Starting phenix.real_space_refine on Sat Sep 12 02:08:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uoe_26646/09_2026/7uoe_26646_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uoe_26646/09_2026/7uoe_26646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uoe_26646/09_2026/7uoe_26646_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uoe_26646/09_2026/7uoe_26646_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uoe_26646/09_2026/7uoe_26646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uoe_26646/09_2026/7uoe_26646.map" } resolution = 2.67 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= 0.000 sd= 0.072 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 74 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 7595 2.51 5 N 2105 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12705 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7478 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1426 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 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: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 697 Classifications: {'RNA': 33} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 32} Chain: "T" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 795 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 21, 'rna3p_pyr': 16} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 33 Unusual residues: {' MG': 2, ' ZN': 2, 'CTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'L2B': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 225 Classifications: {'water': 225} Link IDs: {None: 224} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "T" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2462 SG CYS A 301 34.108 95.946 114.728 1.00 24.16 S ATOM 2503 SG CYS A 306 35.877 99.307 115.464 1.00 49.44 S ATOM 2535 SG CYS A 310 35.918 96.443 118.076 1.00 28.70 S ATOM 3943 SG CYS A 487 33.995 92.897 94.633 1.00 43.34 S ATOM 5196 SG CYS A 645 35.198 96.649 94.646 1.00 31.46 S ATOM 5202 SG CYS A 646 32.961 94.804 97.289 1.00 36.67 S Time building chain proxies: 2.81, per 1000 atoms: 0.22 Number of scatterers: 12705 At special positions: 0 Unit cell: (90.64, 125.66, 170.98, 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 74 15.00 Mg 2 11.99 O 2845 8.00 N 2105 7.00 C 7595 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 569.2 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 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 6 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 56.9% alpha, 13.3% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.592A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.721A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.779A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 200 removed outlier: 4.223A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) 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: 4.086A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.509A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.665A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 321 No H-bonds generated for 'chain 'A' and resid 320 through 321' Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.593A 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 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.740A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.607A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.538A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.730A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.511A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 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 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.545A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.960A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.976A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.465A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (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 9 through 29 removed outlier: 3.783A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 96 Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.664A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.702A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 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: 3.790A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.738A 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 