Starting phenix.real_space_refine on Mon May 4 09:32:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yop_73268/05_2026/9yop_73268.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yop_73268/05_2026/9yop_73268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yop_73268/05_2026/9yop_73268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yop_73268/05_2026/9yop_73268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yop_73268/05_2026/9yop_73268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yop_73268/05_2026/9yop_73268.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 112 5.16 5 C 12353 2.51 5 N 3303 2.21 5 O 3691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19465 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7388 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 31, 'TRANS': 880} Chain breaks: 2 Chain: "B" Number of atoms: 7383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 7383 Classifications: {'peptide': 911} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 2 Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "D" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "E" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.14, per 1000 atoms: 0.21 Number of scatterers: 19465 At special positions: 0 Unit cell: (90.47, 163.51, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 6 15.00 O 3691 8.00 N 3303 7.00 C 12353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 725.9 milliseconds 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4538 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 14 sheets defined 60.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.566A pdb=" N ALA A 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 135 through 142 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.580A pdb=" N ASN A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 4.516A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.626A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.188A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.761A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.968A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 447 Processing helix chain 'A' and resid 472 through 494 Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 517 through 526 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 614 through 621 Processing helix chain 'A' and resid 646 through 664 Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.623A pdb=" N VAL A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 708 Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'A' and resid 737 through 748 removed outlier: 3.684A pdb=" N GLY A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 822 removed outlier: 3.562A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG A 787 " --> pdb=" O ARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 826 Processing helix chain 'A' and resid 827 through 837 removed outlier: 4.089A pdb=" N LYS A 831 " --> pdb=" O TRP A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 943 removed outlier: 3.536A pdb=" N GLU A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 16 removed outlier: 7.353A pdb=" N ALA B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 12 " --> pdb=" O PHE B 9 " (cutoff:3.500A) Proline residue: B 14 - end of helix Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.786A pdb=" N SER B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 removed outlier: 3.976A pdb=" N TYR B 134 " --> pdb=" O LEU B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 200 Processing helix chain 'B' and resid 217 through 232 removed outlier: 4.501A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.857A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.639A pdb=" N VAL B 273 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.883A pdb=" N LEU B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.699A pdb=" N TYR B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 342 through 360 removed outlier: 4.034A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 416 through 448 removed outlier: 3.720A pdb=" N GLY B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 495 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 526 Processing helix chain 'B' and resid 530 through 540 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 614 through 622 Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 723 through 726 Processing helix chain 'B' and resid 737 through 748 Processing helix chain 'B' and resid 768 through 826 removed outlier: 4.094A pdb=" N ASN B 826 " --> pdb=" O MET B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 837 removed outlier: 3.594A pdb=" N LYS B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 943 removed outlier: 3.600A pdb=" N GLU B 846 " --> pdb=" O SER B 842 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 892 " --> pdb=" O GLN B 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 56 through 60 removed outlier: 4.403A pdb=" N THR C 59 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 removed outlier: 3.684A pdb=" N LEU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 93 through 99 removed outlier: 4.181A pdb=" N MET C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN C 98 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.663A pdb=" N LEU D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.919A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 134 removed outlier: 4.043A pdb=" N PHE D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 178 through 187 Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 49 through 57 removed outlier: 3.954A pdb=" N THR E 53 " --> pdb=" O ASP E 49 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.781A pdb=" N MET E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS E 90 " --> pdb=" O MET E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'E' and resid 132 through 140 Processing helix chain 'E' and resid 152 through 162 removed outlier: 4.264A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 84 through 91 Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.934A pdb=" N ILE F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 135 through 142 removed outlier: 3.834A pdb=" N TRP F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 