Starting phenix.real_space_refine on Thu Jul 31 03:28:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7krp_23009/07_2025/7krp_23009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7krp_23009/07_2025/7krp_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_2025/7krp_23009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2025/7krp_23009.map" model { file = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2025/7krp_23009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7krp_23009/07_2025/7krp_23009.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ASN:plan1': 1, 'GLN: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: 20 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: 6 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: 7.82, per 1000 atoms: 0.62 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: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 5.11 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: 5.06 Time building geometry restraints manager: 3.52 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: 7630 30.57 - 61.15: 311 61.15 - 91.72: 65 91.72 - 122.29: 20 122.29 - 152.87: 5 Dihedral angle restraints: 8031 sinusoidal: 3950 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 8028 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.370 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 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 : 17.525 152.867 5389 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.013 0.002 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 726 Details of bonding type rmsd hydrogen bonds : bond 0.14086 ( 631) hydrogen bonds : angle 5.95361 ( 1707) metal coordination : bond 0.00630 ( 8) metal coordination : angle 1.60078 ( 6) covalent geometry : bond 0.00615 (12978) covalent geometry : angle 0.69138 (17967) *********************** 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 : 1.296 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: 0.7102 (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: 0.4996 (t0) outliers start: 50 outliers final: 13 residues processed: 379 average time/residue: 0.2717 time to fit residues: 146.5067 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 : 1.023 ------------------------------------------------------------------------------- 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 119 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 703 ASN 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 = 0.3865 r_free = 0.3865 target = 0.155952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121452 restraints weight = 14940.429| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.48 r_work: 0.3199 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12986 Z= 0.288 Angle : 0.831 13.926 17973 Z= 0.422 Chirality : 0.050 0.313 2101 Planarity : 0.006 0.067 2007 Dihedral : 15.953 162.079 2868 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.77 % Allowed : 13.39 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1365 helix: -0.30 (0.19), residues: 687 sheet: -1.49 (0.44), residues: 125 loop : -1.64 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 182 HIS 0.009 0.002 HIS A 362 PHE 0.024 0.003 PHE D 15 TYR 0.042 0.003 TYR A 32 ARG 0.007 0.001 ARG A 750 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 631) hydrogen bonds : angle 4.76482 ( 1707) metal coordination : bond 0.00894 ( 8) metal coordination : angle 2.89824 ( 6) covalent geometry : bond 0.00646 (12978) covalent geometry : angle 0.82943 (17967) *********************** 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 215 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.8381 (p0) cc_final: 0.7999 (p0) REVERT: A 235 ASP cc_start: 0.7852 (m-30) cc_final: 0.7056 (p0) REVERT: A 251 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 277 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7497 (tp30) REVERT: A 431 GLU cc_start: 0.6955 (tp30) cc_final: 0.6728 (tp30) REVERT: A 440 PHE cc_start: 0.9154 (m-80) cc_final: 0.8792 (m-80) REVERT: A 481 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8008 (t0) REVERT: A 523 