Starting phenix.real_space_refine on Fri Jul 3 08:16:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.map" model { file = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2026/7krp_23009.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.093 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 75 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 7700 2.51 5 N 2111 2.21 5 O 2589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12561 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1416 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 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: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNA': 37} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 36} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 24.703 58.884 80.276 1.00 23.18 S ATOM 2495 SG CYS A 306 25.136 60.110 83.908 1.00 20.09 S ATOM 2527 SG CYS A 310 25.698 56.441 82.999 1.00 17.07 S ATOM 3935 SG CYS A 487 27.719 72.698 66.042 1.00 28.42 S ATOM 5188 SG CYS A 645 27.788 75.074 69.011 1.00 32.11 S ATOM 5194 SG CYS A 646 26.236 71.615 69.477 1.00 29.89 S Time building chain proxies: 3.02, per 1000 atoms: 0.24 Number of scatterers: 12561 At special positions: 0 Unit cell: (95.85, 161.88, 142.71, 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 83 16.00 P 75 15.00 Mg 1 11.99 O 2589 8.00 N 2111 7.00 C 7700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 549.2 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 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " 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 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 6 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 53.4% alpha, 11.3% beta 33 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.534A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.524A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.569A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.631A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.857A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.529A 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 305 through 318 removed outlier: 3.954A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.566A 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 removed outlier: 3.763A pdb=" N TYR A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.487A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.640A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.518A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.955A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.649A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.162A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.566A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 732 removed outlier: 3.717A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.580A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.781A pdb=" N LYS A 807 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 808 " --> pdb=" O LEU A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 804 through 808' Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.684A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 838 " --> pdb=" O PRO A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.625A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.054A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.214A 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 28 removed outlier: 3.757A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 97 removed outlier: 3.761A pdb=" N ARG B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.091A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.733A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.535A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.536A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.838A 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 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 63 removed outlier: 3.744A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.292A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 removed outlier: 4.012A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.662A pdb=" N ASN D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.623A 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 18 through 21 removed outlier: 4.227A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.510A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.528A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.758A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 