959 (tt0) cc_final: 0.8322 (tp30) REVERT: B 672 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8421 (mt-10) REVERT: B 876 ASN cc_start: 0.9343 (m110) cc_final: 0.8997 (m-40) REVERT: B 929 TYR cc_start: 0.8588 (t80) cc_final: 0.8377 (t80) REVERT: B 942 GLU cc_start: 0.8563 (tp30) cc_final: 0.8280 (tp30) REVERT: B 1447 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6540 (ttm110) REVERT: B 1581 ASP cc_start: 0.9237 (m-30) cc_final: 0.8900 (m-30) REVERT: B 1583 ARG cc_start: 0.9095 (ptp90) cc_final: 0.8857 (ptt90) REVERT: B 1590 TYR cc_start: 0.9345 (t80) cc_final: 0.9097 (t80) outliers start: 10 outliers final: 2 residues processed: 173 average time/residue: 0.6993 time to fit residues: 133.4863 Evaluate side-chains 144 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1624 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 42 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 131 optimal weight: 0.0030 chunk 54 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 190 optimal weight: 0.0170 chunk 171 optimal weight: 5.9990 overall best weight: 1.8032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 HIS B 323 HIS B 876 ASN B 908 GLN ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.062155 restraints weight = 33104.588| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.25 r_work: 0.2633 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16604 Z= 0.176 Angle : 0.744 11.906 22532 Z= 0.342 Chirality : 0.067 0.662 2432 Planarity : 0.004 0.057 2774 Dihedral : 11.581 157.140 2464 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.49 % Allowed : 9.05 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1890 helix: 1.94 (0.19), residues: 729 sheet: 0.43 (0.31), residues: 261 loop : -0.14 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 35 TYR 0.014 0.001 TYR B 524 PHE 0.019 0.001 PHE A 491 TRP 0.012 0.001 TRP B 607 HIS 0.003 0.001 HIS A 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (16588) covalent geometry : angle 0.73594 / 0.34 (22511) hydrogen bonds : bond 0.03951 / 2.60 ( 659) hydrogen bonds : angle 4.33487 / 3.09 ( 1923) metal coordination : bond 0.01223 / 0.88 ( 16) metal coordination : angle 3.67487 / 2.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8247 (tp30) REVERT: A 117 ASP cc_start: 0.8883 (m-30) cc_final: 0.8545 (m-30) REVERT: A 138 GLU cc_start: 0.9546 (tp30) cc_final: 0.9103 (tm-30) REVERT: A 139 LYS cc_start: 0.9519 (mmpt) cc_final: 0.9190 (mmmm) REVERT: A 180 MET cc_start: 0.9334 (mmm) cc_final: 0.8986 (mmm) REVERT: A 235 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: A 411 GLU cc_start: 0.9158 (tp30) cc_final: 0.8904 (tp30) REVERT: A 504 LYS cc_start: 0.8806 (ptmm) cc_final: 0.8573 (pptt) REVERT: A 637 ASP cc_start: 0.8342 (p0) cc_final: 0.7903 (p0) REVERT: B 31 MET cc_start: 0.9182 (tpp) cc_final: 0.8910 (tpp) REVERT: B 140 ARG cc_start: 0.8862 (mtp180) cc_final: 0.8505 (mtp85) REVERT: B 273 GLU cc_start: 0.9266 (tp30) cc_final: 0.9012 (mm-30) REVERT: B 283 ASP cc_start: 0.9536 (t70) cc_final: 0.9305 (t0) REVERT: B 672 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8372 (mt-10) REVERT: B 876 ASN cc_start: 0.9378 (m-40) cc_final: 0.8972 (m-40) REVERT: B 938 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: B 942 GLU cc_start: 0.8607 (tp30) cc_final: 0.8317 (tp30) REVERT: B 1560 ASP cc_start: 0.9259 (t0) cc_final: 0.8971 (m-30) REVERT: B 1581 ASP cc_start: 0.9214 (m-30) cc_final: 0.8886 (m-30) REVERT: B 1583 ARG cc_start: 0.9092 (ptp90) cc_final: 0.8851 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9360 (t80) cc_final: 0.9123 (t80) outliers start: 25 outliers final: 4 residues processed: 181 average time/residue: 0.6811 time to fit residues: 136.2008 Evaluate side-chains 