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7277 (t0) REVERT: A 551 LYS cc_start: 0.7411 (ptmm) cc_final: 0.7142 (mmmt) REVERT: A 668 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7404 (tmm) REVERT: A 718 LYS cc_start: 0.8166 (tptt) cc_final: 0.7929 (tptp) REVERT: A 722 ASN cc_start: 0.7954 (t0) cc_final: 0.7500 (t0) REVERT: A 824 ASP cc_start: 0.7760 (p0) cc_final: 0.7447 (t70) REVERT: A 857 GLU cc_start: 0.6960 (mp0) cc_final: 0.6741 (tp30) REVERT: A 926 THR cc_start: 0.8525 (m) cc_final: 0.8285 (p) REVERT: B 165 LYS cc_start: 0.6746 (mptt) cc_final: 0.5824 (tttm) REVERT: B 174 MET cc_start: 0.7595 (mmt) cc_final: 0.7232 (tpt) REVERT: D 50 ASP cc_start: 0.6853 (t0) cc_final: 0.5781 (m-30) REVERT: D 62 MET cc_start: 0.7329 (tpp) cc_final: 0.7097 (ttm) REVERT: D 78 ASP cc_start: 0.7032 (t70) cc_final: 0.6664 (t0) REVERT: D 97 LYS cc_start: 0.8176 (tttm) cc_final: 0.7524 (mttt) outliers start: 45 outliers final: 22 residues processed: 207 average time/residue: 0.2187 time to fit residues: 68.8778 Evaluate side-chains 163 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain A residue 262 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 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 668 MET Chi-restraints excluded: chain A residue 723 LEU 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 124 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 157 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 131 optimal weight: 0.0020 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 210 GLN A 312 ASN A 496 ASN A 497 ASN A 613 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115908 restraints weight = 14960.142| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.62 r_work: 0.3281 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.6671 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= 0.129 Angle : 0.539 8.654 17973 Z= 0.277 Chirality : 0.039 0.222 2101 Planarity : 0.004 0.053 2007 Dihedral : 15.319 138.119 2853 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.26 % Allowed : 14.90 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1365 helix: 0.39 (0.20), residues: 699 sheet: -1.12 (0.45), residues: 124 loop : -1.39 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.014 0.001 PHE D 92 TYR 0.012 0.001 TYR A 788 ARG 0.004 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 631) hydrogen bonds : angle 4.12998 ( 1707) metal coordination : bond 0.00507 ( 8) metal coordination : angle 1.49414 ( 6) covalent geometry : bond 0.00287 (12978) covalent geometry : angle 0.53830 (17967) *********************** 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 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.268 Fit side-chains REVERT: A 69 TYR cc_start: 0.8726 (m-80) cc_final: 0.8501 (m-80) REVERT: A 161 ASP cc_start: 0.8529 (p0) cc_final: 0.8237 (p0) REVERT: A 221 ASP cc_start: 0.8240 (p0) cc_final: 0.7912 (p0) REVERT: A 235 ASP cc_start: 0.7777 (m-30) cc_final: 0.6993 (p0) REVERT: A 277 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7195 (tp30) REVERT: A 551 LYS cc_start: 0.7323 (ptmm) cc_final: 0.7063 (mmtt) REVERT: A 666 MET cc_start: 0.8172 (mtt) cc_final: 0.7639 (mtt) REVERT: A 718 LYS cc_start: 0.7842 (tptt) cc_final: 0.7563 (tptp) REVERT: A 722 ASN cc_start: 0.7739 (t0) cc_final: 0.7372 (t0) REVERT: A 824 ASP cc_start: 0.7894 (p0) cc_final: 0.7379 (t70) REVERT: A 857 GLU cc_start: 0.7003 (mp0) cc_final: 0.6591 (tp30) REVERT: A 911 ASN cc_start: 0.7843 (p0) cc_final: 0.7635 (p0) REVERT: A 926 THR cc_start: 0.8577 (m) cc_final: 0.8204 (p) REVERT: B 105 ASN cc_start: 0.7106 (t0) cc_final: 0.6885 (t0) REVERT: B 165 LYS cc_start: 0.6670 (mptt) cc_final: 0.5959 (tttm) REVERT: B 174 MET cc_start: 0.7661 (mmt) cc_final: 0.7117 (tpt) REVERT: C 38 ASP cc_start: 0.8196 (m-30) cc_final: 0.7858 (m-30) REVERT: D 50 ASP cc_start: 0.6701 (t0) cc_final: 0.5678 (m-30) REVERT: D 62 MET cc_start: 0.7206 (tpp) cc_final: 0.6971 (ttm) REVERT: D 70 MET cc_start: 0.6952 (tpp) cc_final: 0.6670 (mmm) REVERT: D 78 ASP cc_start: 0.6958 (t70) cc_final: 0.6594 (t0) REVERT: D 97 LYS cc_start: 0.8275 (tttm) cc_final: 0.7450 (mttt) REVERT: D 112 ASP cc_start: 0.7529 (m-30) cc_final: 0.7284 (m-30) REVERT: D 164 SER cc_start: 0.7110 (m) cc_final: 0.6603 (t) outliers start: 27 outliers final: 12 residues processed: 163 average time/residue: 0.2674 time to fit residues: 65.7398 Evaluate side-chains 136 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 95 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 136 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 613 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.148178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111758 restraints weight = 14692.627| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.65 r_work: 0.3210 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12986 Z= 0.175 Angle : 0.557 8.246 17973 Z= 0.288 Chirality : 0.040 0.224 2101 Planarity : 0.004 0.050 2007 Dihedral : 15.029 164.631 2847 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.35 % Allowed : 15.06 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1365 helix: 0.57 (0.20), residues: 698 sheet: -1.09 (0.44), residues: 126 loop : -1.28 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.002 PHE D 92 TYR 0.014 0.001 TYR A 32 ARG 0.003 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 631) hydrogen bonds : angle 4.03607 ( 1707) metal coordination : bond 0.00957 ( 8) metal coordination : angle 1.75618 ( 6) covalent geometry : bond 0.00404 (12978) covalent geometry : angle 0.55580 (17967) *********************** 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 177 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7968 (m-30) cc_final: 0.7078 (p0) REVERT: A 277 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6950 (mp0) REVERT: A 497 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8022 (t0) REVERT: A 551 LYS cc_start: 0.7448 (ptmm) cc_final: 0.7244 (mmtt) REVERT: A 608 ASP cc_start: 0.7713 (t0) cc_final: 0.7316 (t0) REVERT: A 718 LYS cc_start: 0.7520 (tptt) cc_final: 0.7196 (tptp) REVERT: A 722 ASN cc_start: 0.7638 (t0) cc_final: 0.7323 (t0) REVERT: A 824 ASP cc_start: 0.8042 (p0) cc_final: 0.7528 (t70) REVERT: A 857 GLU cc_start: 0.7300 (mp0) cc_final: 0.6794 (tp30) REVERT: A 911 ASN cc_start: 0.7911 (p0) cc_final: 0.7681 (p0) REVERT: A 913 SER cc_start: 0.8570 (m) cc_final: 0.8183 (t) REVERT: A 926 THR cc_start: 0.8705 (m) cc_final: 0.8251 (p) REVERT: B 165 LYS cc_start: 0.6708 (mptt) cc_final: 0.6092 (tttm) REVERT: B 174 MET cc_start: 0.7885 (mmt) cc_final: 0.7295 (tpt) REVERT: D 50 ASP cc_start: 0.6821 (t0) cc_final: 0.5860 (m-30) REVERT: D 62 MET cc_start: 0.7348 (tpp) cc_final: 0.7107 (ttm) REVERT: D 70 MET cc_start: 0.7129 (tpp) cc_final: 0.6860 (ttm) REVERT: D 97 LYS cc_start: 0.8326 (tttm) cc_final: 0.7969 (ttmm) REVERT: D 164 SER cc_start: 0.7132 (m) cc_final: 0.6632 (t) outliers start: 40 outliers final: 28 residues processed: 161 average time/residue: 0.3114 time to fit residues: 75.5384 Evaluate side-chains 158 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN 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 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ILE 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 667 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 3 optimal weight: 0.0870 chunk 115 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 408 GLN A 497 ASN A 791 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 = 0.3764 r_free = 0.3764 target = 0.146495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.109837 restraints weight = 14769.207| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.65 r_work: 0.3150 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.8212 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= 0.171 Angle : 0.550 7.854 17973 Z= 0.284 Chirality : 0.040 0.222 2101 Planarity : 0.003 0.048 2007 Dihedral : 15.000 174.189 2847 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.02 % Allowed : 14.56 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1365 helix: 0.71 (0.20), residues: 696 sheet: -1.11 (0.43), residues: 136 loop : -1.24 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.002 PHE A 741 TYR 0.013 0.001 TYR A 80 ARG 