9 through 28 removed outlier: 3.676A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 23 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 Processing helix chain 'D' and resid 82 through 99 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 168 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.767A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 74 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASN A 52 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.767A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.210A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.906A 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: 6.017A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.480A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.157A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.883A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.332A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3858 1.35 - 1.49: 3748 1.49 - 1.62: 5091 1.62 - 1.75: 2 1.75 - 1.89: 129 Bond restraints: 12828 Sorted by residual: bond pdb=" O5' L2B P 101 " pdb=" P L2B P 101 " ideal model delta sigma weight residual 1.612 1.889 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" O3B CTP A1005 " pdb=" PG CTP A1005 " ideal model delta sigma weight residual 1.751 1.581 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" OP1 L2B P 101 " pdb=" P L2B P 101 " ideal model delta sigma weight residual 1.662 1.500 0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C5' L2B P 101 " pdb=" O5' L2B P 101 " ideal model delta sigma weight residual 1.470 1.332 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C1' L2B P 101 " pdb=" N1 L2B P 101 " ideal model delta sigma weight residual 1.500 1.622 -0.122 2.00e-02 2.50e+03 3.75e+01 ... (remaining 12823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17576 2.38 - 4.76: 135 4.76 - 7.14: 11 7.14 - 9.52: 9 9.52 - 11.91: 6 Bond angle restraints: 17737 Sorted by residual: angle pdb=" O5' A P 25 " pdb=" C5' A P 25 " pdb=" C4' A P 25 " ideal model delta sigma weight residual 109.40 113.56 -4.16 8.00e-01 1.56e+00 2.70e+01 angle pdb=" O5' L2B P 101 " pdb=" P L2B P 101 " pdb=" OP2 L2B P 101 " ideal model delta sigma weight residual 118.50 106.59 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O5' U T 103 " pdb=" C5' U T 103 " pdb=" C4' U T 103 " ideal model delta sigma weight residual 109.40 112.57 -3.17 8.00e-01 1.56e+00 1.57e+01 angle pdb=" O5' C P 24 " pdb=" C5' C P 24 " pdb=" C4' C P 24 " ideal model delta sigma weight residual 109.40 112.43 -3.03 8.00e-01 1.56e+00 1.44e+01 angle pdb=" O5' A P 8 " pdb=" C5' A P 8 " pdb=" C4' A P 8 " ideal model delta sigma weight residual 109.40 112.26 -2.86 8.00e-01 1.56e+00 1.28e+01 ... (remaining 17732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.92: 7400 25.92 - 51.84: 287 51.84 - 77.77: 132 77.77 - 103.69: 5 103.69 - 129.61: 1 Dihedral angle restraints: 7825 sinusoidal: 3735 harmonic: 4090 Sorted by residual: dihedral pdb=" CA ASP A 910 " pdb=" C ASP A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual 180.00 143.33 36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA HIS A 75 " pdb=" C HIS A 75 " pdb=" N THR A 76 " pdb=" CA THR A 76 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1828 0.065 - 0.129: 222 0.129 - 0.194: 4 0.194 - 0.258: 1 0.258 - 0.323: 2 Chirality restraints: 2057 Sorted by residual: chirality pdb=" C3' CTP A1005 " pdb=" C2' CTP A1005 " pdb=" C4' CTP A1005 " pdb=" O3' CTP A1005 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' L2B P 101 " pdb=" C1' L2B P 101 " pdb=" C3' L2B P 101 " pdb=" O2' L2B P 101 " both_signs ideal model delta sigma weight residual False -2.83 -2.57 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1' CTP A1005 " pdb=" C2' CTP A1005 " pdb=" N1 CTP A1005 " pdb=" O4' CTP A1005 " both_signs ideal model delta sigma weight residual False 2.35 2.57 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2054 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CTP A1005 " 0.042 2.00e-02 2.50e+03 1.98e-02 8.81e+00 pdb=" C2 CTP A1005 " -0.006 2.00e-02 2.50e+03 pdb=" C4 CTP A1005 " -0.007 2.00e-02 2.50e+03 pdb=" C5 CTP A1005 " -0.013 2.00e-02 2.50e+03 pdb=" C6 CTP A1005 " -0.017 2.00e-02 2.50e+03 pdb=" N1 CTP A1005 " -0.017 2.00e-02 2.50e+03 pdb=" N3 CTP A1005 " 0.003 2.00e-02 2.50e+03 pdb=" N4 CTP A1005 " 0.028 2.00e-02 2.50e+03 pdb=" O2 CTP A1005 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 