Starting phenix.real_space_refine on Sat Oct 24 05:16:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pyw_72038/10_2026/9pyw_72038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pyw_72038/10_2026/9pyw_72038.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 { model { file = "/net/cci-nas-00/data/ceres_data/9pyw_72038/10_2026/9pyw_72038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pyw_72038/10_2026/9pyw_72038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pyw_72038/10_2026/9pyw_72038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pyw_72038/10_2026/9pyw_72038.map" } 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= 0.085 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 58 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 7461 2.51 5 N 2044 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 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: 12115 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2459 SG CYS A 301 56.308 30.660 108.364 1.00 23.75 S ATOM 2500 SG CYS A 306 54.306 27.726 109.395 1.00 27.53 S ATOM 2532 SG CYS A 310 54.274 30.882 111.488 1.00 19.50 S ATOM 3940 SG CYS A 487 56.446 30.947 87.167 1.00 31.56 S ATOM 5193 SG CYS A 645 55.322 27.271 87.734 1.00 36.56 S ATOM 5199 SG CYS A 646 57.349 29.473 90.335 1.00 31.12 S Time building chain proxies: 2.30, per 1000 atoms: 0.19 Number of scatterers: 12115 At special positions: 0 Unit cell: (93.632, 131.936, 163.856, 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 58 15.00 Mg 1 11.99 O 2467 8.00 N 2044 7.00 C 7461 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: 0.82 Conformation dependent library (CDL) restraints added in 480.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " 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: 63 helices and 11 sheets defined 58.6% alpha, 16.1% beta 25 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.884A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.572A 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: 3.837A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.713A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.578A pdb=" N GLN A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 4.252A pdb=" N ASP A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.093A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.422A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.669A 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: 3.810A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.810A 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: 4.728A 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 479 removed outlier: 3.697A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.251A 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: 3.730A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 582 removed outlier: 3.742A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.061A 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: 3.556A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.779A 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 644 removed outlier: 4.648A pdb=" N THR A 644 " --> pdb=" O LYS A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 641 through 644' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.696A 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 774 removed outlier: 3.503A pdb=" N GLN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.636A pdb=" N SER A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.558A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 854 removed outlier: 4.925A pdb=" N GLY A 852 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 853 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.758A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.616A 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: 4.561A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 917 removed outlier: 4.339A pdb=" N THR A 912 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.546A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 11 through 29 removed outlier: 4.005A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 95 removed outlier: 3.826A pdb=" N LYS B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.560A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.104A 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: 3.550A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.558A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 removed outlier: 4.497A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.586A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.076A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.531A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.267A