0.005 0.001 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 631) hydrogen bonds : angle 4.02138 ( 1707) metal coordination : bond 0.00722 ( 8) metal coordination : angle 1.81827 ( 6) covalent geometry : bond 0.00397 (12978) covalent geometry : angle 0.54923 (17967) *********************** 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: 48 poor density : 135 time to evaluate : 1.149 Fit side-chains REVERT: A 235 ASP cc_start: 0.7967 (m-30) cc_final: 0.7149 (p0) REVERT: A 268 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.5356 (m-90) REVERT: A 277 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7118 (mp0) REVERT: A 404 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8152 (p0) REVERT: A 430 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6794 (mmtp) REVERT: A 431 GLU cc_start: 0.7414 (tp30) cc_final: 0.6511 (tt0) REVERT: A 444 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8019 (mm-40) REVERT: A 534 ASN cc_start: 0.8987 (m-40) cc_final: 0.8623 (m-40) REVERT: A 608 ASP cc_start: 0.7742 (t0) cc_final: 0.7293 (t0) REVERT: A 666 MET cc_start: 0.8143 (mtt) cc_final: 0.7636 (mtt) REVERT: A 722 ASN cc_start: 0.7743 (t0) cc_final: 0.7180 (m-40) REVERT: A 824 ASP cc_start: 0.8003 (p0) cc_final: 0.7207 (t0) REVERT: A 857 GLU cc_start: 0.7581 (mp0) cc_final: 0.6925 (tp30) REVERT: A 865 ASP cc_start: 0.8054 (m-30) cc_final: 0.7789 (m-30) REVERT: B 157 GLN cc_start: 0.8312 (mt0) cc_final: 0.7809 (tt0) REVERT: B 164 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8042 (m) REVERT: B 174 MET cc_start: 0.8073 (mmt) cc_final: 0.7517 (tpt) REVERT: C 10 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8668 (p) REVERT: C 21 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7798 (tpp-160) REVERT: C 43 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8131 (mmmt) REVERT: D 50 ASP cc_start: 0.6998 (t0) cc_final: 0.6185 (m-30) REVERT: D 62 MET cc_start: 0.7418 (tpp) cc_final: 0.7060 (ttp) REVERT: D 78 ASP cc_start: 0.7605 (t70) cc_final: 0.7330 (t0) REVERT: D 164 SER cc_start: 0.7050 (m) cc_final: 0.6631 (t) REVERT: D 180 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5634 (tt) outliers start: 48 outliers final: 28 residues processed: 172 average time/residue: 0.2167 time to fit residues: 56.2254 Evaluate side-chains 160 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 223 ILE 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 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 495 VAL 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 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 9 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 164 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 42 optimal weight: 0.0970 chunk 135 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 497 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111770 restraints weight = 14897.305| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.60 r_work: 0.3206 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.8428 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= 0.125 Angle : 0.499 7.676 17973 Z= 0.258 Chirality : 0.038 0.219 2101 Planarity : 0.003 0.043 2007 Dihedral : 14.911 174.121 2847 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.59 % Allowed : 16.90 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1365 helix: 0.95 (0.20), residues: 696 sheet: -0.96 (0.43), residues: 136 loop : -1.14 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.006 0.000 ARG A 750 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 631) hydrogen bonds : angle 3.86600 ( 1707) metal coordination : bond 0.00596 ( 8) metal coordination : angle 1.69261 ( 6) covalent geometry : bond 0.00282 (12978) covalent geometry : angle 0.49862 (17967) *********************** 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 167 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.285 Fit side-chains REVERT: A 235 ASP cc_start: 0.8015 (m-30) cc_final: 0.7303 (p0) REVERT: A 268 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.5421 (m-90) REVERT: A 277 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7110 (mp0) REVERT: A 332 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7791 (ttmm) REVERT: A 430 LYS cc_start: 0.7235 (mmtt) cc_final: 0.6942 (mmtp) REVERT: A 431 GLU cc_start: 0.7387 (tp30) cc_final: 0.6513 (tt0) REVERT: A 444 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: A 534 ASN cc_start: 0.8933 (m-40) cc_final: 0.8546 (m-40) REVERT: A 608 ASP cc_start: 0.7733 (t0) cc_final: 0.7280 (t0) REVERT: A 722 ASN cc_start: 0.7709 (t0) cc_final: 0.7183 (m-40) REVERT: A 824 ASP cc_start: 0.7975 (p0) cc_final: 0.7227 (t0) REVERT: A 857 GLU cc_start: 0.7761 (mp0) cc_final: 0.6790 (tp30) REVERT: A 865 ASP cc_start: 0.7991 (m-30) cc_final: 0.7712 (m-30) REVERT: B 157 GLN cc_start: 0.8484 (mt0) cc_final: 0.7857 (tt0) REVERT: B 164 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.8091 (m) REVERT: B 174 MET cc_start: 0.8069 (mmt) cc_final: 0.7553 (tpt) REVERT: C 21 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7833 (tpp-160) REVERT: C 43 LYS cc_start: 0.8458 (mmtm) cc_final: 0.8076 (mmmt) REVERT: D 50 ASP cc_start: 0.7082 (t0) cc_final: 0.6453 (m-30) REVERT: D 62 MET cc_start: 0.7372 (tpp) cc_final: 0.7043 (ttp) REVERT: D 78 ASP cc_start: 0.7730 (t70) cc_final: 0.7476 (t0) REVERT: D 97 LYS cc_start: 0.8359 (tttm) cc_final: 0.7904 (ttmm) REVERT: D 164 SER cc_start: 0.7142 (m) cc_final: 0.6717 (t) REVERT: D 180 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5251 (tt) outliers start: 31 outliers final: 20 residues processed: 157 average time/residue: 0.2405 time to fit residues: 56.3873 Evaluate side-chains 156 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 223 ILE 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 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 444 GLN 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 710 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 87 MET 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 21 ARG Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 0.0030 chunk 87 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 0.0050 chunk 43 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.149506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112754 restraints weight = 14788.316| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.65 r_work: 0.3156 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.8537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12986 Z= 0.106 Angle : 0.488 7.640 17973 Z= 0.252 Chirality : 0.037 0.217 2101 Planarity : 0.003 0.041 2007 Dihedral : 14.799 159.287 2847 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.18 % Allowed : 16.49 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1365 helix: 1.12 (0.20), residues: 695 sheet: -0.92 (0.41), residues: 141 loop : -1.05 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.013 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG A 750 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 631) hydrogen bonds : angle 3.76989 ( 1707) metal coordination : bond 0.00500 ( 8) metal coordination : angle 1.53399 ( 6) covalent geometry : bond 0.00230 (12978) covalent geometry : angle 0.48772 (17967) *********************** 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 171 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.566 Fit side-chains REVERT: A 235 ASP cc_start: 0.7821 (m-30) cc_final: 0.7088 (p0) REVERT: A 277 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7032 (mp0) REVERT: A 332 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7761 (ttmm) REVERT: A 430 LYS cc_start: 0.7186 (mmtt) cc_final: 0.6908 (mmtp) REVERT: A 431 GLU cc_start: 0.7397 (tp30) cc_final: 0.6487 (tt0) REVERT: A 534 ASN cc_start: 0.8920 (m-40) cc_final: 0.8546 (m-40) REVERT: A 608 ASP cc_start: 0.7719 (t0) cc_final: 0.7285 (t0) REVERT: A 666 MET cc_start: 0.8150 (mtt) cc_final: 0.7607 (mtt) REVERT: A 722 ASN cc_start: 0.7624 (t0) cc_final: 0.7092 (m-40) REVERT: A 824 ASP cc_start: 0.7979 (p0) cc_final: 0.7719 (t70) REVERT: A 857 GLU cc_start: 0.7733 (mp0) cc_final: 0.6706 (tp30) REVERT: A 865 ASP cc_start: 0.7957 (m-30) cc_final: 0.7678 (m-30) REVERT: A 883 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7291 (tp) REVERT: A 911 ASN cc_start: 0.7387 (p0) cc_final: 0.7164 (p0) REVERT: B 67 MET cc_start: 0.5136 (tpp) cc_final: 0.4055 (tmm) REVERT: B 157 GLN cc_start: 0.8469 (mt0) cc_final: 0.7850 (tt0) REVERT: B 174 MET cc_start: 0.8067 (mmt) cc_final: 0.7580 (tpt) REVERT: C 21 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7821 (tpp-160) REVERT: C 43 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8118 (mmmt) REVERT: D 50 ASP cc_start: 0.7051 (t0) cc_final: 0.6454 (m-30) REVERT: D 62 MET cc_start: 0.7327 (tpp) cc_final: 0.7037 (ttp) REVERT: D 78 ASP cc_start: 0.7627 (t70) cc_final: 0.7372 (t0) REVERT: D 97 LYS cc_start: 0.8308 (tttm) cc_final: 0.7886 (ttmm) REVERT: D 112 ASP cc_start: 0.7904 (m-30) cc_final: 0.7406 (m-30) REVERT: D 164 SER cc_start: 0.6986 (m) cc_final: 0.6572 (t) REVERT: D 180 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.5042 (tt) outliers start: 38 outliers final: 24 residues processed: 162 average time/residue: 0.2978 time to fit residues: 72.5588 Evaluate side-chains 154 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 223 ILE 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 372 LEU Chi-restraints excluded: chain A residue 393 THR 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 682 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 776 VAL 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 87 MET 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 C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 408 GLN A 497 ASN A 613 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109108 restraints weight = 14909.390| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.66 r_work: 0.3123 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.8753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12986 Z= 0.172 Angle : 0.541 7.317 17973 Z= 0.280 Chirality : 0.040 0.220 2101 Planarity : 0.003 0.046 2007 Dihedral : 14.781 139.689 2847 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.10 % Allowed : 16.82 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1365 helix: 1.04 (0.20), residues: 695 sheet: -0.96 (0.42), residues: 141 loop : -1.03 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 80 ARG 0.004 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 631) hydrogen bonds : angle 3.89721 ( 1707) metal coordination : bond 0.00691 ( 8) metal coordination : angle 1.62715 ( 6) covalent geometry : bond 0.00400 (12978) covalent geometry : angle 0.54055 (17967) *********************** 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 168 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.275 Fit side-chains REVERT: A 235 ASP cc_start: 0.7874 (m-30) cc_final: 0.7166 (p0) REVERT: A 268 TRP cc_start: 0.8285 (OUTLIER) cc_final: 0.5487 (m-90) REVERT: A 277 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7145 (mp0) REVERT: A 332 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7807 (ttmm) REVERT: A 430 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6973 (mmtp) REVERT: A 431 GLU cc_start: 0.7486 (tp30) cc_final: 0.6627 (tt0) REVERT: A 534 ASN cc_start: 0.9023 (m-40) cc_final: 0.8650 (m-40) REVERT: A 608 ASP cc_start: 0.7734 (t0) cc_final: 0.7221 (t0) REVERT: A 668 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7781 (tmm) REVERT: A 722 ASN cc_start: 0.7717 (t0) cc_final: 0.7186 (m-40) REVERT: A 824 ASP cc_start: 0.7985 (p0) cc_final: 0.7277 (t0) REVERT: A 857 GLU cc_start: 0.7916 (mp0) cc_final: 0.6829 (tp30) REVERT: A 865 ASP cc_start: 0.8008 (m-30) cc_final: 0.7730 (m-30) REVERT: A 883 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7379 (tp) REVERT: A 911 ASN cc_start: 0.7257 (p0) cc_final: 0.6985 (p0) REVERT: B 67 MET cc_start: 0.5169 (tpp) cc_final: 0.4174 (tmm) REVERT: B 157 GLN cc_start: 0.8481 (mt0) cc_final: 0.7869 (tt0) REVERT: B 174 MET cc_start: 0.8066 (mmt) cc_final: 0.7647 (tpt) REVERT: C 43 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8158 (mmmt) REVERT: D 50 ASP cc_start: 0.7175 (t0) cc_final: 0.6621 (m-30) REVERT: D 62 MET cc_start: 0.7399 (tpp) cc_final: 0.7083 (ttp) REVERT: D 78 ASP cc_start: 0.7749 (t70) cc_final: 0.7474 (t0) REVERT: D 97 LYS cc_start: 0.8298 (tttm) cc_final: 0.7943 (ttmm) outliers start: 37 outliers final: 28 residues processed: 157 average time/residue: 0.2309 time to fit residues: 54.9574 Evaluate side-chains 159 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 223 ILE 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 343 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 497 ASN 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 758 LEU Chi-restraints excluded: chain A residue 776 VAL 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 87 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 101 optimal weight: 0.0050 chunk 53 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 312 ASN A 497 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.116331 restraints weight = 14775.450| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.45 r_work: 0.3092 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.8839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12986 Z= 0.119 Angle : 0.505 7.293 17973 Z= 0.261 Chirality : 0.038 0.218 2101 Planarity : 0.003 0.044 2007 Dihedral : 14.688 122.576 2847 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.51 % Allowed : 17.82 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1365 helix: 1.18 (0.20), residues: 694 sheet: -0.88 (0.42), residues: 136 loop : -0.94 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.013 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG D 80 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 631) hydrogen bonds : angle 3.79802 ( 1707) metal coordination : bond 0.00576 ( 8) metal coordination : angle 1.60568 ( 6) covalent geometry : bond 0.00267 (12978) covalent geometry : angle 0.50392 (17967) *********************** 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 151 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.174 Fit side-chains REVERT: A 235 ASP cc_start: 0.7889 (m-30) cc_final: 0.7444 (p0) REVERT: A 268 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.5641 (m-90) REVERT: A 277 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7340 (mp0) REVERT: A 332 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7967 (ttmm) REVERT: A 430 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7212 (mttt) REVERT: A 431 GLU cc_start: 0.7425 (tp30) cc_final: 0.6671 (tt0) REVERT: A 534 ASN cc_start: 0.8959 (m-40) cc_final: 0.8671 (m-40) REVERT: A 608 ASP cc_start: 0.7612 (t0) cc_final: 0.7236 (t0) REVERT: A 722 ASN cc_start: 0.7896 (t0) cc_final: 0.7436 (m-40) REVERT: A 857 GLU cc_start: 0.7856 (mp0) cc_final: 0.6979 (tp30) REVERT: A 865 ASP cc_start: 0.8194 (m-30) cc_final: 0.7956 (m-30) REVERT: A 883 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7716 (tp) REVERT: A 911 ASN cc_start: 0.7414 (p0) cc_final: 0.7133 (p0) REVERT: B 67 MET cc_start: 0.5613 (tpp) cc_final: 0.4576 (tmm) REVERT: B 157 GLN cc_start: 0.8534 (mt0) cc_final: 0.8087 (tt0) REVERT: B 174 MET cc_start: 0.8201 (mmt) cc_final: 0.7869 (tpt) REVERT: C 43 LYS cc_start: 0.8547 (mmtm) cc_final: 0.8251 (mmmt) REVERT: D 62 MET cc_start: 0.7574 (tpp) cc_final: 0.7239 (ttp) REVERT: D 67 MET cc_start: 0.8179 (mtt) cc_final: 0.7921 (mtt) REVERT: D 97 LYS cc_start: 0.8456 (tttm) cc_final: 0.8127 (ttmm) REVERT: D 166 ILE cc_start: 0.6682 (mm) cc_final: 0.6176 (tp) outliers start: 30 outliers final: 24 residues processed: 144 average time/residue: 0.2323 time to fit residues: 50.3575 Evaluate side-chains 147 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 223 ILE 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 343 SER Chi-restraints excluded: chain A residue 372 LEU 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 682 SER Chi-restraints excluded: chain A residue 776 VAL 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 87 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 43 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 0 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.150450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115261 restraints weight = 14667.372| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.43 r_work: 0.3085 