190 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C VAL A 190 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 190 " 0.008 2.00e-02 2.50e+03 pdb=" N GLN A 191 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 189 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C THR A 189 " -0.020 2.00e-02 2.50e+03 pdb=" O THR A 189 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 190 " 0.007 2.00e-02 2.50e+03 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 225 2.60 - 3.17: 10988 3.17 - 3.75: 21225 3.75 - 4.32: 31268 4.32 - 4.90: 49129 Nonbonded interactions: 112835 Sorted by model distance: nonbonded pdb=" OD2 ASP A 36 " pdb=" O HOH A1101 " model vdw 2.022 3.040 nonbonded pdb=" OD2 ASP A 452 " pdb=" OG1 THR A 556 " model vdw 2.026 3.040 nonbonded pdb=" O HOH A1168 " pdb=" O HOH A1303 " model vdw 2.027 3.040 nonbonded pdb=" O LEU A 247 " pdb=" O HOH A1102 " model vdw 2.036 3.040 nonbonded pdb=" O LYS A 545 " pdb=" O HOH A1103 " model vdw 2.039 3.040 ... (remaining 112830 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' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.130 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 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 : 0.006 0.277 12837 Z= 0.279 Angle : 0.627 15.513 17743 Z= 0.382 Chirality : 0.042 0.323 2057 Planarity : 0.003 0.027 2002 Dihedral : 15.688 129.609 5177 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.41 % Favored : 97.37 % Rotamer: Outliers : 1.18 % Allowed : 5.47 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.41 (0.23), residues: 1368 helix: 1.30 (0.20), residues: 696 sheet: -0.98 (0.40), residues: 138 loop : -0.69 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.012 0.001 TYR A 515 PHE 0.015 0.001 PHE A 741 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 0.00539 / 0.27 (12828) covalent geometry : angle 0.61096 / 0.38 (17737) hydrogen bonds : bond 0.13852 / 8.98 ( 658) hydrogen bonds : angle 5.76212 / 3.93 ( 1809) metal coordination : bond 0.04280 / 2.60 ( 8) metal coordination : angle 7.57883 / 3.90 ( 6) Misc. bond : bond 0.04984 / 2.62 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7605 (t70) cc_final: 0.7098 (t0) REVERT: A 64 ASN cc_start: 0.7787 (m-40) cc_final: 0.7202 (m110) REVERT: C 18 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8392 (tm-30) outliers start: 14 outliers final: 2 residues processed: 144 average time/residue: 0.7718 time to fit residues: 119.0249 Evaluate side-chains 114 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN A 650 HIS A 722 ASN D 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.088875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056506 restraints weight = 27158.507| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.52 r_work: 0.2746 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12837 Z= 0.179 Angle : 0.548 7.272 17743 Z= 0.295 Chirality : 0.040 0.264 2057 Planarity : 0.004 0.034 2002 Dihedral : 15.313 131.799 2652 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 1.26 % Allowed : 10.26 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.71 (0.23), residues: 1368 helix: 1.63 (0.20), residues: 687 sheet: -0.80 (0.41), residues: 129 loop : -0.64 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.015 0.002 TYR A 149 PHE 0.017 0.001 PHE A 741 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (12828) covalent geometry : angle 0.54698 / 0.29 (17737) hydrogen bonds : bond 0.04796 / 3.08 ( 658) hydrogen bonds : angle 4.40564 / 3.09 ( 1809) metal coordination : bond 0.00976 / 0.60 ( 8) metal coordination : angle 2.01355 / 1.05 ( 6) Misc. bond : bond 0.00164 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7767 (m-40) cc_final: 0.7226 (p0) REVERT: A 365 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8112 (tpm170) REVERT: B 55 MET cc_start: 0.8425 (pp-130) cc_final: 0.8179 (ppp) REVERT: B 75 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7462 (mpp-170) REVERT: B 155 GLU cc_start: 0.7280 (pp20) cc_final: 0.7055 (pp20) REVERT: C 44 ASP cc_start: 0.7274 (t0) cc_final: 0.5287 (t0) REVERT: C 67 ASP cc_start: 0.7718 (t0) cc_final: 0.7311 (t0) REVERT: D 49 PHE cc_start: 0.7987 (t80) cc_final: 0.7647 (t80) REVERT: D 55 MET cc_start: 0.8928 (tpp) cc_final: 0.8448 (tmm) REVERT: D 62 MET cc_start: 0.8832 (mtp) cc_final: 0.8468 (mmp) REVERT: D 65 GLN cc_start: 0.8101 (pt0) cc_final: 0.7465 (pt0) REVERT: D 73 GLN cc_start: 0.8120 (tt0) cc_final: 0.7618 (tm-30) outliers start: 15 outliers final: 4 residues processed: 120 average time/residue: 0.8610 time to fit residues: 110.1598 Evaluate side-chains 112 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 78 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.088096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.055640 restraints weight = 27253.687| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.53 r_work: 0.2737 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12837 Z= 0.175 Angle : 0.504 6.798 17743 Z= 0.270 Chirality : 0.038 0.245 2057 Planarity : 0.003 0.044 2002 Dihedral : 15.147 134.759 2650 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 1.68 % Allowed : 10.09 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.85 (0.23), residues: 1368 helix: 1.73 (0.20), residues: 696 sheet: -0.67 (0.41), residues: 129 loop : -0.63 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 51 TYR 0.014 0.001 TYR A 149 PHE 0.019 0.001 PHE A 741 TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (12828) covalent geometry : angle 0.50281 / 0.27 (17737) hydrogen bonds : bond 0.04271 / 2.76 ( 658) hydrogen bonds : angle 4.18063 / 2.95 ( 1809) metal coordination : bond 0.00946 / 0.57 ( 8) metal coordination : angle 2.06718 / 1.07 ( 6) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7844 (m-40) cc_final: 0.7404 (p0) REVERT: A 336 ASP cc_start: 0.8517 (t0) cc_final: 0.8257 (t0) REVERT: A 365 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8246 (tpm170) REVERT: A 857 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: B 49 PHE cc_start: 0.7959 (t80) cc_final: 0.7726 (t80) REVERT: B 67 MET cc_start: 0.8433 (ttt) cc_final: 0.7949 (tmm) REVERT: B 69 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 155 GLU cc_start: 0.7512 (pp20) cc_final: 0.7260 (pp20) REVERT: C 44 ASP cc_start: 0.7313 (t0) cc_final: 0.6052 (OUTLIER) REVERT: C 47 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: C 67 ASP cc_start: 0.7805 (t0) cc_final: 0.7301 (t0) REVERT: D 49 PHE cc_start: 0.8092 (t80) cc_final: 0.7754 (t80) REVERT: D 62 MET cc_start: 0.8793 (mtp) cc_final: 0.8420 (mmp) REVERT: D 65 GLN cc_start: 0.8262 (pt0) cc_final: 0.7416 (pt0) REVERT: D 73 GLN cc_start: 0.8138 (tt0) cc_final: 0.7676 (tm-30) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 0.8452 time to fit residues: 115.3638 Evaluate side-chains 121 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 73 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 116 optimal weight: 0.0010 chunk 90 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 chunk 56 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.1780 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.089445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.057022 restraints weight = 27194.083| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.54 r_work: 0.2777 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12837 Z= 0.104 Angle : 0.481 8.448 17743 Z= 0.255 Chirality : 0.036 0.247 2057 Planarity : 0.003 0.034 2002 Dihedral : 15.076 135.580 2649 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.41 % Favored : 97.37 % Rotamer: Outliers : 1.60 % Allowed : 10.77 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1368 helix: 1.79 (0.20), residues: 691 sheet: -0.50 (0.39), residues: 139 loop : -0.64 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 57 TYR 0.012 0.001 TYR A 149 PHE 0.016 0.001 PHE A 741 TRP 0.008 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (12828) covalent geometry : angle 0.48046 / 0.25 (17737) hydrogen bonds : bond 0.03684 / 2.33 ( 658) hydrogen bonds : angle 3.98845 / 2.83 ( 1809) metal coordination : bond 0.00424 / 0.26 ( 8) metal coordination : angle 1.37060 / 0.72 ( 6) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7832 (m-40) cc_final: 0.7363 (p0) REVERT: A 336 ASP cc_start: 0.8469 (t0) cc_final: 0.8189 (t0) REVERT: A 365 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8322 (tpm170) REVERT: A 665 GLU cc_start: 0.8765 (pm20) cc_final: 0.8541 (pm20) REVERT: A 857 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: B 49 PHE cc_start: 0.7944 (t80) cc_final: 0.7658 (t80) REVERT: B 55 MET cc_start: 0.8140 (ppp) cc_final: 0.7885 (ppp) REVERT: B 67 MET cc_start: 0.8420 (ttt) cc_final: 0.7936 (tmm) REVERT: B 69 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8042 (tm-30) REVERT: B 75 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7260 (mpp-170) REVERT: B 155 GLU cc_start: 0.7542 (pp20) cc_final: 0.7269 (pp20) REVERT: C 44 ASP cc_start: 0.7430 (t0) cc_final: 0.6344 (OUTLIER) REVERT: C 47 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: C 67 ASP cc_start: 0.7914 (t0) cc_final: 0.7387 (t0) REVERT: D 49 PHE cc_start: 0.8120 (t80) cc_final: 0.7757 (t80) REVERT: D 55 MET cc_start: 0.8961 (tpp) cc_final: 0.8490 (tmm) REVERT: D 62 MET cc_start: 0.8798 (mtp) cc_final: 0.8455 (mmp) REVERT: D 65 GLN cc_start: 0.8180 (pt0) cc_final: 0.7408 (pt0) REVERT: D 73 GLN cc_start: 0.8140 (tt0) cc_final: 0.7677 (tm-30) outliers start: 19 outliers final: 5 residues processed: 131 average time/residue: 0.8440 time to fit residues: 118.0675 Evaluate side-chains 118 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 73 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 60 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 790 ASN B 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.086163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.053768 restraints weight = 27409.278| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.54 r_work: 0.2702 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12837 Z= 0.269 Angle : 0.558 10.593 17743 Z= 0.293 Chirality : 0.041 0.252 2057 Planarity : 0.003 0.040 2002 Dihedral : 15.031 136.185 2649 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.63 % Favored : 97.15 % Rotamer: Outliers : 1.85 % Allowed : 11.10 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.83 (0.23), residues: 1368 helix: 1.69 (0.20), residues: 702 sheet: -0.56 (0.39), residues: 134 loop : -0.66 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 57 TYR 0.018 0.002 TYR A 289 PHE 0.028 0.002 PHE B 15 TRP 0.010 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (12828) covalent geometry : angle 0.55747 / 0.29 (17737) hydrogen bonds : bond 0.04229 / 2.75 ( 658) hydrogen bonds : angle 4.09830 / 2.90 ( 1809) metal coordination : bond 0.01436 / 0.85 ( 8) metal coordination : angle 1.86476 / 0.97 ( 6) Misc. bond : bond 0.00211 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7894 (m-40) cc_final: 0.7450 (p0) REVERT: A 336 ASP cc_start: 0.8511 (t0) cc_final: 0.8238 (t0) REVERT: A 857 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: B 49 PHE cc_start: 0.8031 (t80) cc_final: 0.7768 (t80) REVERT: B 51 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8496 (tpp80) REVERT: B 55 MET cc_start: 0.8238 (ppp) cc_final: 0.8004 (ppp) REVERT: B 67 MET cc_start: 0.8464 (ttt) cc_final: 0.8002 (tmm) REVERT: B 69 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 75 ARG cc_start: 0.7699 (tpp-160) cc_final: 0.7328 (mpp-170) REVERT: B 155 GLU cc_start: 0.7697 (pp20) cc_final: 0.7422 (pp20) REVERT: C 34 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7466 (tp40) REVERT: C 38 ASP cc_start: 0.8267 (m-30) cc_final: 0.7975 (m-30) REVERT: C 44 ASP cc_start: 0.7486 (t0) cc_final: 0.6086 (OUTLIER) REVERT: C 47 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: C 67 ASP cc_start: 0.7938 (t0) cc_final: 0.7387 (t0) REVERT: D 49 PHE cc_start: 0.8145 (t80) cc_final: 0.7747 (t80) REVERT: D 57 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: D 62 MET cc_start: 0.8809 (mtp) cc_final: 0.8473 (mmp) REVERT: D 65 GLN cc_start: 0.8234 (pt0) cc_final: 0.7292 (pt0) REVERT: D 73 GLN cc_start: 0.8176 (tt0) cc_final: 0.7944 (tm-30) REVERT: D 77 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8154 (tp30) outliers start: 22 outliers final: 12 residues processed: 128 average time/residue: 0.8538 time to fit residues: 116.8284 Evaluate side-chains 122 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 62 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 24 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.087596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.055535 restraints weight = 27099.493| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.53 r_work: 0.2741 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12837 Z= 0.138 Angle : 0.499 9.768 17743 Z= 0.262 Chirality : 0.037 0.254 2057 Planarity : 0.003 0.038 2002 Dihedral : 15.072 136.553 2649 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.41 % Favored : 97.37 % Rotamer: Outliers : 1.43 % Allowed : 12.11 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.92 (0.23), residues: 1368 helix: 1.78 (0.20), residues: 697 sheet: -0.39 (0.39), residues: 144 loop : -0.65 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.015 