Starting phenix.real_space_refine on Sat Oct 24 05:24:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pyz_72053/10_2026/9pyz_72053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pyz_72053/10_2026/9pyz_72053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pyz_72053/10_2026/9pyz_72053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pyz_72053/10_2026/9pyz_72053.map" model { file = "/net/cci-nas-00/data/ceres_data/9pyz_72053/10_2026/9pyz_72053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pyz_72053/10_2026/9pyz_72053.cif" } resolution = 3.1 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= 0.002 sd= 0.080 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 61 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 7470 2.51 5 N 2046 2.21 5 O 2482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12145 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7475 Classifications: {'peptide': 928} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 897} Chain: "B" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1413 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 176} Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1441 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain: "P" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 568 Classifications: {'RNA': 27} Modifications used: {'rna2p': 1, 'rna3p_pur': 13, 'rna3p_pyr': 13} Link IDs: {'rna3p': 26} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 656 Classifications: {'RNA': 31} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 33 Unusual residues: {' MG': 2, ' ZN': 2, 'UTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2459 SG CYS A 301 56.350 29.301 108.567 1.00 23.75 S ATOM 2500 SG CYS A 306 54.331 26.187 109.441 1.00 27.53 S ATOM 2532 SG CYS A 310 54.280 29.496 111.748 1.00 19.50 S ATOM 3940 SG CYS A 487 56.668 29.757 87.313 1.00 31.56 S ATOM 5193 SG CYS A 645 55.623 25.965 88.005 1.00 36.56 S ATOM 5199 SG CYS A 646 57.537 28.164 90.714 1.00 31.12 S Time building chain proxies: 2.53, per 1000 atoms: 0.21 Number of scatterers: 12145 At special positions: 0 Unit cell: (93.632, 130.872, 164.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 61 15.00 Mg 2 11.99 O 2482 8.00 N 2046 7.00 C 7470 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: 0.94 Conformation dependent library (CDL) restraints added in 542.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 306 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 646 " Number of angles added : 6 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 57.3% alpha, 16.4% beta 24 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.774A pdb=" N PHE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.576A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.796A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.515A pdb=" N ALA A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.136A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.428A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.549A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.814A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.595A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.561A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.552A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.671A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.846A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.583A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.741A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.575A pdb=" N SER A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.501A pdb=" N LEU A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 663 " --> pdb=" O CYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.799A pdb=" N ASN A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.523A pdb=" N GLN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 791 Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.618A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 854 removed outlier: 5.003A pdb=" N GLY A 852 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 853 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.764A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 904 removed outlier: 4.335A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 917 removed outlier: 4.221A pdb=" N THR A 912 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 913 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.543A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 29 removed outlier: 3.988A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 95 removed outlier: 3.827A pdb=" N ASP B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.638A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.294A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.664A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.563A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 removed outlier: 4.489A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.706A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'D' and resid 11 through 29 Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.505A pdb=" N ALA D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 removed outlier: 4.103A pdb=" N ARG D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.863A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 4.161A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.307A