815 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.437A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3662 1.34 - 1.46: 2591 1.46 - 1.57: 6398 1.57 - 1.69: 197 1.69 - 1.81: 130 Bond restraints: 12978 Sorted by residual: bond pdb=" C17 1N7 A1005 " pdb=" C18 1N7 A1005 " ideal model delta sigma weight residual 1.528 1.638 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C17 1N7 D 201 " pdb=" C18 1N7 D 201 " ideal model delta sigma weight residual 1.528 1.633 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C17 1N7 A1006 " pdb=" C18 1N7 A1006 " ideal model delta sigma weight residual 1.528 1.630 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 1.346 1.441 -0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C24 1N7 D 201 " pdb=" N1 1N7 D 201 " ideal model delta sigma weight residual 1.346 1.440 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 12973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 17744 2.42 - 4.84: 175 4.84 - 7.26: 39 7.26 - 9.68: 8 9.68 - 12.10: 1 Bond angle restraints: 17967 Sorted by residual: angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C4 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C9 1N7 A1005 " ideal model delta sigma weight residual 117.60 105.50 12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3' C P 25 " pdb=" C3' C P 25 " pdb=" C2' C P 25 " ideal model delta sigma weight residual 113.70 118.97 -5.27 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 115.43 125.06 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C23 1N7 D 201 " pdb=" C24 1N7 D 201 " pdb=" N1 1N7 D 201 " ideal model delta sigma weight residual 115.43 125.03 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 17962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.57: 7404 30.57 - 61.15: 166 61.15 - 91.72: 9 91.72 - 122.29: 0 122.29 - 152.87: 3 Dihedral angle restraints: 7582 sinusoidal: 3501 harmonic: 4081 Sorted by residual: dihedral pdb=" CA SER D 31 " pdb=" C SER D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta harmonic sigma weight residual 0.00 -31.31 31.31 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" C22 1N7 A1005 " pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sinusoidal sigma weight residual 227.30 74.43 152.87 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 2099 1.025 - 2.051: 0 2.051 - 3.076: 0 3.076 - 4.101: 0 4.101 - 5.127: 2 Chirality restraints: 2101 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.70 -5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.56 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.82 -0.42 2.00e-01 2.50e+01 4.37e+00 ... (remaining 2098 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO A 339 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 94 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 338 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL A 338 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 338 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO A 339 " -0.009 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 37 2.41 - 3.03: 7122 3.03 - 3.65: 19487 3.65 - 4.28: 29473 4.28 - 4.90: 48399 Nonbonded interactions: 104518 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.784 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 2.048 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1003 " model vdw 2.065 2.170 nonbonded pdb="MG MG A1003 " pdb=" O1B ADP A1004 " model vdw 2.074 2.170 nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.227 3.040 ... (remaining 104513 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 7 through 191) selection = (chain 'D' and (resid 7 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 23 or (resid 24 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or resi \ d 33 through 38 or (resid 39 and (name N or name CA or name C or name O or name \ CB )) or resid 40 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: 2.970 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.970 Find NCS groups from input model: 0.100 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 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 0.110 12986 Z= 0.299 Angle : 0.692 12.105 17973 Z= 0.371 Chirality : 0.165 5.127 2101 Planarity : 0.003 0.042 2007 Dihedral : 12.670 152.867 4940 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.18 % Allowed : 6.95 % Favored : 88.87 % 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: -1.51 (0.22), residues: 1365 helix: -0.49 (0.20), residues: 672 sheet: -1.31 (0.44), residues: 136 loop : -1.41 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 