146 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1624 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 131 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.060463 restraints weight = 33007.400| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.24 r_work: 0.2579 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16604 Z= 0.246 Angle : 0.771 12.063 22532 Z= 0.356 Chirality : 0.068 0.688 2432 Planarity : 0.004 0.052 2774 Dihedral : 12.112 179.629 2464 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.37 % Allowed : 10.77 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 1890 helix: 1.89 (0.19), residues: 729 sheet: 0.35 (0.31), residues: 256 loop : -0.19 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1639 TYR 0.016 0.001 TYR B 524 PHE 0.022 0.001 PHE A 111 TRP 0.021 0.001 TRP B1596 HIS 0.004 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (16588) covalent geometry : angle 0.76288 / 0.36 (22511) hydrogen bonds : bond 0.04178 / 2.74 ( 659) hydrogen bonds : angle 4.35598 / 3.11 ( 1923) metal coordination : bond 0.01710 / 1.25 ( 16) metal coordination : angle 3.80001 / 2.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8300 (tp30) REVERT: A 117 ASP cc_start: 0.8891 (m-30) cc_final: 0.8557 (m-30) REVERT: A 138 GLU cc_start: 0.9577 (tp30) cc_final: 0.9150 (tm-30) REVERT: A 139 LYS cc_start: 0.9513 (mmpt) cc_final: 0.9217 (mmmm) REVERT: A 180 MET cc_start: 0.9379 (mmm) cc_final: 0.8991 (mmm) REVERT: A 235 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: A 411 GLU cc_start: 0.9190 (tp30) cc_final: 0.8908 (tp30) REVERT: A 637 ASP cc_start: 0.8407 (p0) cc_final: 0.7931 (p0) REVERT: A 682 TYR cc_start: 0.8732 (m-10) cc_final: 0.8413 (m-10) REVERT: A 690 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8370 (mm-30) REVERT: B 31 MET cc_start: 0.9206 (tpp) cc_final: 0.8901 (tpp) REVERT: B 273 GLU cc_start: 0.9299 (tp30) cc_final: 0.9018 (mm-30) REVERT: B 277 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8523 (tm-30) REVERT: B 283 ASP cc_start: 0.9570 (t70) cc_final: 0.9323 (t0) REVERT: B 672 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 876 ASN cc_start: 0.9406 (m-40) cc_final: 0.9007 (m-40) REVERT: B 938 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: B 942 GLU cc_start: 0.8628 (tp30) cc_final: 0.8340 (tp30) REVERT: B 1447 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.7719 (ttp80) REVERT: B 1488 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7728 (pttm) REVERT: B 1508 ASP cc_start: 0.9006 (t70) cc_final: 0.8741 (t70) REVERT: B 1560 ASP cc_start: 0.9304 (t0) cc_final: 0.9010 (m-30) REVERT: B 1581 ASP cc_start: 0.9245 (m-30) cc_final: 0.8916 (m-30) REVERT: B 1583 ARG cc_start: 0.9094 (ptp90) cc_final: 0.8841 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9388 (t80) cc_final: 0.9010 (t80) outliers start: 23 outliers final: 8 residues processed: 169 average time/residue: 0.6734 time to fit residues: 125.5463 Evaluate side-chains 152 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 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 1488 LYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 171 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 190 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.061791 restraints weight = 32988.762| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.31 r_work: 0.2640 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16604 Z= 0.152 Angle : 0.714 10.752 22532 Z= 0.330 Chirality : 0.062 0.600 2432 Planarity : 0.004 0.055 2774 Dihedral : 12.060 177.150 2464 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.25 % Allowed : 12.50 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1890 helix: 1.98 (0.19), residues: 729 sheet: 