pdb=" N PHE A 45 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE A 37 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS A 47 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE A 35 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU A 49 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A 33 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR A 51 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 31 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS A 53 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.652A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 117 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.661A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.380A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.380A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.333A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 665 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 removed outlier: 3.871A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.919A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.637A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2198 1.32 - 1.45: 3393 1.45 - 1.57: 6676 1.57 - 1.70: 119 1.70 - 1.83: 128 Bond restraints: 12514 Sorted by residual: bond pdb=" O3B UTP A1005 " pdb=" PG UTP A1005 " ideal model delta sigma weight residual 1.726 1.600 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C GLY A 503 " pdb=" O GLY A 503 " ideal model delta sigma weight residual 1.237 1.206 0.031 7.00e-03 2.04e+04 2.02e+01 bond pdb=" N ASN A 611 " pdb=" CA ASN A 611 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 2.00e+01 bond pdb=" C ASN A 611 " pdb=" O ASN A 611 " ideal model delta sigma weight residual 1.234 1.251 -0.017 5.00e-03 4.00e+04 1.14e+01 bond pdb=" C GLN A 815 " pdb=" O GLN A 815 " ideal model delta sigma weight residual 1.236 1.196 0.039 1.20e-02 6.94e+03 1.07e+01 ... (remaining 12509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 13563 2.18 - 4.37: 3311 4.37 - 6.55: 355 6.55 - 8.74: 9 8.74 - 10.92: 2 Bond angle restraints: 17240 Sorted by residual: angle pdb=" N PRO A 505 " pdb=" CA PRO A 505 " pdb=" CB PRO A 505 " ideal model delta sigma weight residual 102.60 97.24 5.36 1.10e+00 8.26e-01 2.37e+01 angle pdb=" N VAL A 234 " pdb=" CA VAL A 234 " pdb=" C VAL A 234 " ideal model delta sigma weight residual 109.34 119.35 -10.01 2.08e+00 2.31e-01 2.32e+01 angle pdb=" CB HIS A 439 " pdb=" CG HIS A 439 " pdb=" CD2 HIS A 439 " ideal model delta sigma weight residual 131.20 125.01 6.19 1.30e+00 5.92e-01 2.27e+01 angle pdb=" CB HIS A 642 " pdb=" CG HIS A 642 " pdb=" CD2 HIS A 642 " ideal model delta sigma weight residual 131.20 125.04 6.16 1.30e+00 5.92e-01 2.24e+01 angle pdb=" CA ASP A 736 " pdb=" CB ASP A 736 " pdb=" CG ASP A 736 " ideal model delta sigma weight residual 112.60 117.32 -4.72 1.00e+00 1.00e+00 2.23e+01 ... (remaining 17235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6961 17.73 - 35.45: 461 35.45 - 53.18: 82 53.18 - 70.90: 61 70.90 - 88.63: 27 Dihedral angle restraints: 7592 sinusoidal: 3523 harmonic: 4069 Sorted by residual: dihedral pdb=" CA GLU A 58 " pdb=" C GLU A 58 " pdb=" N LYS A 59 " pdb=" CA LYS A 59 " ideal model delta harmonic sigma weight residual 180.00 152.79 27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA CYS A 464 " pdb=" C CYS A 464 " pdb=" N ASP A 465 " pdb=" CA ASP A 465 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN D 118 " pdb=" C ASN D 118 " pdb=" N ILE D 119 " pdb=" CA ILE D 119 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 7589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1519 0.113 - 0.227: 372 0.227 - 0.340: 34 0.340 - 0.454: 17 0.454 - 0.567: 45 Chirality restraints: 1987 Sorted by residual: chirality pdb=" P U P 4 " pdb=" OP1 U P 4 " pdb=" OP2 U P 4 " pdb=" O5' U P 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" P C T 5 " pdb=" OP1 C T 5 " pdb=" OP2 C T 5 " pdb=" O5' C T 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.55 2.00e-01 2.50e+01 7.70e+00 chirality pdb=" P U P 25 " pdb=" OP1 U P 25 " pdb=" OP2 U P 25 " pdb=" O5' U P 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.64e+00 ... (remaining 1984 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 800 " 0.100 2.00e-02 2.50e+03 5.97e-02 8.91e+01 pdb=" CG TRP A 800 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 800 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 800 " -0.031 2.00e-02 2.50e+03 pdb=" NE1 TRP A 800 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TRP A 800 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 800 " -0.094 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 800 " 0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 800 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP A 800 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 420 " -0.090 2.00e-02 2.50e+03 5.57e-02 6.20e+01 pdb=" CG TYR A 420 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 420 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 420 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR A 420 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 420 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR A 420 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 420 " -0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 689 " 0.078 2.00e-02 2.50e+03 5.09e-02 5.19e+01 pdb=" CG TYR A 689 