0.001 TYR A 149 PHE 0.023 0.001 PHE B 15 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 0.00315 / 0.14 (12828) covalent geometry : angle 0.49869 / 0.26 (17737) hydrogen bonds : bond 0.03674 / 2.35 ( 658) hydrogen bonds : angle 3.94230 / 2.80 ( 1809) metal coordination : bond 0.00705 / 0.41 ( 8) metal coordination : angle 1.40300 / 0.74 ( 6) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7864 (m-40) cc_final: 0.7433 (p0) REVERT: A 336 ASP cc_start: 0.8484 (t0) cc_final: 0.8208 (t0) REVERT: A 365 ARG cc_start: 0.8595 (mmm-85) cc_final: 0.7961 (tpm170) REVERT: A 857 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: B 49 PHE cc_start: 0.8030 (t80) cc_final: 0.7727 (t80) REVERT: B 67 MET cc_start: 0.8469 (ttt) cc_final: 0.7983 (tmm) REVERT: B 69 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8050 (tm-30) REVERT: B 155 GLU cc_start: 0.7725 (pp20) cc_final: 0.7435 (pp20) REVERT: C 34 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7468 (tp40) REVERT: C 38 ASP cc_start: 0.8258 (m-30) cc_final: 0.7882 (m-30) REVERT: C 44 ASP cc_start: 0.7534 (t0) cc_final: 0.7141 (OUTLIER) REVERT: C 67 ASP cc_start: 0.7884 (t0) cc_final: 0.7349 (t0) REVERT: D 49 PHE cc_start: 0.8161 (t80) cc_final: 0.7823 (t80) REVERT: D 55 MET cc_start: 0.8944 (tpp) cc_final: 0.8451 (tmm) REVERT: D 62 MET cc_start: 0.8789 (mtp) cc_final: 0.8449 (mmp) REVERT: D 65 GLN cc_start: 0.8205 (pt0) cc_final: 0.7316 (pt0) REVERT: D 73 GLN cc_start: 0.8197 (tt0) cc_final: 0.7741 (tm-30) outliers start: 17 outliers final: 9 residues processed: 129 average time/residue: 0.7918 time to fit residues: 109.0114 Evaluate side-chains 120 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 60 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 9 optimal weight: 0.0070 chunk 120 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.087656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055585 restraints weight = 26974.514| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.51 r_work: 0.2766 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12837 Z= 0.130 Angle : 0.502 10.108 17743 Z= 0.264 Chirality : 0.037 0.253 2057 Planarity : 0.003 0.046 2002 Dihedral : 15.042 136.572 2649 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.41 % Favored : 97.37 % Rotamer: Outliers : 1.43 % Allowed : 12.70 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.96 (0.23), residues: 1368 helix: 1.79 (0.20), residues: 691 sheet: -0.31 (0.39), residues: 144 loop : -0.60 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 57 TYR 0.014 0.001 TYR A 149 PHE 0.021 0.001 PHE B 15 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 0.00292 / 0.13 (12828) covalent geometry : angle 0.50135 / 0.26 (17737) hydrogen bonds : bond 0.03603 / 2.31 ( 658) hydrogen bonds : angle 3.92611 / 2.78 ( 1809) metal coordination : bond 0.00720 / 0.41 ( 8) metal coordination : angle 1.37657 / 0.73 ( 6) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7889 (m-40) cc_final: 0.7443 (p0) REVERT: A 336 ASP cc_start: 0.8587 (t0) cc_final: 0.8321 (t0) REVERT: A 365 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.7926 (tpm170) REVERT: A 857 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: B 49 PHE cc_start: 0.8054 (t80) cc_final: 0.7755 (t80) REVERT: B 67 MET cc_start: 0.8547 (ttt) cc_final: 0.8077 (tmm) REVERT: B 69 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 155 GLU cc_start: 0.7975 (pp20) cc_final: 0.7673 (pp20) REVERT: C 34 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7630 (tp40) REVERT: C 38 ASP cc_start: 0.8450 (m-30) cc_final: 0.8122 (m-30) REVERT: C 44 ASP cc_start: 0.7605 (t0) cc_final: 0.5636 (OUTLIER) REVERT: C 47 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7907 (mp0) REVERT: C 67 ASP cc_start: 0.7893 (t0) cc_final: 0.7357 (t0) REVERT: D 49 PHE cc_start: 0.8225 (t80) cc_final: 0.7862 (t80) REVERT: D 55 MET cc_start: 0.9043 (tpp) cc_final: 0.8520 (tmm) REVERT: D 62 MET cc_start: 0.8952 (mtp) cc_final: 0.8538 (mpp) REVERT: D 73 GLN cc_start: 0.8345 (tt0) cc_final: 0.7876 (tm-30) REVERT: D 77 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7708 (mt-10) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 0.8221 time to fit residues: 109.7302 Evaluate side-chains 120 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain C residue 73 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.087488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055519 