pdb=" N ARG D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.858A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.761A 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: 5.569A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.341A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.341A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.557A 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: 6.483A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 665 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (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 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 removed outlier: 4.030A 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: 6.400A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 191 " --> pdb=" O TRP D 154 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP D 154 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.400A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA D 191 " --> pdb=" O TRP D 154 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP D 154 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2680 1.33 - 1.46: 3051 1.46 - 1.58: 6511 1.58 - 1.70: 114 1.70 - 1.83: 128 Bond restraints: 12484 Sorted by residual: bond pdb=" N LEU A 90 " pdb=" CA LEU A 90 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.32e-02 5.74e+03 1.19e+01 bond pdb=" CZ ARG A 533 " pdb=" NH2 ARG A 533 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.18e+00 bond pdb=" CZ ARG A 183 " pdb=" NH2 ARG A 183 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.03e+00 bond pdb=" CZ ARG A 279 " pdb=" NH2 ARG A 279 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.99e+00 bond pdb=" CA PRO A 322 " pdb=" C PRO A 322 " ideal model delta sigma weight residual 1.517 1.544 -0.027 9.30e-03 1.16e+04 8.25e+00 ... (remaining 12479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 13821 2.24 - 4.49: 3133 4.49 - 6.73: 228 6.73 - 8.98: 10 8.98 - 11.22: 1 Bond angle restraints: 17193 Sorted by residual: angle pdb=" CA PHE A 222 " pdb=" CB PHE A 222 " pdb=" CG PHE A 222 " ideal model delta sigma weight residual 113.80 118.95 -5.15 1.00e+00 1.00e+00 2.66e+01 angle pdb=" CA ASP B 99 " pdb=" CB ASP B 99 " pdb=" CG ASP B 99 " ideal model delta sigma weight residual 112.60 117.71 -5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" CB HIS A 295 " pdb=" CG HIS A 295 " pdb=" CD2 HIS A 295 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.46e+01 angle pdb=" CB HIS A 872 " pdb=" CG HIS A 872 " pdb=" CD2 HIS A 872 " ideal model delta sigma weight residual 131.20 124.78 6.42 1.30e+00 5.92e-01 2.44e+01 angle pdb=" CA ASP A 377 " pdb=" CB ASP A 377 " pdb=" CG ASP A 377 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.38e+01 ... (remaining 17188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.31: 7283 26.31 - 52.62: 195 52.62 - 78.92: 70 78.92 - 105.23: 5 105.23 - 131.54: 1 Dihedral angle restraints: 7554 sinusoidal: 3485 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 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLY A 228 " pdb=" C GLY A 228 " pdb=" N SER A 229 " pdb=" CA SER A 229 " ideal model delta harmonic sigma weight residual 180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.98e+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 180.00 154.44 25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 7551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1547 0.116 - 0.231: 350 0.231 - 0.347: 27 0.347 - 0.462: 25 0.462 - 0.578: 34 Chirality restraints: 1983 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 -2.99 -0.58 2.00e-01 2.50e+01 8.34e+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 -2.99 -0.58 2.00e-01 2.50e+01 8.28e+00 chirality pdb=" P A P 14 " pdb=" OP1 A P 14 " pdb=" OP2 A P 14 " pdb=" O5' A P 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.41e+00 ... (remaining 1980 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 800 " 0.090 2.00e-02 2.50e+03 5.68e-02 8.05e+01 pdb=" CG TRP A 800 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 800 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 800 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 800 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP A 800 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 800 " -0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 800 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 800 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP A 800 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 