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 689 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 689 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 689 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 689 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR A 689 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 689 " 0.093 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 4 2.48 - 3.09: 7261 3.09 - 3.69: 17855 3.69 - 4.30: 27219 4.30 - 4.90: 44371 Nonbonded interactions: 96710 Sorted by model distance: nonbonded pdb=" OD2 ASP A 760 " pdb="MG MG A1001 " model vdw 1.875 2.170 nonbonded pdb=" OD1 ASP A 618 " pdb="MG MG A1001 " model vdw 1.915 2.170 nonbonded pdb=" OD1 ASP A 761 " pdb="MG MG A1002 " model vdw 1.928 2.170 nonbonded pdb=" O TYR A 619 " pdb="MG MG A1001 " model vdw 2.377 2.170 nonbonded pdb=" N THR A 76 " pdb=" O THR A 76 " model vdw 2.481 2.496 ... (remaining 96705 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 191) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.013 0.335 12522 Z= 0.807 Angle : 1.794 16.600 17246 Z= 1.198 Chirality : 0.122 0.567 1987 Planarity : 0.015 0.222 1993 Dihedral : 14.211 88.626 4958 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.25 % Allowed : 1.08 % Favored : 98.67 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 7.32 % 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: -1.44 (0.20), residues: 1361 helix: -1.27 (0.17), residues: 685 sheet: -0.09 (0.49), residues: 101 loop : -0.46 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 836 TYR 0.099 0.015 TYR A 420 PHE 0.078 0.012 PHE A 859 TRP 0.100 0.023 TRP A 800 HIS 0.012 0.003 HIS A 882 Details of bonding type rmsd/Z covalent geometry : bond 0.01246 / 0.79 (12514) covalent geometry : angle 1.78853 / 1.20 (17240) hydrogen bonds : bond 0.23232 / 15.14 ( 636) hydrogen bonds : angle 7.28386 / 5.06 ( 1749) metal coordination : bond 0.18096 / 8.44 ( 8) metal coordination : angle 7.72391 / 3.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8188 (p) cc_final: 0.7916 (t) REVERT: A 50 LYS cc_start: 0.8109 (tttt) cc_final: 0.7698 (ttpt) REVERT: A 138 ASN cc_start: 0.7320 (t0) cc_final: 0.6861 (m-40) REVERT: A 159 LYS cc_start: 0.7399 (mttt) cc_final: 0.6702 (tttm) REVERT: A 161 ASP cc_start: 0.7787 (m-30) cc_final: 0.7571 (p0) REVERT: A 184 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8295 (mm110) REVERT: A 221 ASP cc_start: 0.8104 (t0) cc_final: 0.6933 (p0) REVERT: A 267 LYS cc_start: 0.8417 (mttt) cc_final: 0.7987 (mptt) REVERT: A 281 LYS cc_start: 0.8423 (tttt) cc_final: 0.7576 (mtpt) REVERT: A 339 PRO cc_start: 0.8935 (Cg_endo) cc_final: 0.8633 (Cg_exo) REVERT: A 418 ASP cc_start: 0.7886 (m-30) cc_final: 0.7563 (m-30) REVERT: A 551 LYS cc_start: 0.7908 (mttt) cc_final: 0.7639 (ptmt) REVERT: A 552 ASN cc_start: 0.8319 (p0) cc_final: 0.7754 (t0) REVERT: A 555 ARG cc_start: 0.7227 (mtm180) cc_final: 0.6591 (ttm-80) REVERT: A 726 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7189 (mmm160) REVERT: A 755 MET cc_start: 0.9191 (mtm) cc_final: 0.8985 (mtt) REVERT: A 846 ASP cc_start: 0.8486 (t0) cc_final: 0.8164 (t0) REVERT: A 855 MET cc_start: 0.6888 (mmm) cc_final: 0.6534 (mmm) REVERT: A 902 MET cc_start: 0.6703 (ttm) cc_final: 0.6284 (ttm) REVERT: B 70 MET cc_start: 0.6893 (mmm) cc_final: 0.6033 (ttp) REVERT: B 79 LYS cc_start: 0.7483 (mttt) cc_final: 0.6937 (mtmt) REVERT: B 94 MET cc_start: 0.8524 (mtm) cc_final: 0.7981 (mtm) REVERT: B 165 LYS cc_start: 0.7763 (mttt) cc_final: 0.6906 (mmtt) REVERT: C 43 LYS cc_start: 0.7873 (mttt) cc_final: 0.7568 (mtmm) REVERT: D 55 MET cc_start: 0.7705 (mtp) cc_final: 0.7483 (tpt) REVERT: D 58 LYS cc_start: 0.7541 (tttt) cc_final: 0.7167 (tttm) REVERT: D 62 MET cc_start: 0.7641 (tpp) cc_final: 0.6845 (mtp) REVERT: D 70 MET cc_start: 0.7527 (ttm) cc_final: 0.7119 (mtp) REVERT: D 87 MET cc_start: 0.8424 (mmt) cc_final: 0.8162 (mmp) REVERT: D 136 ASN cc_start: 0.7997 (t0) cc_final: 0.7418 (m-40) outliers start: 3 outliers final: 1 residues processed: 201 average time/residue: 0.1196 time to fit residues: 33.3909 Evaluate side-chains 142 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 113 HIS A 309 HIS A 613 HIS C 19 GLN D 118 ASN D 192 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.193529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138278 restraints weight = 11552.236| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.61 r_work: 0.3224 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12522 Z= 0.151 Angle : 0.591 7.752 17246 Z= 0.328 Chirality : 0.042 0.148 1987 Planarity : 0.004 0.038 1993 Dihedral : 12.570 73.164 2404 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.83 % Allowed : 4.42 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.01 (0.22), residues: 1361 helix: 0.41 (0.19), residues: 687 sheet: -0.24 (0.40), residues: 159 loop : -0.26 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 74 TYR 0.020 0.002 TYR A 80 PHE 0.024 0.002 PHE A 741 TRP 0.015 0.002 TRP A 916 HIS 0.004 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (12514) covalent geometry : angle 0.58953 / 0.33 (17240) hydrogen bonds : bond 0.06465 / 4.19 ( 636) hydrogen bonds : angle 4.63198 / 3.19 ( 1749) metal coordination : bond 0.01199 / 0.61 ( 8) metal coordination : angle 2.08112 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8314 (tttt) cc_final: 0.7920 (ttpt) REVERT: A 73 LYS cc_start: 0.8101 (tttt) cc_final: 0.7869 (ttpt) REVERT: A 138 ASN cc_start: 0.7298 (t0) cc_final: 0.6723 (m-40) REVERT: A 155 ASP cc_start: 0.7998 (t0) cc_final: 0.7418 (m-30) REVERT: A 159 LYS cc_start: 0.7216 (mttt) cc_final: 0.6598 (tttm) REVERT: A 221 ASP cc_start: 0.7991 (t0) cc_final: 0.6704 (p0) REVERT: A 267 LYS cc_start: 0.8640 (mttt) cc_final: 0.8186 (mptt) REVERT: A 281 LYS cc_start: 0.8258 (tttt) cc_final: 0.7581 (mtmt) REVERT: A 408 GLN cc_start: 0.8196 (tt0) cc_final: 0.7912 (tt0) REVERT: A 477 ASP cc_start: 0.8139 (t0) cc_final: 0.7913 (t0) REVERT: A 551 LYS cc_start: 0.8086 (mttt) cc_final: 0.7731 (ptmt) REVERT: A 552 ASN cc_start: 0.8389 (p0) cc_final: 0.7683 (t0) REVERT: A 555 ARG cc_start: 0.7428 (mtm180) cc_final: 0.6769 (ttm-80) REVERT: A 755 MET cc_start: 0.9120 (mtm) cc_final: 0.8875 (mtt) REVERT: A 782 PHE cc_start: 0.8092 (m-80) cc_final: 0.7385 (t80) REVERT: A 846 ASP cc_start: 0.8289 (t0) cc_final: 0.8085 (t70) REVERT: A 902 MET cc_start: 0.6304 (ttm) cc_final: 0.5898 (ttm) REVERT: A 906 MET cc_start: 0.7803 (tpt) cc_final: 0.7543 (tpt) REVERT: B 70 MET cc_start: 0.6897 (mmm) cc_final: 0.5999 (ttp) REVERT: B 79 LYS cc_start: 0.7303 (mttt) cc_final: 0.6920 (mtmt) REVERT: B 165 LYS cc_start: 0.7899 (mttt) cc_final: 0.7161 (mmtm) REVERT: C 43 LYS cc_start: 0.7552 (mttt) cc_final: 0.7248 (mtmm) REVERT: D 55 MET cc_start: 0.7406 (mtp) cc_final: 0.7067 (tpt) REVERT: D 58 LYS cc_start: 0.7021 (tttt) cc_final: 0.6705 (tttm) REVERT: D 62 MET cc_start: 0.7360 (tpp) cc_final: 0.6610 (mtp) REVERT: D 136 ASN cc_start: 0.7974 (t0) cc_final: 0.7478 (m110) outliers start: 10 outliers final: 7 residues processed: 149 average time/residue: 0.1157 time to fit residues: 24.8422 Evaluate side-chains 134 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [122, 97, 89, 70, 9, 61, 69, 50, 0, 132, 126] chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS A 613 HIS A 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.192946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138532 restraints weight = 11710.572| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.24 r_work: 0.3236 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12522 Z= 0.121 Angle : 0.486 8.065 17246 Z= 0.264 Chirality : 0.039 0.142 1987 Planarity : 0.004 0.034 1993 Dihedral : 12.023 73.397 2401 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.17 % Allowed : 6.01 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.60 (0.23), residues: 1361 helix: 1.12 (0.20), residues: 685 sheet: -0.10 (0.42), residues: 146 loop : -0.29 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 118 TYR 0.014 0.001 TYR A 80 PHE 0.016 0.002 PHE A 571 TRP 0.012 0.002 TRP A 916 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (12514) covalent geometry : angle 0.48465 / 0.26 (17240) hydrogen bonds : bond 0.05023 / 3.26 ( 636) hydrogen bonds : angle 4.03764 / 2.77 ( 1749) metal coordination : bond 0.00995 / 0.65 ( 8) metal coordination : angle 1.78528 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 50 LYS cc_start: 0.8310 (tttt) cc_final: 0.8048 (ttpt) REVERT: A 138 ASN cc_start: 0.7127 (t0) cc_final: 0.6630 (m-40) REVERT: A 155 ASP cc_start: 0.7883 (t0) cc_final: 0.7555 (m-30) REVERT: A 159 LYS cc_start: 0.7322 (mttt) cc_final: 0.6696 (tttp) REVERT: A 221 ASP cc_start: 0.8025 (t0) cc_final: 0.6747 (p0) REVERT: A 267 LYS cc_start: 0.8626 (mttt) cc_final: 0.8162 (mmtt) REVERT: A 281 LYS cc_start: 0.8284 (tttt) cc_final: 0.7583 (mtmt) REVERT: A 408 GLN cc_start: 0.8270 (tt0) cc_final: 0.8028 (tt0) REVERT: A 551 LYS cc_start: 0.8119 (mttt) cc_final: 0.7723 (ptmt) REVERT: A 552 ASN cc_start: 0.8414 (p0) cc_final: 0.7661 (t0) REVERT: A 555 ARG cc_start: 0.7599 (mtm180) cc_final: 0.6877 (ttm-80) REVERT: A 782 PHE cc_start: 0.8100 (m-80) cc_final: 0.7380 (t80) REVERT: A 902 MET cc_start: 0.6245 (ttm) cc_final: 0.5890 (ttm) REVERT: B 70 MET cc_start: 0.6986 (mmm) cc_final: 0.6139 (ttp) REVERT: B 79 LYS cc_start: 0.7291 (mttt) cc_final: 0.6903 (mtmt) REVERT: B 104 ASN cc_start: 0.7902 (m-40) cc_final: 0.7631 (m-40) REVERT: B 165 LYS cc_start: 0.7984 (mttt) cc_final: 0.7220 (mmtm) REVERT: B 176 ASN cc_start: 0.8257 (t0) cc_final: 0.7777 (t0) REVERT: C 43 LYS cc_start: 0.7622 (mttt) cc_final: 0.7317 (mtmm) REVERT: D 58 LYS cc_start: 0.7091 (tttt) cc_final: 0.6781 (tttm) REVERT: D 62 MET cc_start: 0.7585 (tpp) cc_final: 0.6815 (mtp) REVERT: D 70 MET cc_start: 0.7382 (mtp) cc_final: 0.7175 (mtp) REVERT: D 75 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.6826 (mmm-85) REVERT: D 136 ASN cc_start: 0.7999 (t0) cc_final: 0.7590 (m110) outliers start: 14 outliers final: 9 residues processed: 159 average time/residue: 0.1141 time to fit residues: 25.6214 Evaluate side-chains 150 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [76, 86, 24, 74, 116, 42, 22, 112, 43, 121, 53] chunk 76 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.191675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136908 restraints weight = 11578.039| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.32 r_work: 0.3218 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12522 Z= 0.118 Angle : 0.465 8.282 17246 Z= 0.249 Chirality : 0.038 0.133 1987 Planarity : 0.003 0.035 1993 Dihedral : 11.888 73.182 2401 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.33 % Allowed : 7.42 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.73 (0.23), residues: 1361 helix: 1.29 (0.21), residues: 684 sheet: -0.08 (0.41), residues: 147 loop : -0.31 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 654 TYR 0.015 0.001 TYR A 80 PHE 0.016 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (12514) covalent geometry : angle 0.46387 / 0.25 (17240) hydrogen bonds : bond 0.04745 / 3.07 ( 636) hydrogen bonds : angle 3.97629 / 2.72 ( 1749) metal coordination : bond 0.01135 / 0.73 ( 8) metal coordination : angle 1.43808 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8427 (tp) REVERT: A 50 LYS cc_start: 0.8284 (tttt) cc_final: 0.7909 (ttpt) REVERT: A 73 LYS cc_start: 0.7571 (ttpt) cc_final: 0.7275 (tttt) REVERT: A 138 ASN cc_start: 0.7084 (t0) cc_final: 0.6481 (m-40) REVERT: A 159 LYS cc_start: 0.7117 (mttt) cc_final: 0.6339 (tmtt) REVERT: A 205 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7277 (pp) REVERT: A 221 ASP cc_start: 0.8191 (t0) cc_final: 0.6802 (p0) REVERT: A 267 LYS cc_start: 0.8651 (mttt) cc_final: 0.8107 (mmtt) REVERT: A 281 LYS cc_start: 0.8370 (tttt) cc_final: 0.7634 (mtmt) REVERT: A 408 GLN cc_start: 0.8427 (tt0) cc_final: 0.8163 (tt0) REVERT: A 551 LYS cc_start: 0.8141 (mttt) cc_final: 0.7925 (mttm) REVERT: A 552 ASN cc_start: 0.8529 (p0) cc_final: 0.7689 (t0) REVERT: A 555 ARG cc_start: 0.7871 (mtm180) cc_final: 0.6947 (ttm-80) REVERT: A 782 PHE cc_start: 0.8124 (m-80) cc_final: 0.7411 (t80) REVERT: B 70 MET cc_start: 0.7019 (mmm) cc_final: 0.6110 (ttp) REVERT: B 79 LYS cc_start: 0.7246 (mttt) cc_final: 0.6878 (mtpt) REVERT: B 104 ASN cc_start: 0.7895 (m-40) cc_final: 0.7610 (m-40) REVERT: B 165 LYS cc_start: 0.8009 (mttt) cc_final: 0.7233 (mmtm) REVERT: C 43 LYS cc_start: 0.7704 (mttt) cc_final: 0.7294 (mtmm) REVERT: D 58 LYS cc_start: 0.7007 (tttt) cc_final: 0.6743 (tttm) REVERT: D 62 MET cc_start: 0.7709 (tpp) cc_final: 0.6914 (mtp) REVERT: D 75 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6804 (mmm-85) REVERT: D 136 ASN cc_start: 0.8048 (t0) cc_final: 0.7635 (m110) outliers start: 16 outliers final: 10 residues processed: 156 average time/residue: 0.1095 time to fit residues: 24.4013 Evaluate side-chains 154 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain D residue 184 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [11, 32, 133, 71, 73, 57, 134, 67, 84, 92, 96] chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 71 optimal weight: 0.0000 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 50.0000 chunk 96 optimal weight: 7.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.186746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132783 restraints weight = 11561.604| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.60 r_work: 0.3065 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12522 Z= 0.204 Angle : 0.562 9.745 17246 Z= 0.295 Chirality : 0.042 0.168 1987 Planarity : 0.005 0.085 1993 Dihedral : 11.902 73.270 2401 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.58 % Allowed : 8.01 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.50 (0.23), residues: 1361 helix: 1.11 (0.20), residues: 687 sheet: -0.09 (0.42), residues: 147 loop : -0.48 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 654 TYR 0.016 0.002 TYR A 149 PHE 0.024 0.002 PHE A 741 TRP 0.013 0.002 TRP A 916 HIS 0.005 0.001 HIS A 752 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.20 (12514) covalent geometry : angle 0.56104 / 0.30 (17240) hydrogen bonds : bond 0.05770 / 3.73 ( 636) hydrogen bonds : angle 4.09372 / 2.81 ( 1749) metal coordination : bond 0.01943 / 1.28 ( 8) metal coordination : angle 1.58975 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8416 (tttt) cc_final: 0.8134 (ttpt) REVERT: A 138 ASN cc_start: 0.7238 (t0) cc_final: 0.6644 (m-40) REVERT: A 155 ASP cc_start: 0.7999 (t0) cc_final: 0.7620 (m-30) REVERT: A 159 LYS cc_start: 0.7359 (mttt) cc_final: 0.6798 (tttp) REVERT: A 205 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7147 (pp) REVERT: A 221 ASP cc_start: 0.8169 (t0) cc_final: 0.6819 (p0) REVERT: A 267 LYS cc_start: 0.8724 (mttt) cc_final: 0.8226 (mmtt) REVERT: A 281 LYS cc_start: 0.8296 (tttt) cc_final: 0.7602 (mtmt) REVERT: A 408 GLN cc_start: 0.8400 (tt0) cc_final: 0.8152 (tt0) REVERT: A 551 LYS cc_start: 0.8214 (mttt) cc_final: 0.7938 (mtmm) REVERT: A 553 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.7245 (tmt170) REVERT: A 555 ARG cc_start: 0.7919 (mtm180) cc_final: 0.6885 (ttm-80) REVERT: A 782 PHE cc_start: 0.8096 (m-80) cc_final: 0.7508 (t80) REVERT: B 70 MET cc_start: 0.6912 (mmm) cc_final: 0.6021 (ttp) REVERT: B 79 LYS cc_start: 0.7358 (mttt) cc_final: 0.6963 (mtmt) REVERT: B 104 ASN cc_start: 0.7946 (m-40) cc_final: 0.7670 (m-40) REVERT: B 165 LYS cc_start: 0.8213 (mttt) cc_final: 0.7517 (mmtm) REVERT: C 43 LYS cc_start: 0.7722 (mttt) cc_final: 0.7429 (mtmm) REVERT: D 58 LYS cc_start: 0.7165 (tttt) cc_final: 0.6828 (tttm) REVERT: D 62 MET cc_start: 0.7718 (tpp) cc_final: 0.6902 (mtm) REVERT: D 75 ARG cc_start: 0.7386 (ttm-80) cc_final: 0.6882 (mmm-85) REVERT: D 136 ASN cc_start: 0.7953 (t0) cc_final: 0.7548 (m-40) outliers start: 19 outliers final: 12 residues processed: 152 average time/residue: 0.1131 time to fit residues: 24.4529 Evaluate side-chains 149 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 148 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [80, 68, 93, 31, 103, 37, 59, 124, 1, 132, 56] chunk 80 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.188559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.133210 