0.42 (0.31), residues: 256 loop : -0.18 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1639 TYR 0.016 0.001 TYR B 929 PHE 0.019 0.001 PHE A 111 TRP 0.024 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16588) covalent geometry : angle 0.70754 / 0.33 (22511) hydrogen bonds : bond 0.03669 / 2.42 ( 659) hydrogen bonds : angle 4.16075 / 2.97 ( 1923) metal coordination : bond 0.00961 / 0.69 ( 16) metal coordination : angle 3.21093 / 1.78 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8270 (tp30) REVERT: A 111 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8065 (m-10) REVERT: A 117 ASP cc_start: 0.8909 (m-30) cc_final: 0.8576 (m-30) REVERT: A 138 GLU cc_start: 0.9544 (tp30) cc_final: 0.9153 (tm-30) REVERT: A 139 LYS cc_start: 0.9512 (mmpt) cc_final: 0.9182 (mmmm) REVERT: A 180 MET cc_start: 0.9285 (mmm) cc_final: 0.9018 (mmm) REVERT: A 235 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: A 392 GLU cc_start: 0.8673 (mp0) cc_final: 0.8403 (pm20) REVERT: A 411 GLU cc_start: 0.9181 (tp30) cc_final: 0.8895 (tp30) REVERT: A 637 ASP cc_start: 0.8337 (p0) cc_final: 0.7841 (p0) REVERT: A 682 TYR cc_start: 0.8795 (m-10) cc_final: 0.8566 (m-10) REVERT: A 690 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8523 (mm-30) REVERT: B 31 MET cc_start: 0.9115 (tpp) cc_final: 0.8786 (tpp) REVERT: B 273 GLU cc_start: 0.9272 (tp30) cc_final: 0.8985 (mm-30) REVERT: B 277 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 283 ASP cc_start: 0.9567 (t70) cc_final: 0.9322 (t0) REVERT: B 384 TYR cc_start: 0.9003 (t80) cc_final: 0.8733 (t80) REVERT: B 583 MET cc_start: 0.9031 (tpp) cc_final: 0.8742 (mmm) REVERT: B 672 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8343 (mt-10) REVERT: B 876 ASN cc_start: 0.9423 (m-40) cc_final: 0.9035 (m110) REVERT: B 938 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: B 942 GLU cc_start: 0.8600 (tp30) cc_final: 0.8271 (tp30) REVERT: B 1488 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7762 (pttm) REVERT: B 1507 MET cc_start: 0.8639 (mtp) cc_final: 0.8334 (tpt) REVERT: B 1560 ASP cc_start: 0.9262 (t0) cc_final: 0.8992 (m-30) REVERT: B 1581 ASP cc_start: 0.9259 (m-30) cc_final: 0.8882 (m-30) REVERT: B 1583 ARG cc_start: 0.9091 (ptp90) cc_final: 0.8839 (ptt90) REVERT: B 1590 TYR cc_start: 0.9356 (t80) cc_final: 0.9114 (t80) REVERT: B 1591 GLN cc_start: 0.9172 (mm110) cc_final: 0.8899 (mp10) REVERT: B 1635 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7437 (mp0) outliers start: 21 outliers final: 5 residues processed: 177 average time/residue: 0.6918 time to fit residues: 135.1534 Evaluate side-chains 155 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Chi-restraints excluded: chain B residue 1635 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1487 GLN ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.061548 restraints weight = 32689.552| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.31 r_work: 0.2618 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16604 Z= 0.181 Angle : 0.731 10.709 22532 Z= 0.339 Chirality : 0.063 0.590 2432 Planarity : 0.004 0.049 2774 Dihedral : 12.116 176.154 2464 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.25 % Allowed : 13.33 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1890 helix: 1.95 (0.19), residues: 729 sheet: 0.38 (0.31), residues: 257 loop : -0.15 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1639 TYR 0.014 0.001 TYR B 385 PHE 0.020 0.001 PHE A 111 TRP 0.040 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (16588) covalent geometry : angle 0.72511 / 0.34 (22511) hydrogen bonds : bond 0.03779 / 2.49 ( 659) hydrogen bonds : angle 4.19326 / 3.00 ( 1923) metal coordination : bond 0.01249 / 0.91 ( 16) metal coordination : angle 3.18788 / 1.