restraints weight = 26897.416| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.50 r_work: 0.2776 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12837 Z= 0.139 Angle : 0.510 11.945 17743 Z= 0.266 Chirality : 0.037 0.254 2057 Planarity : 0.004 0.072 2002 Dihedral : 15.026 136.618 2649 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.49 % Favored : 97.30 % Rotamer: Outliers : 1.35 % Allowed : 13.37 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1368 helix: 1.85 (0.20), residues: 693 sheet: -0.25 (0.39), residues: 145 loop : -0.53 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 57 TYR 0.014 0.001 TYR A 149 PHE 0.019 0.001 PHE A 741 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 0.00317 / 0.14 (12828) covalent geometry : angle 0.50953 / 0.27 (17737) hydrogen bonds : bond 0.03526 / 2.27 ( 658) hydrogen bonds : angle 3.86329 / 2.74 ( 1809) metal coordination : bond 0.00794 / 0.45 ( 8) metal coordination : angle 1.38506 / 0.73 ( 6) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7872 (m-40) cc_final: 0.7411 (p0) REVERT: A 336 ASP cc_start: 0.8461 (t0) cc_final: 0.8182 (t0) REVERT: A 365 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.7970 (tpm170) REVERT: A 857 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: B 49 PHE cc_start: 0.8051 (t80) cc_final: 0.7759 (t80) REVERT: B 65 GLN cc_start: 0.8299 (mt0) cc_final: 0.7981 (mt0) REVERT: B 67 MET cc_start: 0.8493 (ttt) cc_final: 0.8017 (tmm) REVERT: B 69 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 75 ARG cc_start: 0.7645 (mpp-170) cc_final: 0.7301 (mpp-170) REVERT: B 111 ARG cc_start: 0.8171 (ptp90) cc_final: 0.7765 (ppt-90) REVERT: B 155 GLU cc_start: 0.7762 (pp20) cc_final: 0.7459 (pp20) REVERT: C 34 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7539 (tp40) REVERT: C 44 ASP cc_start: 0.7533 (t0) cc_final: 0.5428 (t0) REVERT: C 47 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7838 (mp0) REVERT: C 67 ASP cc_start: 0.7942 (t0) cc_final: 0.7386 (t0) REVERT: D 49 PHE cc_start: 0.8249 (t80) cc_final: 0.7945 (t80) REVERT: D 55 MET cc_start: 0.9034 (tpp) cc_final: 0.8483 (tmm) REVERT: D 56 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 57 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7491 (mtm-85) REVERT: D 62 MET cc_start: 0.8927 (mtp) cc_final: 0.8568 (mmp) REVERT: D 65 GLN cc_start: 0.8441 (pt0) cc_final: 0.7556 (pt0) REVERT: D 73 GLN cc_start: 0.8223 (tt0) cc_final: 0.7768 (tm-30) outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 0.8473 time to fit residues: 113.8599 Evaluate side-chains 124 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 60 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 0.0070 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.087459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055513 restraints weight = 26991.943| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.53 r_work: 0.2760 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12837 Z= 0.140 Angle : 0.517 11.628 17743 Z= 0.269 Chirality : 0.037 0.255 2057 Planarity : 0.003 0.056 2002 Dihedral : 15.021 136.634 2649 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.56 % Favored : 97.22 % Rotamer: Outliers : 1.01 % Allowed : 13.62 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1368 helix: 1.82 (0.20), residues: 694 sheet: -0.23 (0.39), residues: 145 loop : -0.48 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 57 TYR 0.014 0.001 TYR A 149 PHE 0.019 0.001 PHE A 741 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 0.00320 / 0.14 (12828) covalent geometry : angle 0.51600 / 0.27 (17737) hydrogen bonds : bond 0.03549 / 2.26 ( 658) hydrogen bonds : angle 3.85745 / 2.73 ( 1809) metal coordination : bond 0.00759 / 0.43 ( 8) metal coordination : angle 1.35343 / 0.71 ( 6) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7875 (m-40) cc_final: 0.7416 (p0) REVERT: A 336 ASP cc_start: 0.8455 (t0) cc_final: 0.8179 (t0) REVERT: A 365 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.7972 (tpm170) REVERT: A 857 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: B 67 MET cc_start: 0.8508 (ttt) cc_final: 0.8028 (tmm) REVERT: B 69 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 75 ARG cc_start: 0.7672 (tpp-160) cc_final: 0.7282 (mpp-170) REVERT: B 111 ARG cc_start: 0.8150 (ptp90) cc_final: 0.7751 (ppt-90) REVERT: B 155 GLU cc_start: 0.7793 (pp20) cc_final: 0.7493 (pp20) REVERT: C 34 