restraints weight = 11510.896| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.91 r_work: 0.3189 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12522 Z= 0.132 Angle : 0.478 9.186 17246 Z= 0.254 Chirality : 0.038 0.137 1987 Planarity : 0.004 0.073 1993 Dihedral : 11.827 73.317 2401 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.83 % Allowed : 8.17 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.65 (0.23), residues: 1361 helix: 1.25 (0.21), residues: 691 sheet: -0.03 (0.41), residues: 147 loop : -0.45 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.015 0.001 TYR A 80 PHE 0.017 0.001 PHE A 694 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12514) covalent geometry : angle 0.47783 / 0.25 (17240) hydrogen bonds : bond 0.04922 / 3.18 ( 636) hydrogen bonds : angle 3.95482 / 2.72 ( 1749) metal coordination : bond 0.01240 / 0.79 ( 8) metal coordination : angle 1.29919 / 0.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8483 (tp) REVERT: A 50 LYS cc_start: 0.8420 (tttt) cc_final: 0.8114 (ttpt) REVERT: A 138 ASN cc_start: 0.7194 (t0) cc_final: 0.6589 (m-40) REVERT: A 159 LYS cc_start: 0.7252 (mttt) cc_final: 0.6704 (tttp) REVERT: A 205 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7270 (pp) REVERT: A 221 ASP cc_start: 0.8203 (t0) cc_final: 0.6804 (p0) REVERT: A 267 LYS cc_start: 0.8741 (mttt) cc_final: 0.8212 (mmtt) REVERT: A 281 LYS cc_start: 0.8288 (tttt) cc_final: 0.7574 (mtmt) REVERT: A 408 GLN cc_start: 0.8448 (tt0) cc_final: 0.8196 (tt0) REVERT: A 551 LYS cc_start: 0.8187 (mttt) cc_final: 0.7908 (mtmm) REVERT: A 553 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7200 (tmt170) REVERT: A 555 ARG cc_start: 0.7933 (mtm180) cc_final: 0.6818 (ttm-80) REVERT: A 782 PHE cc_start: 0.8129 (m-80) cc_final: 0.7478 (t80) REVERT: B 70 MET cc_start: 0.6971 (mmm) cc_final: 0.6102 (ttp) REVERT: B 79 LYS cc_start: 0.7324 (mttt) cc_final: 0.6933 (mtmt) REVERT: B 104 ASN cc_start: 0.7849 (m-40) cc_final: 0.7569 (m-40) REVERT: B 165 LYS cc_start: 0.8184 (mttt) cc_final: 0.7486 (mmtm) REVERT: C 43 LYS cc_start: 0.7701 (mttt) cc_final: 0.7292 (mtmm) REVERT: D 58 LYS cc_start: 0.7086 (tttt) cc_final: 0.6767 (tttm) REVERT: D 62 MET cc_start: 0.7826 (tpp) cc_final: 0.6997 (mtm) REVERT: D 75 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.6831 (mmm-85) REVERT: D 136 ASN cc_start: 0.8017 (t0) cc_final: 0.7650 (m-40) outliers start: 22 outliers final: 15 residues processed: 156 average time/residue: 0.1109 time to fit residues: 24.8915 Evaluate side-chains 153 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 170 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [106, 18, 59, 38, 76, 120, 74, 127, 124, 96, 19] chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.185711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144093 restraints weight = 11524.569| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.24 r_work: 0.3070 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12522 Z= 0.237 Angle : 0.583 9.909 17246 Z= 0.305 Chirality : 0.043 0.172 1987 Planarity : 0.005 0.096 1993 Dihedral : 11.877 73.287 2401 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.09 % Allowed : 8.51 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.39 (0.23), residues: 1361 helix: 1.09 (0.21), residues: 682 sheet: -0.10 (0.41), residues: 147 loop : -0.64 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.017 0.002 TYR A 149 PHE 0.024 0.002 PHE A 741 TRP 0.013 0.002 TRP A 916 HIS 0.006 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.24 (12514) covalent geometry : angle 0.58231 / 0.30 (17240) hydrogen bonds : bond 0.05933 / 3.85 ( 636) hydrogen bonds : angle 4.10001 / 2.83 ( 1749) metal coordination : bond 0.01894 / 1.24 ( 8) metal coordination : angle 1.19120 / 0.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.339 Fit side-chains REVERT: A 50 LYS cc_start: 0.8433 (tttt) cc_final: 0.8214 (ttpt) REVERT: A 75 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.6018 (m-70) REVERT: A 138 ASN cc_start: 0.7300 (t0) cc_final: 0.6793 (m-40) REVERT: A 155 ASP cc_start: 0.8136 (t0) cc_final: 0.7784 (m-30) REVERT: A 159 LYS cc_start: 0.7342 (mttt) cc_final: 0.7066 (tttp) REVERT: A 205 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7261 (pp) REVERT: A 221 ASP cc_start: 0.8208 (t0) cc_final: 0.7052 (p0) REVERT: A 267 LYS cc_start: 0.8811 (mttt) cc_final: 0.8356 (mmtt) REVERT: A 281 LYS cc_start: 0.8293 (tttt) cc_final: 0.7675 (mtmt) REVERT: A 408 GLN cc_start: 0.8446 (tt0) cc_final: 0.8239 (tt0) REVERT: A 551 LYS cc_start: 0.8332 (mttt) cc_final: 0.8076 (mtmm) REVERT: A 553 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7481 (tmt170) REVERT: A 555 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7050 (ttm-80) REVERT: A 782 PHE cc_start: 0.8099 (m-80) cc_final: 0.7584 (t80) REVERT: B 70 MET cc_start: 0.7141 (mmm) cc_final: 0.6352 (ttp) REVERT: B 79 LYS cc_start: 0.7612 (mttt) cc_final: 0.7236 (mtmt) REVERT: B 104 ASN cc_start: 0.8019 (m-40) cc_final: 0.7744 (m-40) REVERT: B 165 LYS cc_start: 0.8268 (mttt) cc_final: 0.7704 (mmtm) REVERT: C 43 LYS cc_start: 0.7787 (mttt) cc_final: 0.7545 (mtmm) REVERT: D 58 LYS cc_start: 0.7782 (tttt) cc_final: 0.7399 (tttm) REVERT: D 62 MET cc_start: 0.8127 (tpp) cc_final: 0.7407 (mtm) REVERT: D 75 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7034 (mmm-85) REVERT: D 136 