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.8305 (tmm-80) cc_final: 0.7885 (tmt170) REVERT: A 95 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8244 (tp30) REVERT: A 102 GLU cc_start: 0.8922 (tp30) cc_final: 0.8242 (tp30) REVERT: A 111 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: A 117 ASP cc_start: 0.8915 (m-30) cc_final: 0.8592 (m-30) REVERT: A 138 GLU cc_start: 0.9563 (tp30) cc_final: 0.9157 (tm-30) REVERT: A 139 LYS cc_start: 0.9498 (mmpt) cc_final: 0.9191 (mmmm) REVERT: A 180 MET cc_start: 0.9316 (mmm) cc_final: 0.9057 (mmm) REVERT: A 235 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: A 392 GLU cc_start: 0.8652 (mp0) cc_final: 0.8410 (pm20) REVERT: A 411 GLU cc_start: 0.9173 (tp30) cc_final: 0.8842 (tp30) REVERT: A 512 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8731 (mt-10) REVERT: A 637 ASP cc_start: 0.8371 (p0) cc_final: 0.7802 (p0) REVERT: A 639 MET cc_start: 0.8882 (mpp) cc_final: 0.8599 (mmm) REVERT: A 682 TYR cc_start: 0.8783 (m-10) cc_final: 0.8575 (m-10) REVERT: A 690 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 31 MET cc_start: 0.9153 (tpp) cc_final: 0.8821 (tpp) REVERT: B 273 GLU cc_start: 0.9281 (tp30) cc_final: 0.9001 (mm-30) REVERT: B 277 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 283 ASP cc_start: 0.9559 (t70) cc_final: 0.9328 (t0) REVERT: B 384 TYR cc_start: 0.9030 (t80) cc_final: 0.8737 (t80) REVERT: B 583 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8851 (mmm) REVERT: B 672 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 876 ASN cc_start: 0.9440 (m-40) cc_final: 0.9032 (m-40) REVERT: B 938 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: B 942 GLU cc_start: 0.8590 (tp30) cc_final: 0.8270 (tp30) REVERT: B 1396 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8768 (mmpt) REVERT: B 1488 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7679 (pttm) REVERT: B 1560 ASP cc_start: 0.9280 (t0) cc_final: 0.9046 (m-30) REVERT: B 1581 ASP cc_start: 0.9226 (m-30) cc_final: 0.8841 (m-30) REVERT: B 1583 ARG cc_start: 0.9074 (ptp90) cc_final: 0.8811 (ptt90) REVERT: B 1590 TYR cc_start: 0.9382 (t80) cc_final: 0.9026 (t80) REVERT: B 1635 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7509 (mp0) outliers start: 21 outliers final: 7 residues processed: 176 average time/residue: 0.6493 time to fit residues: 126.5001 Evaluate side-chains 158 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 542 PHE 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 1488 LYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Chi-restraints excluded: chain B residue 1635 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 37 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.060744 restraints weight = 32979.041| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.28 r_work: 0.2609 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16604 Z= 0.218 Angle : 0.761 12.116 22532 Z= 0.353 Chirality : 0.064 0.657 2432 Planarity : 0.004 0.048 2774 Dihedral : 12.260 176.707 2464 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.25 % Allowed : 14.52 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1890 helix: 1.87 (0.19), residues: 730 sheet: 0.35 (0.32), residues: 257 loop : -0.15 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1639 TYR 0.012 0.001 TYR A 607 PHE 0.019 0.001 PHE A 111 TRP 0.036 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (16588) covalent geometry : angle 0.75298 / 0.35 (22511) hydrogen bonds : bond 0.03924 / 2.58 ( 659) hydrogen bonds : angle 4.26585 / 3.05 ( 1923) metal coordination : bond 0.01448 / 1.05 ( 16) metal coordination : angle 3.62734 / 2.