726 TYR 0.014 0.001 TYR A 788 PHE 0.013 0.002 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.30 (12978) covalent geometry : angle 0.69138 / 0.37 (17967) hydrogen bonds : bond 0.14086 / 9.47 ( 631) hydrogen bonds : angle 5.95361 / 4.12 ( 1707) metal coordination : bond 0.00630 / 0.33 ( 8) metal coordination : angle 1.60078 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 344 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7637 (m-10) cc_final: 0.7386 (m-10) REVERT: A 450 ILE cc_start: 0.7101 (tp) cc_final: 0.6844 (tp) REVERT: A 481 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6739 (t0) REVERT: A 666 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5429 (mtt) REVERT: A 755 MET cc_start: 0.6677 (ttm) cc_final: 0.6449 (ttp) REVERT: A 768 SER cc_start: 0.5726 (m) cc_final: 0.5466 (m) REVERT: B 165 LYS cc_start: 0.5807 (mptt) cc_final: 0.5396 (tmtt) REVERT: D 176 ASN cc_start: 0.5391 (OUTLIER) cc_final: 0.4997 (t0) outliers start: 50 outliers final: 13 residues processed: 379 average time/residue: 0.1156 time to fit residues: 63.1442 Evaluate side-chains 228 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 113 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 613 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 HIS A 767 ASN B 157 GLN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127609 restraints weight = 14869.663| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.43 r_work: 0.3424 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12986 Z= 0.216 Angle : 0.729 9.327 17973 Z= 0.373 Chirality : 0.046 0.310 2101 Planarity : 0.005 0.064 2007 Dihedral : 8.665 171.091 2419 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.26 % Allowed : 13.31 % Favored : 83.43 % 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: -1.08 (0.22), residues: 1365 helix: 0.00 (0.19), residues: 698 sheet: -1.35 (0.43), residues: 136 loop : -1.39 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 249 TYR 0.031 0.002 TYR A 32 PHE 0.020 0.003 PHE A 741 TRP 0.019 0.002 TRP A 598 HIS 0.007 0.002 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (12978) covalent geometry : angle 0.72827 / 0.37 (17967) hydrogen bonds : bond 0.04254 / 2.79 ( 631) hydrogen bonds : angle 4.40909 / 3.07 ( 1707) metal coordination : bond 0.00884 / 0.43 ( 8) metal coordination : angle 2.38688 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.449 Fit side-chains REVERT: A 221 ASP cc_start: 0.8279 (p0) cc_final: 0.7974 (p0) REVERT: A 235 ASP cc_start: 0.7646 (m-30) cc_final: 0.7010 (p0) REVERT: A 415 PHE cc_start: 0.8133 (t80) cc_final: 0.7851 (t80) REVERT: A 440 PHE cc_start: 0.8519 (m-80) cc_final: 0.7952 (m-80) REVERT: A 455 TYR cc_start: 0.8262 (m-10) cc_final: 0.8044 (m-10) REVERT: A 481 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8008 (t0) REVERT: A 523 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7305 (t0) REVERT: A 551 LYS cc_start: 0.7057 (ptmm) cc_final: 0.6832 (mmmt) REVERT: A 629 MET cc_start: 0.8643 (mmm) cc_final: 0.8396 (mmm) REVERT: A 722 ASN cc_start: 0.8025 (t0) cc_final: 0.7708 (t0) REVERT: A 922 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6952 (tt0) REVERT: B 70 MET cc_start: 0.6534 (tpp) cc_final: 0.6278 (ttm) REVERT: B 90 MET cc_start: 0.8434 (tmm) cc_final: 0.8225 (ttp) REVERT: B 165 LYS cc_start: 0.6784 (mptt) cc_final: 0.5943 (tttm) REVERT: C 49 PHE cc_start: 0.7842 (m-80) cc_final: 0.7639 (m-80) REVERT: D 62 MET cc_start: 0.6944 (tpp) cc_final: 0.6708 (ttm) REVERT: D 78 ASP cc_start: 0.6772 (t70) cc_final: 0.6433 (t0) REVERT: D 119 ILE cc_start: 0.8319 (mt) cc_final: 0.8026 (mt) REVERT: D 164 SER cc_start: 0.7483 (m) cc_final: 0.6805 (t) outliers start: 39 outliers final: 21 residues processed: 247 average time/residue: 0.0944 time to fit residues: 36.1433 Evaluate side-chains 197 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 48 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN A 613 HIS A 789 GLN B 136 ASN D 65 GLN D 158 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116600 restraints weight = 14937.099| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.62 r_work: 0.3313 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12986 Z= 0.159 Angle : 0.567 9.292 17973 Z= 0.291 Chirality : 0.040 0.218 2101 Planarity : 0.004 0.057 2007 Dihedral : 8.280 179.329 2407 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.26 % Allowed : 14.81 % Favored : 81.92 % 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: -0.52 (0.22), residues: 1365 helix: 0.50 (0.20), residues: 700 sheet: -1.03 (0.45), residues: 124 loop : -1.23 