ASN cc_start: 0.8199 (t0) cc_final: 0.7696 (m110) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.1132 time to fit residues: 25.0773 Evaluate side-chains 155 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 170 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [24, 117, 105, 75, 100, 30, 45, 22, 76, 88, 132] chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.187538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.132111 restraints weight = 11418.675| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.90 r_work: 0.3174 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12522 Z= 0.146 Angle : 0.499 9.804 17246 Z= 0.263 Chirality : 0.039 0.146 1987 Planarity : 0.004 0.063 1993 Dihedral : 11.827 73.352 2401 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.00 % Allowed : 8.59 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.51 (0.23), residues: 1361 helix: 1.17 (0.21), residues: 689 sheet: -0.03 (0.41), residues: 147 loop : -0.59 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.015 0.002 TYR A 149 PHE 0.018 0.002 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (12514) covalent geometry : angle 0.49879 / 0.26 (17240) hydrogen bonds : bond 0.05087 / 3.30 ( 636) hydrogen bonds : angle 3.99476 / 2.75 ( 1749) metal coordination : bond 0.01255 / 0.81 ( 8) metal coordination : angle 1.20738 / 0.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8426 (tttt) cc_final: 0.8115 (ttpt) REVERT: A 73 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7532 (tttt) REVERT: A 75 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.5835 (m-70) REVERT: A 138 ASN cc_start: 0.7208 (t0) cc_final: 0.6585 (m-40) REVERT: A 155 ASP cc_start: 0.8032 (t0) cc_final: 0.7633 (m-30) REVERT: A 159 LYS cc_start: 0.7159 (mttt) cc_final: 0.6819 (tttm) REVERT: A 205 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7352 (pp) REVERT: A 221 ASP cc_start: 0.8252 (t0) cc_final: 0.6952 (p0) REVERT: A 267 LYS cc_start: 0.8779 (mttt) cc_final: 0.8217 (mmtt) REVERT: A 281 LYS cc_start: 0.8258 (tttt) cc_final: 0.7524 (mtmt) REVERT: A 408 GLN cc_start: 0.8469 (tt0) cc_final: 0.8216 (tt0) REVERT: A 551 LYS cc_start: 0.8261 (mttt) cc_final: 0.7952 (mtmm) REVERT: A 553 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7297 (tmt170) REVERT: A 555 ARG cc_start: 0.7960 (mtm180) cc_final: 0.6862 (ttm-80) REVERT: A 782 PHE cc_start: 0.8079 (m-80) cc_final: 0.7501 (t80) REVERT: B 70 MET cc_start: 0.6945 (mmm) cc_final: 0.6062 (ttp) REVERT: B 79 LYS cc_start: 0.7328 (mttt) cc_final: 0.6939 (mtmt) REVERT: B 104 ASN cc_start: 0.7842 (m-40) cc_final: 0.7566 (m-40) REVERT: B 165 LYS cc_start: 0.8146 (mttt) cc_final: 0.7463 (mmtm) REVERT: B 176 ASN cc_start: 0.8337 (t0) cc_final: 0.7957 (t0) REVERT: C 43 LYS cc_start: 0.7736 (mttt) cc_final: 0.7400 (mtmm) REVERT: D 58 LYS cc_start: 0.7159 (tttt) cc_final: 0.6829 (tttm) REVERT: D 62 MET cc_start: 0.7889 (tpp) cc_final: 0.7111 (mtm) REVERT: D 75 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.6838 (mmm-85) REVERT: D 136 ASN cc_start: 0.8172 (t0) cc_final: 0.7644 (m110) outliers start: 24 outliers final: 20 residues processed: 155 average time/residue: 0.1142 time to fit residues: 25.5140 Evaluate side-chains 157 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [37, 2, 31, 60, 91, 69, 97, 50, 109, 133, 72] chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.189937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135353 restraints weight = 11393.874| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.08 r_work: 0.3166 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12522 Z= 0.107 Angle : 0.451 9.537 17246 Z= 0.240 Chirality : 0.037 0.132 1987 Planarity : 0.004 0.061 1993 Dihedral : 11.774 73.388 2401 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.58 % Allowed : 9.17 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.73 (0.23), residues: 1361 helix: 1.38 (0.21), residues: 686 sheet: 0.06 (0.41), residues: 147 loop : -0.50 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.014 0.001 TYR A 788 PHE 0.015 0.001 PHE A 694 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (12514) covalent geometry : angle 0.45080 / 0.24 (17240) hydrogen bonds : bond 0.04474 / 2.89 ( 636) hydrogen bonds : angle 3.87052 / 2.67 ( 1749) metal coordination : bond 0.00915 / 0.56 ( 8) metal coordination : angle 1.35607 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8417 (tttt) cc_final: 0.8197 (ttpt) REVERT: A 73 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7525 (ttpt) REVERT: A 75 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.5868 (m-70) REVERT: A 138 ASN cc_start: 0.7136 (t0) cc_final: 0.6641 (m-40) REVERT: A 159 LYS cc_start: 0.7184 (mttt) cc_final: 0.6924 (tttp) REVERT: A 205 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7206 (pp) REVERT: A 221 ASP cc_start: 0.8152 (t0) cc_final: 0.6849 (p0) REVERT: A 267 LYS cc_start: 0.8769 (mttt) cc_final: 0.8268 (mmtt) REVERT: A 281 LYS cc_start: 0.8176 (tttt) cc_final: 0.7503 (mtmt) REVERT: A 408 GLN cc_start: 0.8386 (tt0) cc_final: 0.8140 (tt0) REVERT: A 551 LYS cc_start: 0.8191 (mttt) cc_final: 0.7907 (mtmm) REVERT: A 553 ARG cc_start: 0.7670 (mtt-85) cc_final: 0.7220 (tmt170) REVERT: A 555 ARG cc_start: 0.7808 (mtm180) cc_final: 0.6879 (ttm-80) REVERT: A 782 PHE cc_start: 0.8029 (m-80) cc_final: 0.7477 (t80) REVERT: B 70 MET cc_start: 0.6809 (mmm) cc_final: 0.5924 (ttp) REVERT: B 79 LYS