289 " 0.102 2.00e-02 2.50e+03 5.98e-02 7.16e+01 pdb=" CG TYR A 289 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 289 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 289 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A 289 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 289 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 289 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 289 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 916 " 0.086 2.00e-02 2.50e+03 4.82e-02 5.81e+01 pdb=" CG TRP A 916 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 916 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 916 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP A 916 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP A 916 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A 916 " -0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 916 " 0.047 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 916 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 916 " 0.062 2.00e-02 2.50e+03 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 3 2.52 - 3.11: 7780 3.11 - 3.71: 17768 3.71 - 4.30: 26584 4.30 - 4.90: 43432 Nonbonded interactions: 95567 Sorted by model distance: nonbonded pdb=" OD1 ASP A 761 " pdb="MG MG A1003 " model vdw 1.924 2.170 nonbonded pdb=" O LEU A 758 " pdb=" O3' UAR P 30 " model vdw 2.445 3.040 nonbonded pdb=" O2' C P 8 " pdb=" OP1 U P 9 " model vdw 2.489 3.040 nonbonded pdb=" OG SER A 501 " pdb=" OP1 C T 7 " model vdw 2.527 3.040 nonbonded pdb=" O GLY A 683 " pdb=" O2' A T 8 " model vdw 2.527 3.040 ... (remaining 95562 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 0.396 12492 Z= 0.790 Angle : 1.767 12.424 17199 Z= 1.184 Chirality : 0.119 0.578 1983 Planarity : 0.013 0.125 1991 Dihedral : 13.740 131.539 4920 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.17 % Allowed : 0.25 % Favored : 99.58 % 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: -1.08 (0.20), residues: 1361 helix: -1.10 (0.17), residues: 669 sheet: 0.64 (0.49), residues: 100 loop : -0.26 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 75 TYR 0.102 0.017 TYR A 289 PHE 0.069 0.012 PHE A 859 TRP 0.090 0.022 TRP A 800 HIS 0.011 0.003 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.01223 / 0.77 (12484) covalent geometry : angle 1.76315 / 1.18 (17193) hydrogen bonds : bond 0.23193 / 15.56 ( 663) hydrogen bonds : angle 7.09006 / 4.89 ( 1839) metal coordination : bond 0.20860 / 13.94 ( 8) metal coordination : angle 6.29855 / 3.16 ( 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 189 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8980 (mt) cc_final: 0.8772 (mp) REVERT: A 110 MET cc_start: 0.6468 (mmm) cc_final: 0.6127 (mmm) REVERT: A 167 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7587 (mp0) REVERT: A 360 ASN cc_start: 0.7640 (m-40) cc_final: 0.7297 (m-40) REVERT: A 377 ASP cc_start: 0.8391 (t0) cc_final: 0.8187 (m-30) REVERT: A 542 MET cc_start: 0.8602 (mmt) cc_final: 0.8391 (mmt) REVERT: A 551 LYS cc_start: 0.8296 (mttt) cc_final: 0.7928 (mttm) REVERT: A 675 VAL cc_start: 0.9256 (t) cc_final: 0.9027 (m) REVERT: A 718 LYS cc_start: 0.8374 (mttt) cc_final: 0.7860 (mmmt) REVERT: A 798 LYS cc_start: 0.7919 (mttt) cc_final: 0.7539 (ptpt) REVERT: A 821 LYS cc_start: 0.8575 (tttt) cc_final: 0.8184 (tttp) REVERT: A 826 TYR cc_start: 0.8675 (m-80) cc_final: 0.8320 (m-80) REVERT: B 78 ASP cc_start: 0.7715 (t0) cc_final: 0.7377 (t0) REVERT: B 151 SER cc_start: 0.8658 (m) cc_final: 0.8399 (t) REVERT: B 166 ILE cc_start: 0.9008 (mt) cc_final: 0.8685 (mm) REVERT: B 174 MET cc_start: 0.8147 (tpp) cc_final: 0.7733 (tpt) REVERT: B 176 ASN cc_start: 0.8620 (t0) cc_final: 0.8324 (t0) REVERT: C 21 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7828 (mtm110) REVERT: C 62 MET cc_start: 0.8597 (mtm) cc_final: 0.8265 (mtm) REVERT: D 46 LYS cc_start: 0.5684 (tttt) cc_final: 0.5292 (ttpt) REVERT: D 52 ASP cc_start: 0.7432 (m-30) cc_final: 0.7038 (m-30) REVERT: D 64 ASP cc_start: 0.6692 (t70) cc_final: 0.6210 (m-30) REVERT: D 72 LYS cc_start: 0.6841 (mttt) cc_final: 0.6570 (mttm) REVERT: D 97 LYS cc_start: 0.8221 (mttt) cc_final: 0.7996 (mtmm) REVERT: D 134 ASP cc_start: 0.7420 (t0) cc_final: 0.7210 (p0) outliers start: 2 outliers final: 0 residues processed: 189 average time/residue: 0.1315 time to fit residues: 34.0212 Evaluate side-chains 141 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.181935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122329 restraints weight = 12118.150| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.06 r_work: 0.3143 