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 889 TYR 0.014 0.002 TYR A 32 PHE 0.016 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (12978) covalent geometry : angle 0.56684 / 0.29 (17967) hydrogen bonds : bond 0.03772 / 2.45 ( 631) hydrogen bonds : angle 4.05784 / 2.83 ( 1707) metal coordination : bond 0.00518 / 0.27 ( 8) metal coordination : angle 1.17541 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8395 (p0) cc_final: 0.8107 (p0) REVERT: A 196 MET cc_start: 0.8166 (mtm) cc_final: 0.7907 (mtm) REVERT: A 221 ASP cc_start: 0.8329 (p0) cc_final: 0.7995 (p0) REVERT: A 235 ASP cc_start: 0.7780 (m-30) cc_final: 0.6920 (p0) REVERT: A 246 THR cc_start: 0.7978 (p) cc_final: 0.7758 (p) REVERT: A 431 GLU cc_start: 0.6856 (tp30) cc_final: 0.6348 (tp30) REVERT: A 440 PHE cc_start: 0.8646 (m-80) cc_final: 0.7934 (m-80) REVERT: A 441 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8497 (t80) REVERT: A 551 LYS cc_start: 0.7415 (ptmm) cc_final: 0.7134 (mmtt) REVERT: A 629 MET cc_start: 0.8668 (mmm) cc_final: 0.8416 (mmm) REVERT: A 666 MET cc_start: 0.8120 (mtt) cc_final: 0.7710 (mtt) REVERT: A 668 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7418 (tmm) REVERT: A 775 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8561 (mt) REVERT: A 911 ASN cc_start: 0.7842 (p0) cc_final: 0.7617 (p0) REVERT: A 926 THR cc_start: 0.8396 (m) cc_final: 0.8041 (p) REVERT: B 143 ASP cc_start: 0.6896 (p0) cc_final: 0.6663 (t70) REVERT: B 165 LYS cc_start: 0.6698 (mptt) cc_final: 0.5923 (tttm) REVERT: C 23 GLU cc_start: 0.8757 (tt0) cc_final: 0.8553 (tt0) REVERT: D 50 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.5578 (m-30) REVERT: D 62 MET cc_start: 0.7158 (tpp) cc_final: 0.6950 (ttm) REVERT: D 70 MET cc_start: 0.7286 (tpp) cc_final: 0.6960 (mmm) REVERT: D 97 LYS cc_start: 0.8096 (tttm) cc_final: 0.7263 (mttt) REVERT: D 164 SER cc_start: 0.7112 (m) cc_final: 0.6815 (t) REVERT: D 173 SER cc_start: 0.6644 (m) cc_final: 0.6241 (p) REVERT: D 185 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7884 (mt) outliers start: 39 outliers final: 20 residues processed: 195 average time/residue: 0.0942 time to fit residues: 28.6845 Evaluate side-chains 173 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 97 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 GLN A 496 ASN A 613 HIS A 722 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114542 restraints weight = 14859.948| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.60 r_work: 0.3280 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12986 Z= 0.148 Angle : 0.549 9.262 17973 Z= 0.280 Chirality : 0.039 0.222 2101 Planarity : 0.004 0.049 2007 Dihedral : 7.987 176.992 2398 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.26 % Allowed : 15.73 % Favored : 81.00 % 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: -0.25 (0.22), residues: 1365 helix: 0.77 (0.20), residues: 698 sheet: -0.94 (0.44), residues: 126 loop : -1.15 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.013 0.001 TYR A 788 PHE 0.015 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (12978) covalent geometry : angle 0.54762 / 0.28 (17967) hydrogen bonds : bond 0.03322 / 2.19 ( 631) hydrogen bonds : angle 3.90915 / 2.73 ( 1707) metal coordination : bond 0.01428 / 0.75 ( 8) metal coordination : angle 2.08055 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8245 (p0) cc_final: 0.7941 (p0) REVERT: A 235 ASP cc_start: 0.8009 (m-30) cc_final: 0.7102 (p0) REVERT: A 431 GLU cc_start: 0.7147 (tp30) cc_final: 0.6790 (tp30) REVERT: A 440 PHE cc_start: 0.8856 (m-80) cc_final: 0.8123 (m-80) REVERT: A 551 LYS cc_start: 0.7404 (ptmm) cc_final: 0.7198 (mmtt) REVERT: A 666 MET cc_start: 0.8078 (mtt) cc_final: 0.7792 (mtt) REVERT: A 703 ASN cc_start: 0.8199 (m110) cc_final: 0.7691 (m110) REVERT: A 722 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7085 (t0) REVERT: A 750 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8132 (mmt90) REVERT: A 828 TYR cc_start: 0.9056 (m-80) cc_final: 0.8792 (m-80) REVERT: A 911 ASN cc_start: 0.7916 (p0) cc_final: 0.7650 (p0) REVERT: A 926 THR cc_start: 0.8598 (m) cc_final: 0.8154 (p) REVERT: B 92 PHE cc_start: 0.6595 (m-80) cc_final: 0.6324 (m-80) REVERT: B 165 LYS cc_start: 0.6975 (mptt) cc_final: 0.6156 (tttm) REVERT: D 50 ASP cc_start: 0.6693 (t0) cc_final: 0.5654 (m-30) REVERT: D 62 MET cc_start: 0.7125 (tpp) cc_final: 0.6711 (ttp) REVERT: D 70 MET cc_start: 0.7113 (tpp) cc_final: 0.6852 (mmm) REVERT: D 78 ASP cc_start: 0.7069 (t70) cc_final: 0.6738 (t0) REVERT: D 97 LYS cc_start: 0.8304 (tttm) cc_final: 0.8038 (ttmm) REVERT: D 164 SER cc_start: 0.7334 (m) cc_final: 0.6663 (t) REVERT: D 185 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7920 (mt) outliers start: 39 outliers final: 22 residues processed: 182 average time/residue: 0.0985 time to fit residues: 27.4741 Evaluate side-chains 158 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A 613 HIS A 703 ASN A 722 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113759 restraints weight = 14855.282| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.61 r_work: 0.3241 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12986 Z= 0.136 Angle : 0.520 7.920 17973 Z= 0.266 Chirality : 0.039 0.218 2101 Planarity : 0.003 0.047 2007 Dihedral : 7.897 170.705 2398 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.43 % Allowed : 16.40 % Favored : 80.17 % 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: -0.04 (0.23), residues: 1365 helix: 0.92 (0.20), residues: 699 sheet: -0.81 (0.45), residues: 126 loop : -1.03 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 726 TYR 0.014 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12978) covalent geometry : angle 0.51921 / 0.27 (17967) hydrogen bonds : bond 0.03257 / 2.15 ( 631) hydrogen bonds : angle 3.83918 / 2.69 ( 1707) metal coordination : bond 0.00512 / 0.27 ( 8) metal coordination : angle 1.52277 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.428 Fit side-chains REVERT: A 235 ASP cc_start: 0.7959 (m-30) cc_final: 0.7125 (p0) REVERT: A 431 GLU cc_start: 0.7253 (tp30) cc_final: 0.7026 (tp30) REVERT: A 440 PHE cc_start: 0.8858 (m-80) cc_final: 0.8060 (m-80) REVERT: A 522 GLU cc_start: 0.8048 (tt0) cc_final: 0.7847 (tt0) REVERT: A 608 ASP cc_start: 0.7628 (t0) cc_final: 0.7266 (t0) REVERT: A 666 MET cc_start: 0.8128 (mtt) cc_final: 0.7818 (mtt) REVERT: A 668 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7669 (tmm) REVERT: A 718 LYS cc_start: 0.7792 (tptp) cc_final: 0.7584 (tptp) REVERT: A 750 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7956 (mmt90) REVERT: A 911 ASN cc_start: 0.7949 (p0) cc_final: 0.7726 (p0) REVERT: A 926 THR cc_start: 0.8574 (m) cc_final: 0.8158 (p) REVERT: B 157 GLN cc_start: 0.8325 (mt0) cc_final: 0.7786 (tt0) REVERT: C 21 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7776 (tpp-160) REVERT: C 75 MET cc_start: 0.4215 (ptt) cc_final: 0.3980 (ptt) REVERT: D 50 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.5842 (m-30) REVERT: D 62 MET cc_start: 0.7399 (tpp) cc_final: 0.6983 (ttp) REVERT: D 70 MET cc_start: 0.7198 (tpp) cc_final: 0.6913 (ttm) REVERT: D 78 ASP cc_start: 0.7212 (t70) cc_final: 0.6943 (t0) REVERT: D 97 LYS cc_start: 0.8391 (tttm) cc_final: 0.8028 (ttmm) REVERT: D 164 SER cc_start: 0.7335 (m) cc_final: 0.6936 (t) outliers start: 41 outliers final: 19 residues processed: 171 average time/residue: 0.1084 time to fit residues: 27.5670 Evaluate side-chains 154 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 497 ASN A 613 HIS D 43 ASN D 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112017 restraints weight = 14749.757| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.64 r_work: 0.3212 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12986 Z= 0.145 Angle : 0.517 7.402 17973 Z= 0.266 Chirality : 0.039 0.219 2101 Planarity : 0.003 0.045 2007 Dihedral : 7.809 164.655 2398 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.68 % Allowed : 16.40 % Favored : 79.92 % 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: 0.05 (0.23), residues: 1365 helix: 1.00 (0.20), residues: 705 sheet: -0.78 (0.43), residues: 136 loop : -1.01 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.013 0.001 TYR A 788 PHE 0.015 0.001 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (12978) covalent geometry : angle 0.51595 / 0.27 (17967) hydrogen bonds : bond 0.03248 / 2.12 ( 631) hydrogen bonds : angle 3.79882 / 2.65 ( 1707) metal coordination : bond 0.00676 / 0.36 ( 8) metal coordination : angle 1.65060 / 0.