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8296 (tp30) REVERT: A 102 GLU cc_start: 0.8910 (tp30) cc_final: 0.8240 (tp30) REVERT: A 111 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8051 (m-10) REVERT: A 117 ASP cc_start: 0.8903 (m-30) cc_final: 0.8562 (m-30) REVERT: A 138 GLU cc_start: 0.9561 (tp30) cc_final: 0.9155 (tm-30) REVERT: A 139 LYS cc_start: 0.9496 (mmpt) cc_final: 0.9206 (mmmm) REVERT: A 180 MET cc_start: 0.9380 (mmm) cc_final: 0.9116 (mmm) REVERT: A 235 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: A 332 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 392 GLU cc_start: 0.8669 (mp0) cc_final: 0.8421 (pm20) REVERT: A 411 GLU cc_start: 0.9168 (tp30) cc_final: 0.8834 (tp30) REVERT: A 512 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8726 (mt-10) REVERT: A 637 ASP cc_start: 0.8374 (p0) cc_final: 0.7854 (p0) REVERT: A 639 MET cc_start: 0.8862 (mpp) cc_final: 0.8506 (mmm) REVERT: A 690 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8717 (mm-30) REVERT: B 31 MET cc_start: 0.9169 (tpp) cc_final: 0.8832 (tpp) REVERT: B 273 GLU cc_start: 0.9296 (tp30) cc_final: 0.9013 (mm-30) REVERT: B 277 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8520 (tm-30) REVERT: B 283 ASP cc_start: 0.9608 (t70) cc_final: 0.9318 (t0) REVERT: B 672 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 876 ASN cc_start: 0.9448 (m-40) cc_final: 0.9045 (m-40) REVERT: B 938 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: B 942 GLU cc_start: 0.8639 (tp30) cc_final: 0.8325 (tp30) REVERT: B 1396 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8783 (mmpt) REVERT: B 1488 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7775 (pttm) REVERT: B 1507 MET cc_start: 0.8815 (mtp) cc_final: 0.8425 (tpt) REVERT: B 1554 SER cc_start: 0.9493 (m) cc_final: 0.9255 (p) REVERT: B 1560 ASP cc_start: 0.9287 (t0) cc_final: 0.9027 (m-30) REVERT: B 1581 ASP cc_start: 0.9255 (m-30) cc_final: 0.8878 (m-30) REVERT: B 1583 ARG cc_start: 0.9098 (ptp90) cc_final: 0.8819 (ptt90) REVERT: B 1590 TYR cc_start: 0.9385 (t80) cc_final: 0.9042 (t80) REVERT: B 1635 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7505 (mp0) outliers start: 21 outliers final: 8 residues processed: 167 average time/residue: 0.7117 time to fit residues: 130.7510 Evaluate side-chains 163 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Chi-restraints excluded: chain B residue 1635 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 ASN ** B1444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.091485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.062977 restraints weight = 32822.406| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.32 r_work: 0.2655 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 16604 Z= 0.143 Angle : 0.732 11.856 22532 Z= 0.341 Chirality : 0.060 0.548 2432 Planarity : 0.004 0.053 2774 Dihedral : 12.259 172.649 2464 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.25 % Allowed : 14.58 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1890 helix: 1.96 (0.19), residues: 729 sheet: 0.35 (0.32), residues: 259 loop : -0.11 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1639 TYR 0.011 0.001 TYR B 385 PHE 0.018 0.001 PHE A 111 TRP 0.023 0.001 TRP B1596 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (16588) covalent geometry : angle 0.72652 / 0.34 (22511) hydrogen bonds : bond 0.03540 / 2.34 ( 659) hydrogen bonds : angle 4.14238 / 2.97 ( 1923) metal coordination : bond 0.00893 / 0.64 ( 16) metal coordination : angle 3.00145 / 1.