cc_start: 0.7267 (mttt) cc_final: 0.6844 (mtmt) REVERT: B 104 ASN cc_start: 0.7895 (m-40) cc_final: 0.7618 (m-40) REVERT: B 165 LYS cc_start: 0.8120 (mttt) cc_final: 0.7474 (mmtm) REVERT: B 176 ASN cc_start: 0.8405 (t0) cc_final: 0.8035 (t0) REVERT: C 43 LYS cc_start: 0.7643 (mttt) cc_final: 0.7404 (mtmm) REVERT: D 58 LYS cc_start: 0.7032 (tttt) cc_final: 0.6759 (tttm) REVERT: D 62 MET cc_start: 0.7742 (tpp) cc_final: 0.7031 (mtp) REVERT: D 75 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6804 (mmm-85) REVERT: D 136 ASN cc_start: 0.8137 (t0) cc_final: 0.7612 (m110) outliers start: 19 outliers final: 16 residues processed: 151 average time/residue: 0.1173 time to fit residues: 25.0946 Evaluate side-chains 154 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 23 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [113, 134, 69, 60, 0, 135, 51, 11, 72, 6, 117] chunk 113 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 GLN A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.187290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144328 restraints weight = 11491.058| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.27 r_work: 0.3094 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12522 Z= 0.168 Angle : 0.514 10.188 17246 Z= 0.269 Chirality : 0.040 0.165 1987 Planarity : 0.004 0.068 1993 Dihedral : 11.793 73.376 2401 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.58 % Allowed : 9.09 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.62 (0.23), residues: 1361 helix: 1.32 (0.21), residues: 684 sheet: 0.05 (0.41), residues: 147 loop : -0.61 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.015 0.002 TYR A 149 PHE 0.020 0.002 PHE A 741 TRP 0.012 0.002 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (12514) covalent geometry : angle 0.51370 / 0.27 (17240) hydrogen bonds : bond 0.05125 / 3.32 ( 636) hydrogen bonds : angle 3.95937 / 2.72 ( 1749) metal coordination : bond 0.01314 / 0.87 ( 8) metal coordination : angle 1.23989 / 0.70 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2722 Ramachandran restraints generated. 1361 Oldfield, 0 Emsley, 1361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.414 Fit side-chains REVERT: A 73 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7644 (ttpt) REVERT: A 75 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.5875 (m-70) REVERT: A 138 ASN cc_start: 0.7303 (t0) cc_final: 0.6812 (m-40) REVERT: A 159 LYS cc_start: 0.7325 (mttt) cc_final: 0.7090 (tttm) REVERT: A 205 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7415 (pp) REVERT: A 221 ASP cc_start: 0.8162 (t0) cc_final: 0.7098 (p0) REVERT: A 267 LYS cc_start: 0.8773 (mttt) cc_final: 0.8337 (mmtt) REVERT: A 281 LYS cc_start: 0.8226 (tttt) cc_final: 0.7628 (mtmt) REVERT: A 360 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7585 (t0) REVERT: A 408 GLN cc_start: 0.8494 (tt0) cc_final: 0.8249 (tt0) REVERT: A 551 LYS cc_start: 0.8265 (mttt) cc_final: 0.8035 (mtmm) REVERT: A 553 ARG cc_start: 0.7794 (mtt-85) cc_final: 0.7431 (tmt170) REVERT: A 555 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7049 (ttm-80) REVERT: A 782 PHE cc_start: 0.8088 (m-80) cc_final: 0.7578 (t80) REVERT: B 70 MET cc_start: 0.7063 (mmm) cc_final: 0.6281 (ttp) REVERT: B 79 LYS cc_start: 0.7578 (mttt) cc_final: 0.7191 (mtmt) REVERT: B 104 ASN cc_start: 0.7998 (m-40) cc_final: 0.7712 (m-40) REVERT: B 165 LYS cc_start: 0.8236 (mttt) cc_final: 0.7637 (mmtm) REVERT: B 176 ASN cc_start: 0.8534 (t0) cc_final: 0.8159 (t0) REVERT: C 43 LYS cc_start: 0.7778 (mttt) cc_final: 0.7524 (mtmm) REVERT: D 58 LYS cc_start: 0.7722 (tttt) cc_final: 0.7369 (tttm) REVERT: D 62 MET cc_start: 0.7969 (tpp) cc_final: 0.7382 (mtp) REVERT: D 75 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.6951 (mmm-85) REVERT: D 136 ASN cc_start: 0.8178 (t0) cc_final: 0.7695 (m110) outliers start: 19 outliers final: 15 residues processed: 148 average time/residue: 0.1086 time to fit residues: 22.9032 Evaluate side-chains 151 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [14, 86, 118, 16, 90, 109, 110, 84, 46, 35, 74] chunk 14 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 109 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.187552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133862 restraints weight = 11416.024| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.56 r_work: 0.3089 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 12522 Z= 0.201 Angle : 0.816 59.199 17246 Z= 0.488 Chirality : 0.039 0.144 1987 Planarity : 0.004 0.065 1993 Dihedral : 11.795 73.371 2401 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.50 % Allowed : 9.01 % Favored : 89.49 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.32 % 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: 0.62 (0.23), residues: 1361 helix: 1.32 (0.21), residues: 684 sheet: 0.05 (0.41), residues: 147 loop : -0.64 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.015 0.002 TYR A 149 PHE 0.020 0.002 PHE A 694 TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (12514) covalent geometry : angle 0.81612 / 0.49 (17240) hydrogen bonds : bond 0.05028 / 3.26 ( 636) hydrogen bonds : angle 3.96505 / 2.73 ( 1749) metal coordination : bond 0.01220 / 0.80 ( 8) metal coordination : angle 1.24856 / 0.71 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3059.82 seconds wall clock time: 53 minutes 6.60 seconds (3186.60 seconds total)