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.430 Fit side-chains REVERT: A 40 ASP cc_start: 0.8243 (m-30) cc_final: 0.7801 (p0) REVERT: A 235 ASP cc_start: 0.7913 (m-30) cc_final: 0.7041 (p0) REVERT: A 268 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.5216 (m-90) REVERT: A 277 GLU cc_start: 0.7646 (tp30) cc_final: 0.7129 (mp0) REVERT: A 404 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8181 (p0) REVERT: A 431 GLU cc_start: 0.7116 (tp30) cc_final: 0.6913 (tp30) REVERT: A 522 GLU cc_start: 0.8001 (tt0) cc_final: 0.7787 (tt0) REVERT: A 608 ASP cc_start: 0.7700 (t0) cc_final: 0.7286 (t0) REVERT: A 668 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7686 (tmm) REVERT: A 722 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7145 (m-40) REVERT: A 865 ASP cc_start: 0.8014 (m-30) cc_final: 0.7693 (m-30) REVERT: A 906 MET cc_start: 0.6998 (mtt) cc_final: 0.6786 (mtp) REVERT: A 911 ASN cc_start: 0.7841 (p0) cc_final: 0.7599 (p0) REVERT: B 157 GLN cc_start: 0.8290 (mt0) cc_final: 0.7741 (tt0) REVERT: C 21 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (tpp-160) REVERT: D 50 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.5889 (m-30) REVERT: D 62 MET cc_start: 0.7387 (tpp) cc_final: 0.7008 (ttp) REVERT: D 78 ASP cc_start: 0.7362 (t70) cc_final: 0.7096 (t0) REVERT: D 164 SER cc_start: 0.7299 (m) cc_final: 0.6664 (t) REVERT: D 180 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5276 (tt) outliers start: 44 outliers final: 24 residues processed: 162 average time/residue: 0.1066 time to fit residues: 25.9617 Evaluate side-chains 159 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 78 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 408 GLN A 613 HIS D 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109985 restraints weight = 14806.300| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.64 r_work: 0.3166 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.8386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12986 Z= 0.173 Angle : 0.545 7.408 17973 Z= 0.280 Chirality : 0.040 0.220 2101 Planarity : 0.003 0.046 2007 Dihedral : 7.797 157.291 2397 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.68 % Allowed : 17.15 % Favored : 79.16 % 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: 0.00 (0.23), residues: 1365 helix: 0.98 (0.20), residues: 704 sheet: -0.82 (0.42), residues: 141 loop : -1.05 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 750 TYR 0.013 0.001 TYR A 80 PHE 0.015 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (12978) covalent geometry : angle 0.54391 / 0.28 (17967) hydrogen bonds : bond 0.03441 / 2.26 ( 631) hydrogen bonds : angle 3.84632 / 2.69 ( 1707) metal coordination : bond 0.00663 / 0.35 ( 8) metal coordination : angle 1.75002 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.436 Fit side-chains REVERT: A 40 ASP cc_start: 0.8347 (m-30) cc_final: 0.7908 (p0) REVERT: A 235 ASP cc_start: 0.8038 (m-30) cc_final: 0.7212 (p0) REVERT: A 268 TRP cc_start: 0.8142 (OUTLIER) cc_final: 0.5310 (m-90) REVERT: A 277 GLU cc_start: 0.7688 (tp30) cc_final: 0.7176 (mp0) REVERT: A 404 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8214 (p0) REVERT: A 430 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6916 (mmtp) REVERT: A 431 GLU cc_start: 0.7235 (tp30) cc_final: 0.7024 (tp30) REVERT: A 608 ASP cc_start: 0.7747 (t0) cc_final: 0.7343 (t0) REVERT: A 668 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7699 (tmm) REVERT: A 815 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: A 865 ASP cc_start: 0.7916 (m-30) cc_final: 0.7541 (m-30) REVERT: A 911 ASN cc_start: 0.7802 (p0) cc_final: 0.7578 (p0) REVERT: B 157 GLN cc_start: 0.8302 (mt0) cc_final: 0.7789 (tt0) REVERT: C 21 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7857 (tpp-160) REVERT: C 43 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8286 (mmmt) REVERT: D 50 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.5921 (m-30) REVERT: D 62 MET cc_start: 0.7339 (tpp) cc_final: 0.6957 (ttp) REVERT: D 78 ASP cc_start: 0.7619 (t70) cc_final: 0.7300 (t0) REVERT: D 164 SER cc_start: 0.7284 (m) cc_final: 0.6862 (t) REVERT: D 180 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5472 (tt) outliers start: 44 outliers final: 31 residues processed: 162 average time/residue: 0.0992 time to fit residues: 24.5364 Evaluate side-chains 165 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110741 restraints weight = 14684.704| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.63 r_work: 0.3196 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.8650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12986 Z= 0.141 Angle : 0.522 7.287 17973 Z= 0.266 Chirality : 0.039 0.219 2101 Planarity : 0.003 0.045 2007 Dihedral : 7.701 150.815 2397 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.35 % Allowed : 17.82 % Favored : 78.83 % 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: 0.10 (0.23), residues: 1365 helix: 1.07 (0.20), residues: 702 sheet: -0.84 (0.42), residues: 141 loop : -1.00 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 750 TYR 0.013 0.001 TYR A 788 PHE 0.014 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12978) covalent geometry : angle 0.52066 / 0.27 (17967) hydrogen bonds : bond 0.03231 / 2.11 ( 631) hydrogen bonds : angle 3.76185 / 2.63 ( 1707) metal coordination : bond 0.00614 / 0.32 ( 8) metal coordination : angle 1.77425 / 0.