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12492 Z= 0.152 Angle : 0.593 7.462 17199 Z= 0.333 Chirality : 0.042 0.250 1983 Planarity : 0.004 0.043 1991 Dihedral : 12.095 127.446 2363 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.42 % Allowed : 2.92 % Favored : 96.66 % 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: 0.20 (0.22), residues: 1361 helix: 0.63 (0.20), residues: 692 sheet: 0.15 (0.41), residues: 147 loop : -0.40 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 118 TYR 0.017 0.002 TYR A 32 PHE 0.021 0.002 PHE A 652 TRP 0.014 0.002 TRP A 916 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (12484) covalent geometry : angle 0.59141 / 0.33 (17193) hydrogen bonds : bond 0.06475 / 4.22 ( 663) hydrogen bonds : angle 4.60592 / 3.18 ( 1839) metal coordination : bond 0.01276 / 0.70 ( 8) metal coordination : angle 2.27391 / 1.42 ( 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: 5 poor density : 150 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7632 (m-40) cc_final: 0.7296 (m-40) REVERT: A 380 MET cc_start: 0.8488 (mmm) cc_final: 0.7943 (mmm) REVERT: A 821 LYS cc_start: 0.8463 (tttt) cc_final: 0.8147 (tttp) REVERT: A 913 SER cc_start: 0.8692 (t) cc_final: 0.8246 (m) REVERT: B 109 ASN cc_start: 0.7675 (m-40) cc_final: 0.7292 (m-40) REVERT: B 151 SER cc_start: 0.8766 (m) cc_final: 0.8533 (t) REVERT: B 166 ILE cc_start: 0.9020 (mt) cc_final: 0.8781 (mm) REVERT: B 176 ASN cc_start: 0.8533 (t0) cc_final: 0.8127 (t0) REVERT: C 21 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7512 (mtm110) REVERT: D 52 ASP cc_start: 0.7433 (m-30) cc_final: 0.7091 (m-30) REVERT: D 64 ASP cc_start: 0.6808 (t70) cc_final: 0.6306 (m-30) REVERT: D 94 MET cc_start: 0.8613 (mtp) cc_final: 0.8398 (mtm) REVERT: D 134 ASP cc_start: 0.7151 (t0) cc_final: 0.6653 (p0) outliers start: 5 outliers final: 4 residues processed: 153 average time/residue: 0.1121 time to fit residues: 24.6011 Evaluate side-chains 140 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [114, 42, 0, 47, 91, 14, 78, 60, 41, 21, 137] chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.0470 chunk 91 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.0040 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.180640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120743 restraints weight = 12144.584| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.13 r_work: 0.3107 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12492 Z= 0.116 Angle : 0.480 7.394 17199 Z= 0.263 Chirality : 0.038 0.238 1983 Planarity : 0.004 0.036 1991 Dihedral : 11.909 126.739 2363 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.50 % Allowed : 3.92 % Favored : 95.58 % 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: 0.77 (0.22), residues: 1361 helix: 1.20 (0.20), residues: 692 sheet: 0.13 (0.40), residues: 147 loop : -0.19 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.013 0.001 TYR A 80 PHE 0.016 0.001 PHE A 753 TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS A 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (12484) covalent geometry : angle 0.47892 / 0.26 (17193) hydrogen bonds : bond 0.04837 / 3.16 ( 663) hydrogen bonds : angle 4.07996 / 2.82 ( 1839) metal coordination : bond 0.00517 / 0.32 ( 8) metal coordination : angle 1.53120 / 0.99 ( 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 137 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 39 ASN cc_start: 0.6933 (t0) cc_final: 0.6692 (t0) REVERT: A 40 ASP cc_start: 0.7223 (m-30) cc_final: 0.7001 (m-30) REVERT: A 110 MET cc_start: 0.6107 (mmm) cc_final: 0.5742 (mmm) REVERT: A 205 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7706 (pp) REVERT: A 360 ASN cc_start: 0.7623 (m-40) cc_final: 0.7348 (m-40) REVERT: A 380 MET cc_start: 0.8267 (mmm) cc_final: 0.7877 (mmm) REVERT: A 821 LYS cc_start: 0.8453 (tttt) cc_final: 0.8078 (tttp) REVERT: A 913 SER cc_start: 0.8688 (t) cc_final: 0.8205 (m) REVERT: B 109 ASN cc_start: 0.7586 (m-40) cc_final: 0.7259 (m-40) REVERT: B 151 SER cc_start: 0.8795 (m) cc_final: 0.8508 (t) REVERT: B 166 ILE cc_start: 0.9045 (mt) cc_final: 0.8818 (mm) REVERT: C 21 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7443 (mtm110) REVERT: D 52 ASP cc_start: 0.7345 (m-30) cc_final: 0.6954 (m-30) REVERT: D 99 ASP cc_start: 0.7678 (t0) cc_final: 0.7424 (t0) REVERT: D 134 ASP cc_start: 0.7000 (t0) cc_final: 0.6488 (p0) outliers start: 6 outliers final: 2 residues processed: 134 average time/residue: 0.1111 time to fit residues: 21.1789 Evaluate side-chains 126 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [55, 44, 70, 80, 5, 83, 107, 15, 56, 