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.8940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12986 Z= 0.147 Angle : 0.526 8.560 17973 Z= 0.269 Chirality : 0.039 0.219 2101 Planarity : 0.003 0.046 2007 Dihedral : 14.657 122.121 2847 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.59 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1365 helix: 1.10 (0.20), residues: 701 sheet: -0.87 (0.43), residues: 136 loop : -0.94 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.012 0.001 TYR A 788 ARG 0.008 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 631) hydrogen bonds : angle 3.84499 ( 1707) metal coordination : bond 0.00619 ( 8) metal coordination : angle 1.55649 ( 6) covalent geometry : bond 0.00340 (12978) covalent geometry : angle 0.52548 (17967) ********************** 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 155 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.281 Fit side-chains REVERT: A 235 ASP cc_start: 0.7844 (m-30) cc_final: 0.7398 (p0) REVERT: A 268 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.5628 (m-90) REVERT: A 277 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7377 (mp0) REVERT: A 332 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7981 (ttmm) REVERT: A 430 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7247 (mttt) REVERT: A 431 GLU cc_start: 0.7489 (tp30) cc_final: 0.7250 (tp30) REVERT: A 534 ASN cc_start: 0.8990 (m-40) cc_final: 0.8675 (m-40) REVERT: A 553 ARG cc_start: 0.8370 (ttm110) cc_final: 0.8089 (mtm-85) REVERT: A 608 ASP cc_start: 0.7584 (t0) cc_final: 0.7190 (t0) REVERT: A 722 ASN cc_start: 0.7916 (t0) cc_final: 0.7465 (m-40) REVERT: A 857 GLU cc_start: 0.7904 (mp0) cc_final: 0.6979 (tp30) REVERT: A 865 ASP cc_start: 0.8217 (m-30) cc_final: 0.7972 (m-30) REVERT: A 883 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 911 ASN cc_start: 0.7430 (p0) cc_final: 0.7137 (p0) REVERT: B 67 MET cc_start: 0.5601 (tpp) cc_final: 0.4600 (tmm) REVERT: B 157 GLN cc_start: 0.8543 (mt0) cc_final: 0.8088 (tt0) REVERT: B 174 MET cc_start: 0.8228 (mmt) cc_final: 0.7962 (tpt) REVERT: C 43 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8307 (mmtt) REVERT: D 62 MET cc_start: 0.7512 (tpp) cc_final: 0.7263 (ttp) REVERT: D 67 MET cc_start: 0.8225 (mtt) cc_final: 0.7978 (mtt) REVERT: D 97 LYS cc_start: 0.8443 (tttm) cc_final: 0.8109 (ttmm) REVERT: D 166 ILE cc_start: 0.6701 (mm) cc_final: 0.6184 (tp) outliers start: 31 outliers final: 27 residues processed: 148 average time/residue: 0.2401 time to fit residues: 52.9504 Evaluate side-chains 152 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 223 ILE 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 343 SER Chi-restraints excluded: chain A residue 372 LEU 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 682 SER 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 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 87 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN D 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114411 restraints weight = 14673.901| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.43 r_work: 0.3056 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.9078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12986 Z= 0.156 Angle : 0.531 7.551 17973 Z= 0.273 Chirality : 0.039 0.219 2101 Planarity : 0.003 0.047 2007 Dihedral : 14.656 122.141 2847 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.85 % Allowed : 17.57 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1365 helix: 1.05 (0.20), residues: 703 sheet: -0.92 (0.43), residues: 136 loop : -0.94 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.013 0.001 TYR A 80 ARG 0.008 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 631) hydrogen bonds : angle 3.87549 ( 1707) metal coordination : bond 0.00617 ( 8) metal coordination : angle 1.58970 ( 6) covalent geometry : bond 0.00363 (12978) covalent geometry : angle 0.53019 (17967) =============================================================================== Job complete usr+sys time: 7428.17 seconds wall clock time: 133 minutes 53.03 seconds (8033.03 seconds total)