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.457 Fit side-chains REVERT: A 40 ASP cc_start: 0.8387 (m-30) cc_final: 0.7890 (p0) REVERT: A 235 ASP cc_start: 0.7803 (m-30) cc_final: 0.7087 (p0) REVERT: A 268 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.5270 (m-90) REVERT: A 277 GLU cc_start: 0.7738 (tp30) cc_final: 0.7259 (mp0) REVERT: A 332 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7768 (ttmm) REVERT: A 430 LYS cc_start: 0.7278 (mmtt) cc_final: 0.6965 (mmtp) REVERT: A 431 GLU cc_start: 0.7205 (tp30) cc_final: 0.6967 (tp30) REVERT: A 608 ASP cc_start: 0.7728 (t0) cc_final: 0.7280 (t0) REVERT: A 668 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7734 (tmm) REVERT: A 815 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: A 865 ASP cc_start: 0.7868 (m-30) cc_final: 0.7510 (m-30) REVERT: A 911 ASN cc_start: 0.7803 (p0) cc_final: 0.7585 (p0) REVERT: B 67 MET cc_start: 0.5038 (tpp) cc_final: 0.4040 (tmm) REVERT: B 157 GLN cc_start: 0.8418 (mt0) cc_final: 0.7786 (tt0) REVERT: B 164 SER cc_start: 0.8321 (t) cc_final: 0.8104 (m) REVERT: B 174 MET cc_start: 0.8052 (mmt) cc_final: 0.7542 (tpt) REVERT: C 43 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8309 (mmmt) REVERT: D 50 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6255 (m-30) REVERT: D 62 MET cc_start: 0.7324 (tpp) cc_final: 0.6968 (ttp) REVERT: D 97 LYS cc_start: 0.8323 (tttm) cc_final: 0.7933 (ttmm) REVERT: D 164 SER cc_start: 0.7070 (m) cc_final: 0.6543 (t) REVERT: D 180 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5271 (tt) outliers start: 40 outliers final: 25 residues processed: 157 average time/residue: 0.1082 time to fit residues: 25.3067 Evaluate side-chains 163 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 408 GLN A 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.148263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111653 restraints weight = 14773.685| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.64 r_work: 0.3111 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.8806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12986 Z= 0.122 Angle : 0.509 7.323 17973 Z= 0.260 Chirality : 0.038 0.217 2101 Planarity : 0.003 0.044 2007 Dihedral : 7.605 143.561 2397 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.01 % Allowed : 17.82 % Favored : 79.16 % 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: 0.25 (0.23), residues: 1365 helix: 1.16 (0.20), residues: 703 sheet: -0.84 (0.42), residues: 141 loop : -0.85 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 750 TYR 0.014 0.001 TYR A 788 PHE 0.013 0.001 PHE D 92 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12978) covalent geometry : angle 0.50834 / 0.26 (17967) hydrogen bonds : bond 0.03102 / 2.03 ( 631) hydrogen bonds : angle 3.69355 / 2.59 ( 1707) metal coordination : bond 0.00483 / 0.25 ( 8) metal coordination : angle 1.66591 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.442 Fit side-chains REVERT: A 40 ASP cc_start: 0.8379 (m-30) cc_final: 0.7938 (p0) REVERT: A 235 ASP cc_start: 0.7868 (m-30) cc_final: 0.7159 (p0) REVERT: A 268 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.5446 (m-90) REVERT: A 277 GLU cc_start: 0.7803 (tp30) cc_final: 0.7307 (mp0) REVERT: A 332 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7819 (ttmm) REVERT: A 430 LYS cc_start: 0.7305 (mmtt) cc_final: 0.6821 (mttt) REVERT: A 431 GLU cc_start: 0.7217 (tp30) cc_final: 0.6386 (tt0) REVERT: A 608 ASP cc_start: 0.7691 (t0) cc_final: 0.7244 (t0) REVERT: A 668 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7757 (tmm) REVERT: A 815 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: A 865 ASP cc_start: 0.7974 (m-30) cc_final: 0.7603 (m-30) REVERT: A 883 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7489 (tp) REVERT: A 911 ASN cc_start: 0.7830 (p0) cc_final: 0.7566 (p0) REVERT: B 67 MET cc_start: 0.5130 (tpp) cc_final: 0.4145 (tmm) REVERT: B 157 GLN cc_start: 0.8470 (mt0) cc_final: 0.7870 (tt0) REVERT: B 174 MET cc_start: 0.8105 (mmt) cc_final: 0.7613 (tpt) REVERT: C 43 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8319 (mmmt) REVERT: D 50 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6457 (m-30) REVERT: D 62 MET cc_start: 0.7404 (tpp) cc_final: 0.7066 (ttp) REVERT: D 78 ASP cc_start: 0.7803 (t70) cc_final: 0.7478 (t0) REVERT: D 97 LYS cc_start: 0.8297 (tttm) cc_final: 0.7923 (ttmm) REVERT: D 164 SER cc_start: 0.7159 (m) cc_final: 0.6729 (t) REVERT: D 180 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5100 (tt) outliers start: 36 outliers final: 25 residues processed: 166 average time/residue: 0.1125 time to fit residues: 27.5812 Evaluate side-chains 160 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 27 optimal weight: 0.0040 chunk 14 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111700 restraints weight = 14769.043| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.64 r_work: 0.3193 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.8914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12986 Z= 0.118 Angle : 0.508 7.332 17973 Z= 0.260 Chirality : 0.038 0.217 2101 Planarity : 0.003 0.044 2007 Dihedral : 7.533 136.901 2397 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.85 % Allowed : 18.24 % Favored : 78.91 % 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: 0.31 (0.23), residues: 1365 helix: 1.21 (0.20), residues: 704 sheet: -0.81 (0.42), residues: 141 loop : -0.83 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 80 TYR 0.014 0.001 TYR A 788 PHE 0.013 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12978) covalent geometry : angle 0.50729 / 0.26 (17967) hydrogen bonds : bond 0.03076 / 2.02 ( 631) hydrogen bonds : angle 3.65804 / 2.56 ( 1707) metal coordination : bond 0.00491 / 0.26 ( 8) metal coordination : angle 1.59691 / 0.84 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.443 Fit side-chains REVERT: A 40 ASP cc_start: 0.8351 (m-30) cc_final: 0.7944 (p0) REVERT: A 235 ASP cc_start: 0.7834 (m-30) cc_final: 0.7134 (p0) REVERT: A 268 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.5429 (m-90) REVERT: A 277 GLU cc_start: 0.7748 (tp30) cc_final: 0.7243 (mp0) REVERT: A 332 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7874 (ttmm) REVERT: A 430 LYS cc_start: 0.7223 (mmtt) cc_final: 0.6786 (mttt) REVERT: A 431 GLU cc_start: 0.7224 (tp30) cc_final: 0.6395 (tt0) REVERT: A 553 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7888 (mtm-85) REVERT: A 608 ASP cc_start: 0.7694 (t0) cc_final: 0.7202 (t0) REVERT: A 668 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7779 (tmm) REVERT: A 815 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: A 865 ASP cc_start: 0.7883 (m-30) cc_final: 0.7536 (m-30) REVERT: A 883 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7455 (tp) REVERT: A 911 ASN cc_start: 0.7765 (p0) cc_final: 0.7512 (p0) REVERT: B 67 MET cc_start: 0.5078 (tpp) cc_final: 0.4118 (tmm) REVERT: B 157 GLN cc_start: 0.8478 (mt0) cc_final: 0.7894 (tt0) REVERT: B 174 MET cc_start: 0.8131 (mmt) cc_final: 0.7659 (tpt) REVERT: C 43 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8310 (mmmt) REVERT: D 50 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6486 (m-30) REVERT: D 62 MET cc_start: 0.7315 (tpp) cc_final: 0.7008 (ttp) REVERT: D 70 MET cc_start: 0.7856 (ttm) cc_final: 0.7650 (ttm) REVERT: D 78 ASP cc_start: 0.7586 (t70) cc_final: 0.7273 (t0) REVERT: D 97 LYS cc_start: 0.8245 (tttm) cc_final: 0.7873 (ttmm) REVERT: D 164 SER cc_start: 0.7191 (m) cc_final: 0.6752 (t) outliers start: 34 outliers final: 25 residues processed: 157 average time/residue: 0.1056 time to fit residues: 25.1041 Evaluate side-chains 154 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS D 65 GLN D 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107460 restraints weight = 14873.632| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.64 r_work: 0.3100 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.9156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12986 Z= 0.200 Angle : 0.587 10.784 17973 Z= 0.298 Chirality : 0.042 0.221 2101 Planarity : 0.004 0.051 2007 Dihedral : 7.702 124.171 2397 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.35 % Allowed : 17.74 % Favored : 78.91 % 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: -0.02 (0.23), residues: 1365 helix: 0.95 (0.20), residues: 705 sheet: -1.00 (0.42), residues: 138 loop : -0.99 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 750 TYR 0.014 0.002 TYR A 831 PHE 0.017 0.002 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (12978) covalent geometry : angle 0.58615 / 0.30 (17967) hydrogen bonds : bond 0.03695 / 2.46 ( 631) hydrogen bonds : angle 3.87958 / 2.71 ( 1707) metal coordination : bond 0.00858 / 0.45 ( 8) metal coordination : angle 1.94142 / 1.17 ( 6) =============================================================================== Job complete usr+sys time: 3539.91 seconds wall clock time: 61 minutes 36.83 seconds (3696.83 seconds total)