113, 33] chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.179441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119533 restraints weight = 12131.689| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.86 r_work: 0.3042 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12492 Z= 0.140 Angle : 0.497 5.751 17199 Z= 0.270 Chirality : 0.040 0.262 1983 Planarity : 0.004 0.044 1991 Dihedral : 11.878 125.580 2363 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.83 % Allowed : 5.00 % Favored : 94.16 % 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: 0.90 (0.23), residues: 1361 helix: 1.32 (0.20), residues: 692 sheet: 0.18 (0.40), residues: 147 loop : -0.13 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.015 0.001 TYR A 515 PHE 0.016 0.002 PHE A 571 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (12484) covalent geometry : angle 0.49611 / 0.27 (17193) hydrogen bonds : bond 0.05074 / 3.29 ( 663) hydrogen bonds : angle 4.02068 / 2.77 ( 1839) metal coordination : bond 0.01167 / 0.72 ( 8) metal coordination : angle 1.74239 / 1.10 ( 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 138 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 39 ASN cc_start: 0.6966 (t0) cc_final: 0.6744 (t0) REVERT: A 110 MET cc_start: 0.6100 (mmm) cc_final: 0.5683 (mmm) REVERT: A 221 ASP cc_start: 0.7730 (t0) cc_final: 0.7527 (t0) REVERT: A 360 ASN cc_start: 0.7718 (m-40) cc_final: 0.7451 (m-40) REVERT: A 380 MET cc_start: 0.8295 (mmm) cc_final: 0.7812 (mmm) REVERT: A 758 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8805 (tt) REVERT: A 821 LYS cc_start: 0.8564 (tttt) cc_final: 0.8223 (tttp) REVERT: B 109 ASN cc_start: 0.7686 (m-40) cc_final: 0.7367 (m-40) REVERT: B 166 ILE cc_start: 0.9086 (mt) cc_final: 0.8868 (mm) REVERT: C 21 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7574 (mtm110) REVERT: C 27 LYS cc_start: 0.8500 (tptp) cc_final: 0.8253 (ttmm) REVERT: D 52 ASP cc_start: 0.7273 (m-30) cc_final: 0.6912 (m-30) REVERT: D 99 ASP cc_start: 0.7950 (t0) cc_final: 0.7614 (t0) REVERT: D 118 ASN cc_start: 0.8158 (m-40) cc_final: 0.7956 (m110) REVERT: D 134 ASP cc_start: 0.7035 (t0) cc_final: 0.6515 (p0) outliers start: 10 outliers final: 7 residues processed: 134 average time/residue: 0.0982 time to fit residues: 19.0579 Evaluate side-chains 134 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 70 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [12, 39, 77, 61, 19, 37, 64, 132, 122, 85, 139] chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.0060 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 50.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.181285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123180 restraints weight = 12066.783| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.67 r_work: 0.3072 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12492 Z= 0.107 Angle : 0.443 5.803 17199 Z= 0.242 Chirality : 0.038 0.260 1983 Planarity : 0.003 0.034 1991 Dihedral : 11.838 125.910 2363 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.83 % Allowed : 5.67 % Favored : 93.49 % 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: 1.03 (0.23), residues: 1361 helix: 1.46 (0.21), residues: 697 sheet: 0.23 (0.40), residues: 147 loop : -0.14 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.013 0.001 TYR A 80 PHE 0.014 0.001 PHE A 753 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (12484) covalent geometry : angle 0.44222 / 0.24 (17193) hydrogen bonds : bond 0.04439 / 2.90 ( 663) hydrogen bonds : angle 3.91022 / 2.69 ( 1839) metal coordination : bond 0.00795 / 0.44 ( 8) metal coordination : angle 1.51550 / 0.97 ( 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 142 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.262 Fit side-chains REVERT: A 205 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7503 (pp) REVERT: A 221 ASP cc_start: 0.7686 (t0) cc_final: 0.7401 (t0) REVERT: A 235 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7704 (t0) REVERT: A 360 ASN cc_start: 0.7698 (m-40) cc_final: 0.7455 (m-40) REVERT: A 380 MET cc_start: 0.8199 (mmm) cc_final: 0.7797 (mmm) REVERT: A 821 LYS cc_start: 0.8552 (tttt) cc_final: 0.8213 (tttp) REVERT: A 877 TYR cc_start: 0.8958 (m-10) cc_final: 0.8720 (m-10) REVERT: A 913 SER cc_start: 0.8774 (t) cc_final: 0.8387 (m) REVERT: B 109 ASN cc_start: 0.7602 (m-40) cc_final: 0.7233 (m-40) REVERT: C 21 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7540 (mtm110) REVERT: C 27 LYS cc_start: 0.8368 (tptp) cc_final: 0.8167 (ttmm) REVERT: D 52 ASP cc_start: 0.7233 (m-30) cc_final: 0.6839 (m-30) REVERT: D 99 ASP cc_start: 0.7864 (t0) cc_final: 0.7492 (t0) REVERT: D 118 ASN cc_start: 0.8080 (m-40) cc_final: 0.7808 (m110) REVERT: D 134 ASP cc_start: 0.6989 (t0) cc_final: 0.6506 (p0) REVERT: D 174 MET cc_start: 0.7264 (tmm) cc_final: 0.6816 (mtp) outliers start: 10 outliers final: 4 residues processed: 139 average time/residue: 0.1081 time to fit residues: 21.2898 Evaluate side-chains 136 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [62, 21, 43, 51, 124, 122, 55, 61, 139, 13, 37] chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 61 optimal weight: 0.0020 chunk 139 optimal weight: 50.0000 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117967 restraints weight = 11994.484| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.74 r_work: 0.3039 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12492 Z= 0.198 Angle : 0.537 6.823 17199 Z= 0.289 Chirality : 0.042 0.264 1983 Planarity : 0.005 0.075 1991 Dihedral : 11.872 125.612 2363 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.75 % Allowed : 6.34 % Favored : 92.91 % 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: 0.79 (0.23), residues: 1361 helix: 1.27 (0.20), residues: 698 sheet: 0.26 (0.41), residues: 142 loop : -0.32 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 10 TYR 0.017 0.002 TYR A 515 PHE 0.022 0.002 PHE A 571 TRP 0.010 0.002 TRP A 916 HIS 0.009 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (12484) covalent geometry : angle 0.53602 / 0.29 (17193) hydrogen bonds : bond 0.05609 / 3.66 ( 663) hydrogen bonds : angle 4.01345 / 2.75 ( 1839) metal coordination : bond 0.01589 / 0.94 ( 8) metal coordination : angle 1.61233 / 1.01 ( 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 142 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7663 (pp) REVERT: A 221 ASP cc_start: 0.7919 (t0) cc_final: 0.7638 (t0) REVERT: A 360 ASN cc_start: 0.7793 (m-40) cc_final: 0.7563 (m-40) REVERT: A 380 MET cc_start: 0.8315 (mmm) cc_final: 0.7840 (mmm) REVERT: A 519 MET cc_start: 0.8408 (mtm) cc_final: 0.8054 (mtm) REVERT: A 821 LYS cc_start: 0.8667 (tttt) cc_final: 0.8307 (tttp) REVERT: A 913 SER cc_start: 0.8911 (t) cc_final: 0.8525 (m) REVERT: B 109 ASN cc_start: 0.7752 (m-40) cc_final: 0.7400 (m-40) REVERT: C 21 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7797 (mtm110) REVERT: C 27 LYS cc_start: 0.8536 (tptp) cc_final: 0.8329 (ttmm) REVERT: D 52 ASP cc_start: 0.7295 (m-30) cc_final: 0.6947 (m-30) REVERT: D 64 ASP cc_start: 0.6761 (t70) cc_final: 0.6305 (m-30) REVERT: D 80 ARG cc_start: 0.7983 (ttm110) cc_final: 0.7745 (mtm-85) REVERT: D 99 ASP cc_start: 0.8234 (t0) cc_final: 0.7785 (t0) REVERT: D 118 ASN cc_start: 0.8191 (m-40) cc_final: 0.7926 (m110) REVERT: D 134 ASP cc_start: 0.7095 (t0) cc_final: 0.6612 (p0) REVERT: D 174 MET cc_start: 0.7318 (tmm) cc_final: 0.6857 (mtp) outliers start: 9 outliers final: 7 residues processed: 137 average time/residue: 0.1194 time to fit residues: 23.1185 Evaluate side-chains 139 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [26, 56, 11, 119, 34, 43, 0, 55, 104, 97, 22] chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.179580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123051 restraints weight = 11997.834| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.80 r_work: 0.2998 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12492 Z= 0.107 Angle : 0.443 5.589 17199 Z= 0.242 Chirality : 0.038 0.266 1983 Planarity : 0.003 0.036 1991 Dihedral : 11.835 125.379 2363 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.92 % Allowed : 7.01 % Favored : 92.08 % 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: 0.99 (0.23), residues: 1361 helix: 1.46 (0.21), residues: 697 sheet: 0.34 (0.40), residues: 142 loop : -0.25 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.013 0.001 TYR A 80 PHE 0.014 0.001 PHE A 753 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (12484) covalent geometry : angle 0.44165 / 0.24 (17193) hydrogen bonds : bond 0.04515 / 2.95 ( 663) hydrogen bonds : angle 3.92395 / 2.70 ( 1839) metal coordination : bond 0.00744 / 0.41 ( 8) metal coordination : angle 1.56441 / 0.99 ( 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 138 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.402 Fit side-chains REVERT: A 205 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7435 (pp) REVERT: A 221 ASP cc_start: 0.7828 (t0) cc_final: 0.7518 (t0) REVERT: A 360 ASN cc_start: 0.7758 (m-40) cc_final: 0.7534 (m-40) REVERT: A 380 MET cc_start: 0.8242 (mmm) cc_final: 0.7714 (mmm) REVERT: A 463 MET cc_start: 0.8695 (ttt) cc_final: 0.8443 (ttt) REVERT: A 821 LYS cc_start: 0.8570 (tttt) cc_final: 