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7552 (tp40) REVERT: C 44 ASP cc_start: 0.7527 (t0) cc_final: 0.5410 (t0) REVERT: C 47 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7836 (mp0) REVERT: C 67 ASP cc_start: 0.7953 (t0) cc_final: 0.7395 (t0) REVERT: D 49 PHE cc_start: 0.8240 (t80) cc_final: 0.7872 (t80) REVERT: D 62 MET cc_start: 0.8941 (mtp) cc_final: 0.8561 (mmp) REVERT: D 65 GLN cc_start: 0.8316 (pt0) cc_final: 0.7800 (pt0) REVERT: D 73 GLN cc_start: 0.8227 (tt0) cc_final: 0.7978 (tm-30) REVERT: D 77 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8138 (tp30) outliers start: 12 outliers final: 9 residues processed: 126 average time/residue: 0.8409 time to fit residues: 113.1448 Evaluate side-chains 123 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain C residue 73 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.087420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055876 restraints weight = 27329.238| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.51 r_work: 0.2772 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12837 Z= 0.168 Angle : 0.538 12.892 17743 Z= 0.279 Chirality : 0.038 0.258 2057 Planarity : 0.003 0.068 2002 Dihedral : 15.037 136.649 2649 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 1.01 % Allowed : 13.46 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.09 (0.23), residues: 1368 helix: 1.83 (0.20), residues: 700 sheet: -0.18 (0.39), residues: 145 loop : -0.48 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 57 TYR 0.015 0.001 TYR A 149 PHE 0.018 0.001 PHE A 741 TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12828) covalent geometry : angle 0.53747 / 0.28 (17737) hydrogen bonds : bond 0.03613 / 2.33 ( 658) hydrogen bonds : angle 3.86142 / 2.74 ( 1809) metal coordination : bond 0.00915 / 0.52 ( 8) metal coordination : angle 1.47139 / 0.77 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7887 (m-40) cc_final: 0.7436 (p0) REVERT: A 336 ASP cc_start: 0.8472 (t0) cc_final: 0.8202 (t0) REVERT: A 365 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.7962 (tpm170) REVERT: A 857 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: B 67 MET cc_start: 0.8546 (ttt) cc_final: 0.8066 (tmm) REVERT: B 69 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 75 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7355 (mpp-170) REVERT: B 111 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7701 (ppt-90) REVERT: B 155 GLU cc_start: 0.7831 (pp20) cc_final: 0.7526 (pp20) REVERT: C 34 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7525 (tp40) REVERT: C 44 ASP cc_start: 0.7554 (t0) cc_final: 0.5387 (t0) REVERT: C 47 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7778 (mp0) REVERT: C 67 ASP cc_start: 0.7968 (t0) cc_final: 0.7406 (t0) REVERT: D 49 PHE cc_start: 0.8264 (t80) cc_final: 0.7982 (t80) REVERT: D 55 MET cc_start: 0.8989 (tpp) cc_final: 0.8419 (tmm) REVERT: D 73 GLN cc_start: 0.8233 (tt0) cc_final: 0.7986 (tm-30) outliers start: 12 outliers final: 8 residues processed: 124 average time/residue: 0.8721 time to fit residues: 115.2212 Evaluate side-chains 121 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain C residue 73 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 138 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.087389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.055842 restraints weight = 26381.167| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.33 r_work: 0.2736 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12837 Z= 0.130 Angle : 0.534 12.240 17743 Z= 0.278 Chirality : 0.037 0.258 2057 Planarity : 0.003 0.080 2002 Dihedral : 15.050 136.574 2649 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 0.93 % Allowed : 13.88 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1368 helix: 1.84 (0.20), residues: 699 sheet: -0.25 (0.39), residues: 149 loop : -0.45 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 51 TYR 0.014 0.001 TYR A 149 PHE 0.018 0.001 PHE A 741 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 0.00298 / 0.13 (12828) covalent geometry : angle 0.53325 / 0.28 (17737) hydrogen bonds : bond 0.03423 / 2.20 ( 658) hydrogen bonds : angle 3.83058 / 2.72 ( 1809) metal coordination : bond 0.00734 / 0.41 ( 8) metal coordination : angle 1.30748 / 0.69 ( 6) Misc. bond : bond 0.00002 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4916.13 seconds wall clock time: 84 minutes 35.39 seconds (5075.39 seconds total)