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8165 (tp30) REVERT: A 102 GLU cc_start: 0.8893 (tp30) cc_final: 0.8223 (tp30) REVERT: A 111 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: A 117 ASP cc_start: 0.8894 (m-30) cc_final: 0.8572 (m-30) REVERT: A 138 GLU cc_start: 0.9551 (tp30) cc_final: 0.9166 (tm-30) REVERT: A 139 LYS cc_start: 0.9493 (mmpt) cc_final: 0.9202 (mmmm) REVERT: A 235 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 328 LEU cc_start: 0.8605 (tp) cc_final: 0.7884 (tt) REVERT: A 332 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 392 GLU cc_start: 0.8651 (mp0) cc_final: 0.8381 (pm20) REVERT: A 411 GLU cc_start: 0.9151 (tp30) cc_final: 0.8813 (tp30) REVERT: A 637 ASP cc_start: 0.8366 (p0) cc_final: 0.7819 (p0) REVERT: A 639 MET cc_start: 0.8863 (mpp) cc_final: 0.8377 (mmp) REVERT: A 690 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8766 (mm-30) REVERT: B 31 MET cc_start: 0.9108 (tpp) cc_final: 0.8777 (tpp) REVERT: B 273 GLU cc_start: 0.9293 (tp30) cc_final: 0.9008 (mm-30) REVERT: B 277 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 283 ASP cc_start: 0.9607 (t70) cc_final: 0.9331 (t0) REVERT: B 384 TYR cc_start: 0.9008 (t80) cc_final: 0.8774 (t80) REVERT: B 672 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 876 ASN cc_start: 0.9450 (m-40) cc_final: 0.9041 (m-40) REVERT: B 938 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: B 942 GLU cc_start: 0.8631 (tp30) cc_final: 0.8341 (tp30) REVERT: B 1488 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7730 (pttm) REVERT: B 1507 MET cc_start: 0.8614 (mtp) cc_final: 0.8391 (tpt) REVERT: B 1554 SER cc_start: 0.9467 (m) cc_final: 0.9257 (p) REVERT: B 1560 ASP cc_start: 0.9274 (t0) cc_final: 0.9037 (m-30) REVERT: B 1581 ASP cc_start: 0.9250 (m-30) cc_final: 0.8877 (m-30) REVERT: B 1583 ARG cc_start: 0.9084 (ptp90) cc_final: 0.8796 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9342 (t80) cc_final: 0.8981 (t80) REVERT: B 1635 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7586 (mp0) outliers start: 21 outliers final: 7 residues processed: 177 average time/residue: 0.6970 time to fit residues: 136.0710 Evaluate side-chains 160 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 1624 LEU Chi-restraints excluded: chain B residue 1626 VAL Chi-restraints excluded: chain B residue 1635 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 34 optimal weight: 0.1980 chunk 90 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 94 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.063605 restraints weight = 32602.530| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.31 r_work: 0.2677 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2559 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= 0.139 Angle : 0.738 12.790 22532 Z= 0.343 Chirality : 0.059 0.545 2432 Planarity : 0.004 0.052 2774 Dihedral : 12.224 174.531 2464 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.01 % Allowed : 15.54 % Favored : 83.45 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1890 helix: 2.02 (0.19), residues: 729 sheet: 0.40 (0.32), residues: 259 loop : -0.10 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1639 TYR 0.017 0.001 TYR B 385 PHE 0.023 0.001 PHE A 491 TRP 0.011 0.001 TRP B1625 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (16588) covalent geometry : angle 0.73334 / 0.34 (22511) hydrogen bonds : bond 0.03443 / 2.28 ( 659) hydrogen bonds : angle 4.08127 / 2.93 ( 1923) metal coordination : bond 0.00776 / 0.55 ( 16) metal coordination : angle 2.82756 / 1.62 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8174 (tp30) REVERT: A 102 GLU cc_start: 0.8866 (tp30) cc_final: 0.8174 (tp30) REVERT: A 105 ASP cc_start: 0.9189 (t70) cc_final: 0.8792 (t0) REVERT: A 111 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: A 117 ASP cc_start: 0.8924 (m-30) cc_final: 0.8629 (m-30) REVERT: A 138 GLU cc_start: 0.9533 (tp30) cc_final: 0.9156 (tm-30) REVERT: A 139 LYS cc_start: 0.9492 (mmpt) cc_final: 