0.8223 (tttp) REVERT: A 913 SER cc_start: 0.8846 (t) cc_final: 0.8479 (m) REVERT: B 79 LYS cc_start: 0.7059 (mmtp) cc_final: 0.5627 (ptmt) REVERT: B 109 ASN cc_start: 0.7674 (m-40) cc_final: 0.7332 (m-40) REVERT: C 21 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7617 (mtm110) REVERT: D 52 ASP cc_start: 0.7233 (m-30) cc_final: 0.6849 (m-30) REVERT: D 80 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7761 (mtm-85) REVERT: D 99 ASP cc_start: 0.8002 (t0) cc_final: 0.7567 (t0) REVERT: D 134 ASP cc_start: 0.6999 (t0) cc_final: 0.6522 (p0) REVERT: D 174 MET cc_start: 0.7392 (tmm) cc_final: 0.6900 (mtp) outliers start: 11 outliers final: 9 residues processed: 133 average time/residue: 0.1240 time to fit residues: 22.7396 Evaluate side-chains 135 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [92, 62, 137, 121, 37, 93, 50, 63, 25, 54, 116] chunk 92 optimal weight: 40.0000 chunk 62 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 116 optimal weight: 0.0470 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.182077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123993 restraints weight = 12131.062| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.68 r_work: 0.3130 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12492 Z= 0.092 Angle : 0.412 5.585 17199 Z= 0.224 Chirality : 0.037 0.268 1983 Planarity : 0.003 0.034 1991 Dihedral : 11.799 125.520 2363 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.83 % Allowed : 7.17 % Favored : 91.99 % 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: 1.25 (0.23), residues: 1361 helix: 1.69 (0.21), residues: 689 sheet: 0.34 (0.40), residues: 142 loop : -0.08 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.013 0.001 TYR A 826 PHE 0.015 0.001 PHE A 753 TRP 0.010 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (12484) covalent geometry : angle 0.41122 / 0.22 (17193) hydrogen bonds : bond 0.03965 / 2.59 ( 663) hydrogen bonds : angle 3.78208 / 2.60 ( 1839) metal coordination : bond 0.00679 / 0.37 ( 8) metal coordination : angle 1.34353 / 0.86 ( 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 139 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 39 ASN cc_start: 0.6901 (t0) cc_final: 0.6677 (t0) REVERT: A 221 ASP cc_start: 0.7726 (t0) cc_final: 0.7451 (t0) REVERT: A 380 MET cc_start: 0.8241 (mmm) cc_final: 0.7676 (mmm) REVERT: A 821 LYS cc_start: 0.8535 (tttt) cc_final: 0.8167 (tttp) REVERT: A 913 SER cc_start: 0.8854 (t) cc_final: 0.8486 (m) REVERT: B 79 LYS cc_start: 0.7103 (mmtp) cc_final: 0.5614 (ptmt) REVERT: B 109 ASN cc_start: 0.7553 (m-40) cc_final: 0.7200 (m-40) REVERT: B 174 MET cc_start: 0.8248 (tpp) cc_final: 0.7433 (ttp) REVERT: C 21 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7614 (mtm110) REVERT: D 52 ASP cc_start: 0.7160 (m-30) cc_final: 0.6813 (m-30) REVERT: D 80 ARG cc_start: 0.7943 (ttm110) cc_final: 0.7735 (mtm-85) REVERT: D 99 ASP cc_start: 0.8021 (t0) cc_final: 0.7690 (t0) REVERT: D 134 ASP cc_start: 0.6983 (t0) cc_final: 0.6529 (p0) outliers start: 10 outliers final: 6 residues processed: 133 average time/residue: 0.1205 time to fit residues: 22.4395 Evaluate side-chains 129 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [118, 46, 11, 16, 40, 131, 33, 130, 41, 28, 36] chunk 118 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.177055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.118452 restraints weight = 11996.661| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.76 r_work: 0.3039 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12492 Z= 0.195 Angle : 0.533 8.116 17199 Z= 0.285 Chirality : 0.042 0.267 1983 Planarity : 0.005 0.081 1991 Dihedral : 11.832 125.399 2363 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.83 % Allowed : 7.51 % Favored : 91.66 % 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: 0.97 (0.23), residues: 1361 helix: 1.43 (0.21), residues: 691 sheet: 0.50 (0.42), residues: 137 loop : -0.29 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 467 TYR 0.017 0.002 TYR A 788 PHE 0.023 0.002 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.010 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (12484) covalent geometry : angle 0.53239 / 0.28 (17193) hydrogen bonds : bond 0.05454 / 3.56 ( 663) hydrogen bonds : angle 3.96624 / 2.72 ( 1839) metal coordination : bond 0.01363 / 0.82 ( 8) metal coordination : angle 1.59285 / 0.99 ( 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 138 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.7891 (t0) cc_final: 0.7617 (t0) REVERT: A 380 MET cc_start: 0.8343 (mmm) cc_final: 0.7808 (mmm) REVERT: A 463 MET cc_start: 0.8799 (ttt) cc_final: 0.8556 (ttt) REVERT: A 821 LYS cc_start: 0.8682 (tttt) cc_final: 0.8333 (tttp) REVERT: A 913 SER cc_start: 0.8959 (t) cc_final: 0.8555 (m) REVERT: B 79 LYS cc_start: 0.7174 (mmtp) cc_final: 0.5652 (ptpt) REVERT: B 109 ASN cc_start: 0.7799 (m-40) cc_final: 0.7428 (m-40) REVERT: B 174 MET cc_start: 0.8308 (tpp) cc_final: 0.7499 (ttp) REVERT: C 21 ARG cc_start: 0.8415 (mtt180) cc_final: 0.7855 (mtm110) REVERT: D 52 ASP cc_start: 0.7214 (m-30) cc_final: 0.6856 (m-30) REVERT: D 80 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7746 (mtm-85) REVERT: D 99 ASP cc_start: 0.8383 (t0) cc_final: 0.7954 (t0) REVERT: D 134 ASP cc_start: 0.7071 (t0) cc_final: 0.6627 (p0) REVERT: D 174 MET cc_start: 0.7024 (pmm) cc_final: 0.6782 (mtp) outliers start: 10 outliers final: 9 residues processed: 133 average time/residue: 0.1183 time to fit residues: 22.1564 Evaluate side-chains 136 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [75, 2, 8, 51, 33, 119, 16, 126, 41, 120, 103] chunk 75 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.0040 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.179713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121138 restraints weight = 12100.837| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.69 r_work: 0.3034 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12492 Z= 0.109 Angle : 0.446 6.905 17199 Z= 0.243 Chirality : 0.038 0.269 1983 Planarity : 0.003 0.035 1991 Dihedral : 11.800 125.203 2363 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.50 % Allowed : 7.67 % Favored : 91.83 % 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: 1.12 (0.23), residues: 1361 helix: 1.57 (0.21), residues: 689 sheet: 0.42 (0.41), residues: 142 loop : -0.19 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.013 0.001 TYR A 80 PHE 0.012 0.001 PHE A 753 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12484) covalent geometry : angle 0.44570 / 0.24 (17193) hydrogen bonds : bond 0.04456 / 2.92 ( 663) hydrogen bonds : angle 3.87402 / 2.66 ( 1839) metal coordination : bond 0.00797 / 0.45 ( 8) metal coordination : angle 1.48533 / 0.94 ( 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 131 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.7879 (t0) cc_final: 0.7624 (t0) REVERT: A 380 MET cc_start: 0.8309 (mmm) cc_final: 0.7754 (mmm) REVERT: A 463 MET cc_start: 0.8750 (ttt) cc_final: 0.8488 (ttt) REVERT: A 821 LYS cc_start: 0.8604 (tttt) cc_final: 0.8264 (tttp) REVERT: A 913 SER cc_start: 0.8897 (t) cc_final: 0.8549 (m) REVERT: B 79 LYS cc_start: 0.7250 (mmtp) cc_final: 0.5740 (ptmt) REVERT: B 109 ASN cc_start: 0.7784 (m-40) cc_final: 0.7431 (m-40) REVERT: B 174 MET cc_start: 0.8378 (tpp) cc_final: 0.7592 (ttp) REVERT: C 21 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7720 (mtm110) REVERT: D 52 ASP cc_start: 0.7341 (m-30) cc_final: 0.6973 (m-30) REVERT: D 80 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7775 (mtm-85) REVERT: D 99 ASP cc_start: 0.8318 (t0) cc_final: 0.7879 (t0) REVERT: D 134 ASP cc_start: 0.7018 (t0) cc_final: 0.6616 (p0) REVERT: D 174 MET cc_start: 0.6994 (pmm) cc_final: 0.6687 (mtp) outliers start: 6 outliers final: 6 residues processed: 128 average time/residue: 0.1171 time to fit residues: 21.2497 Evaluate side-chains 130 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [128, 64, 87, 109, 22, 91, 114, 17, 62, 77, 16] chunk 128 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS C 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.180355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121980 restraints weight = 12092.454| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.65 r_work: 0.3103 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12492 Z= 0.109 Angle : 0.443 7.251 17199 Z= 0.239 Chirality : 0.038 0.269 1983 Planarity : 0.003 0.036 1991 Dihedral : 11.781 125.328 2363 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.58 % Allowed : 8.17 % 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: 1.20 (0.23), residues: 1361 helix: 1.65 (0.21), residues: 689 sheet: 0.54 (0.41), residues: 137 loop : -0.19 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 654 TYR 0.012 0.001 TYR A 515 PHE 0.013 0.001 PHE A 753 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12484) covalent geometry : angle 0.44194 / 0.24 (17193) hydrogen bonds : bond 0.04304 / 2.82 ( 663) hydrogen bonds : angle 3.80617 / 2.62 ( 1839) metal coordination : bond 0.00826 / 0.45 ( 8) metal coordination : angle 1.39342 / 0.90 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.21 seconds wall clock time: 58 minutes 3.34 seconds (3483.34 seconds total)