0.9198 (mmmm) REVERT: A 235 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: A 328 LEU cc_start: 0.8612 (tp) cc_final: 0.7894 (tt) REVERT: A 332 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8331 (mt-10) REVERT: A 392 GLU cc_start: 0.8637 (mp0) cc_final: 0.8372 (pm20) REVERT: A 411 GLU cc_start: 0.9171 (tp30) cc_final: 0.8816 (tp30) REVERT: A 512 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8709 (mt-10) REVERT: A 637 ASP cc_start: 0.8361 (p0) cc_final: 0.7792 (p0) REVERT: A 639 MET cc_start: 0.8879 (mpp) cc_final: 0.8415 (mmp) REVERT: A 682 TYR cc_start: 0.8674 (m-10) cc_final: 0.8351 (m-10) REVERT: B 31 MET cc_start: 0.9050 (tpp) cc_final: 0.8740 (tpp) REVERT: B 273 GLU cc_start: 0.9306 (tp30) cc_final: 0.9018 (mm-30) REVERT: B 277 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 283 ASP cc_start: 0.9604 (t70) cc_final: 0.9333 (t0) REVERT: B 384 TYR cc_start: 0.9032 (t80) cc_final: 0.8749 (t80) REVERT: B 524 TYR cc_start: 0.8613 (m-80) cc_final: 0.8265 (m-80) REVERT: B 672 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8332 (mt-10) REVERT: B 693 ASP cc_start: 0.8725 (m-30) cc_final: 0.8347 (m-30) REVERT: B 748 ASP cc_start: 0.8863 (m-30) cc_final: 0.8561 (m-30) REVERT: B 876 ASN cc_start: 0.9448 (m-40) cc_final: 0.9039 (m-40) REVERT: B 938 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: B 942 GLU cc_start: 0.8639 (tp30) cc_final: 0.8348 (tp30) REVERT: B 1394 LEU cc_start: 0.8600 (tp) cc_final: 0.8138 (tt) REVERT: B 1488 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7691 (pttm) REVERT: B 1507 MET cc_start: 0.8672 (mtp) cc_final: 0.8436 (tpt) REVERT: B 1554 SER cc_start: 0.9468 (m) cc_final: 0.9224 (p) REVERT: B 1581 ASP cc_start: 0.9243 (m-30) cc_final: 0.8863 (m-30) REVERT: B 1583 ARG cc_start: 0.9085 (ptp90) cc_final: 0.8805 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9303 (t80) cc_final: 0.8897 (t80) outliers start: 17 outliers final: 7 residues processed: 178 average time/residue: 0.6668 time to fit residues: 131.6612 Evaluate side-chains 164 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 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 15 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 125 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 919 HIS B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.063442 restraints weight = 32433.116| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.29 r_work: 0.2672 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2610 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= 0.147 Angle : 0.747 12.115 22532 Z= 0.348 Chirality : 0.059 0.534 2432 Planarity : 0.004 0.061 2774 Dihedral : 12.223 179.096 2464 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.83 % Allowed : 16.13 % Favored : 83.04 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1890 helix: 2.03 (0.19), residues: 729 sheet: 0.45 (0.32), residues: 259 loop : -0.11 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B1639 TYR 0.011 0.001 TYR A 607 PHE 0.025 0.001 PHE A 491 TRP 0.014 0.001 TRP A 687 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (16588) covalent geometry : angle 0.74297 / 0.35 (22511) hydrogen bonds : bond 0.03449 / 2.29 ( 659) hydrogen bonds : angle 4.10042 / 2.96 ( 1923) metal coordination : bond 0.00837 / 0.61 ( 16) metal coordination : angle 2.65719 / 1.55 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8255 (tp30) REVERT: A 102 GLU cc_start: 0.8870 (tp30) cc_final: 0.8176 (tp30) REVERT: A 105 ASP cc_start: 0.9188 (t70) cc_final: 0.8784 (t0) REVERT: A 111 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: A 117 ASP cc_start: 0.8927 (m-30) cc_final: 0.8628 (m-30) REVERT: A 138 GLU cc_start: 0.9542 (tp30) cc_final: 0.9167 (tm-30) REVERT: A 139 LYS cc_start: 0.9490 (mmpt) cc_final: 0.9199 (mmmm) REVERT: A 235 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: A 327 ARG cc_start: 0.8045 (mpp80) cc_final: 0.7722 (mpt-90) REVERT: A 328 LEU cc_start: 0.8625 (tp) cc_final: 0.7877 (tt) REVERT: A 332 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8346 (mt-10) REVERT: A 392 GLU cc_start: 0.8653 (mp0) cc_final: 0.8384 (pm20) REVERT: A 411 GLU cc_start: 0.9170 (tp30) cc_final: 0.8820 (tp30) REVERT: A 512 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8707 (mt-10) REVERT: A 587 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8313 (pt0) REVERT: A 637 ASP cc_start: 0.8360 (p0) cc_final: 0.7810 (p0) REVERT: A 639 MET cc_start: 0.8883 (mpp) cc_final: 0.8418 (mmp) REVERT: A 682 TYR cc_start: 0.8694 (m-10) cc_final: 0.8359 (m-10) REVERT: B 31 MET cc_start: 0.9068 (tpp) cc_final: 0.8752 (tpp) REVERT: B 273 GLU cc_start: 0.9331 (tp30) cc_final: 0.9033 (mm-30) REVERT: B 277 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 283 ASP cc_start: 0.9606 (t70) cc_final: 0.9339 (t0) REVERT: B 384 TYR cc_start: 0.9055 (t80) cc_final: 0.8795 (t80) REVERT: B 524 TYR cc_start: 0.8610 (m-80) cc_final: 0.8257 (m-80) REVERT: B 583 MET cc_start: 0.9416 (mmm) cc_final: 0.9175 (mmm) REVERT: B 672 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 693 ASP cc_start: 0.8722 (m-30) cc_final: 0.8341 (m-30) REVERT: B 748 ASP cc_start: 0.8861 (m-30) cc_final: 0.8558 (m-30) REVERT: B 876 ASN cc_start: 0.9451 (m-40) cc_final: 0.9055 (m110) REVERT: B 938 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: B 942 GLU cc_start: 0.8633 (tp30) cc_final: 0.8340 (tp30) REVERT: B 1488 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7760 (pttm) REVERT: B 1507 MET cc_start: 0.8658 (mtp) cc_final: 0.8430 (tpt) REVERT: B 1554 SER cc_start: 0.9470 (m) cc_final: 0.9230 (p) REVERT: B 1581 ASP cc_start: 0.9242 (m-30) cc_final: 0.8859 (m-30) REVERT: B 1583 ARG cc_start: 0.9088 (ptp90) cc_final: 0.8810 (ptp-170) REVERT: B 1590 TYR cc_start: 0.9315 (t80) cc_final: 0.8936 (t80) outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 0.6862 time to fit residues: 120.0080 Evaluate side-chains 157 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 938 GLU Chi-restraints excluded: chain B residue 951 CYS Chi-restraints excluded: chain B residue 1488 LYS Chi-restraints excluded: chain B residue 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 158 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 986 ASN ** B1479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.091427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.063664 restraints weight = 32305.221| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.22 r_work: 0.2664 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 16604 Z= 0.161 Angle : 0.754 12.326 22532 Z= 0.350 Chirality : 0.060 0.552 2432 Planarity : 0.004 0.059 2774 Dihedral : 12.210 177.003 2464 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.89 % Allowed : 16.19 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1890 helix: 2.00 (0.19), residues: 729 sheet: 0.46 (0.32), residues: 258 loop : -0.10 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B1639 TYR 0.011 0.001 TYR A 607 PHE 0.025 0.001 PHE A 491 TRP 0.014 0.001 TRP B1625 HIS 0.006 0.001 HIS B1616 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (16588) covalent geometry : angle 0.74935 / 0.35 (22511) hydrogen bonds : bond 0.03540 / 2.35 ( 659) hydrogen bonds : angle 4.11612 / 2.97 ( 1923) metal coordination : bond 0.00958 / 0.70 ( 16) metal coordination : angle 2.83521 / 1.64 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5055.51 seconds wall clock time: 87 minutes 17.96 seconds (5237.96 seconds total)