5.620A pdb=" N ILE A 51 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A 62 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 6.512A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN A 172 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LEU A 460 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 174 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY A 245 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 711 through 714 removed outlier: 4.063A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.481A pdb=" N ILE B 51 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B 62 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 53 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 117 removed outlier: 6.870A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN B 172 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU B 460 " --> pdb=" O GLN B 172 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 174 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY B 245 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 264 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 262 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 260 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AB1, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.762A pdb=" N ASN B 711 " --> pdb=" O PHE B 765 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 757 " --> pdb=" O PHE B 764 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'D' and resid 140 through 142 1094 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 2.32 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: 6420 1.34 - 1.46: 3932 1.46 - 1.58: 9267 1.58 - 1.70: 6 1.70 - 1.82: 198 Bond restraints: 19823 Sorted by residual: bond pdb=" C GLN B 815 " pdb=" N TRP B 816 " ideal model delta sigma weight residual 1.335 1.434 -0.100 1.31e-02 5.83e+03 5.78e+01 bond pdb=" C LEU A 277 " pdb=" N LYS A 278 " ideal model delta sigma weight residual 1.332 1.412 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" C4 ADP B1401 " pdb=" C5 ADP B1401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP A1401 " pdb=" C5 ADP A1401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C5 ADP A1401 " pdb=" C6 ADP A1401 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 19818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 25439 2.15 - 4.30: 1116 4.30 - 6.46: 81 6.46 - 8.61: 20 8.61 - 10.76: 11 Bond angle restraints: 26667 Sorted by residual: angle pdb=" C CYS F 128 " pdb=" CA CYS F 128 " pdb=" CB CYS F 128 " ideal model delta sigma weight residual 116.54 110.91 5.63 1.15e+00 7.56e-01 2.40e+01 angle pdb=" O SER B 782 " pdb=" C SER B 782 " pdb=" N ARG B 783 " ideal model delta sigma weight residual 122.07 127.10 -5.03 1.03e+00 9.43e-01 2.38e+01 angle pdb=" C GLN B 815 " pdb=" N TRP B 816 " pdb=" CA TRP B 816 " ideal model delta sigma weight residual 120.28 113.98 6.30 1.34e+00 5.57e-01 2.21e+01 angle pdb=" C LYS A 707 " pdb=" N GLY A 708 " pdb=" CA GLY A 708 " ideal model delta sigma weight residual 122.43 118.36 4.07 8.90e-01 1.26e+00 2.09e+01 angle pdb=" N VAL F 147 " pdb=" CA VAL F 147 " pdb=" C VAL F 147 " ideal model delta sigma weight residual 112.43 108.24 4.19 9.20e-01 1.18e+00 2.08e+01 ... (remaining 26662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.34: 11399 28.34 - 56.68: 602 56.68 - 85.02: 94 85.02 - 113.35: 9 113.35 - 141.69: 5 Dihedral angle restraints: 12109 sinusoidal: 5096 harmonic: 7013 Sorted by residual: dihedral pdb=" O2A ADP A1401 " pdb=" O3A ADP A1401 " pdb=" PA ADP A1401 " pdb=" PB ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 81.69 -141.69 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" C5' ADP A1401 " pdb=" O5' ADP A1401 " pdb=" PA ADP A1401 " pdb=" O2A ADP A1401 " ideal model delta sinusoidal sigma weight residual -60.00 -179.90 119.91 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" O1B ADP B1401 " pdb=" O3A ADP B1401 " pdb=" PB ADP B1401 " pdb=" PA ADP B1401 " ideal model delta sinusoidal sigma weight residual -60.00 -179.74 119.74 1 2.00e+01 2.50e-03 3.59e+01 ... (remaining 12106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2061 0.050 - 0.101: 566 0.101 - 0.151: 214 0.151 - 0.202: 37 0.202 - 0.252: 11 Chirality restraints: 2889 Sorted by residual: chirality pdb=" CA ILE B 521 " pdb=" N ILE B 521 " pdb=" C ILE B 521 " pdb=" CB ILE B 521 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE A 713 " pdb=" N ILE A 713 " pdb=" C ILE A 713 " pdb=" CB ILE A 713 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE B 736 " pdb=" N ILE B 736 " pdb=" C ILE B 736 " pdb=" CB ILE B 736 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2886 not shown) Planarity restraints: 3463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 777 " 0.469 9.50e-02 1.11e+02 2.10e-01 2.71e+01 pdb=" NE ARG B 777 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 777 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 777 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 777 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 780 " 0.450 9.50e-02 1.11e+02 2.02e-01 2.49e+01 pdb=" NE ARG A 780 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 780 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 780 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 780 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 783 " -0.445 9.50e-02 1.11e+02 2.00e-01 2.45e+01 pdb=" NE ARG B 783 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 783 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 783 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 783 " -0.014 2.00e-02 2.50e+03 ... (remaining 3460 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 283 2.64 - 3.20: 19388 3.20 - 3.77: 32236 3.77 - 4.33: 43698 4.33 - 4.90: 69671 Nonbonded interactions: 165276 Sorted by model distance: nonbonded pdb=" CB LEU A 908 " pdb=" NZ LYS B 912 " model vdw 2.069 3.520 nonbonded pdb=" O ALA A 233 " pdb=" OG SER A 241 " model vdw 2.170 3.040 nonbonded pdb=" OH TYR A 287 " pdb=" O ILE A 313 " model vdw 2.175 3.040 nonbonded pdb=" OE1 GLN A 44 " pdb=" OH TYR A 65 " model vdw 2.196 3.040 nonbonded pdb=" OE2 GLU A 179 " pdb=" NH2 ARG A 237 " model vdw 2.201 3.120 ... (remaining 165271 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 'A' and (resid 4 through 626 or resid 643 through 1402)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.007 0.109 19823 Z= 0.456 Angle : 0.909 10.762 26667 Z= 0.604 Chirality : 0.056 0.252 2889 Planarity : 0.011 0.210 3463 Dihedral : 17.150 141.692 7571 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 1.05 % Allowed : 17.10 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2391 helix: 0.67 (0.14), residues: 1328 sheet: -1.63 (0.38), residues: 170 loop : -1.33 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 808 TYR 0.016 0.002 TYR A 283 PHE 0.018 0.002 PHE A 312 TRP 0.017 0.002 TRP A 816 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00707 (19823) covalent geometry : angle 0.90920 (26667) hydrogen bonds : bond 0.14531 ( 1094) hydrogen bonds : angle 6.37724 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 293 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.7791 (mtm110) cc_final: 0.7327 (mtm110) REVERT: A 410 TYR cc_start: 0.8611 (m-80) cc_final: 0.8342 (m-80) REVERT: A 690 MET cc_start: 0.9116 (mmm) cc_final: 0.8832 (mmm) REVERT: D 110 MET cc_start: 0.4857 (tpp) cc_final: 0.4574 (tpp) REVERT: E 26 GLN cc_start: 0.6435 (mm-40) cc_final: 0.5976 (tm-30) REVERT: F 140 TRP cc_start: 0.6283 (m-10) cc_final: 0.6034 (m-10) outliers start: 22 outliers final: 7 residues processed: 308 average time/residue: 0.1360 time to fit residues: 65.5761 Evaluate side-chains 245 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 238 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 131 PHE Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.0270 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 276 GLN A 408 ASN A 492 HIS A 907 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 251 HIS B 815 GLN B 885 ASN B 923 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN F 127 GLN F 138 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.138305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096047 restraints weight = 46321.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095200 restraints weight = 28401.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094833 restraints weight = 21421.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095360 restraints weight = 21953.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095410 restraints weight = 19580.578| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19823 Z= 0.171 Angle : 0.617 14.357 26667 Z= 0.315 Chirality : 0.042 0.245 2889 Planarity : 0.004 0.052 3463 Dihedral : 7.046 123.516 2623 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.63 % Allowed : 16.62 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2391 helix: 1.16 (0.14), residues: 1355 sheet: -1.27 (0.40), residues: 147 loop : -1.19 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 904 TYR 0.019 0.002 TYR B 624 PHE 0.020 0.002 PHE D 107 TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00378 (19823) covalent geometry : angle 0.61706 (26667) hydrogen bonds : bond 0.04405 ( 1094) hydrogen bonds : angle 5.02786 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 260 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 785 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8049 (tp) REVERT: A 800 GLU cc_start: 0.8503 (tp30) cc_final: 0.8248 (tp30) REVERT: B 43 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7607 (tppt) REVERT: B 230 PHE cc_start: 0.8307 (m-10) cc_final: 0.8063 (m-10) REVERT: B 300 MET cc_start: 0.8121 (ppp) cc_final: 0.7844 (ppp) REVERT: B 720 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8732 (tm-30) REVERT: C 43 LYS cc_start: 0.6597 (tptt) cc_final: 0.6051 (tppt) REVERT: D 97 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6301 (mmm) REVERT: D 107 PHE cc_start: 0.4495 (p90) cc_final: 0.3842 (p90) REVERT: D 110 MET cc_start: 0.6076 (tpp) cc_final: 0.5792 (tpp) REVERT: D 119 ASP cc_start: 0.7167 (t0) cc_final: 0.6824 (t0) REVERT: E 26 GLN cc_start: 0.6474 (mm-40) cc_final: 0.6169 (tm-30) REVERT: F 131 PHE cc_start: 0.3384 (OUTLIER) cc_final: 0.2980 (m-80) REVERT: F 139 MET cc_start: 0.6027 (ptt) cc_final: 0.5490 (ptm) outliers start: 76 outliers final: 33 residues processed: 313 average time/residue: 0.1233 time to fit residues: 62.1764 Evaluate side-chains 269 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 131 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 157 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 92 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 149 optimal weight: 0.4980 chunk 164 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 217 optimal weight: 20.0000 chunk 129 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 454 GLN B 911 ASN B 914 GLN C 112 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.139802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097334 restraints weight = 46324.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096961 restraints weight = 29372.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096945 restraints weight = 20984.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097395 restraints weight = 20230.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097541 restraints weight = 18607.981| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19823 Z= 0.117 Angle : 0.571 10.168 26667 Z= 0.287 Chirality : 0.040 0.242 2889 Planarity : 0.004 0.052 3463 Dihedral : 6.587 116.127 2615 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.82 % Allowed : 18.05 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2391 helix: 1.35 (0.14), residues: 1352 sheet: -1.11 (0.42), residues: 148 loop : -1.04 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.017 0.001 TYR B 624 PHE 0.021 0.001 PHE D 181 TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00247 (19823) covalent geometry : angle 0.57054 (26667) hydrogen bonds : bond 0.03841 ( 1094) hydrogen bonds : angle 4.73648 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8367 (tp30) cc_final: 0.8041 (mm-30) REVERT: A 403 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7995 (mtp85) REVERT: A 785 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 800 GLU cc_start: 0.8513 (tp30) cc_final: 0.8272 (tp30) REVERT: A 890 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8337 (tm-30) REVERT: B 43 LYS cc_start: 0.8104 (tmtt) cc_final: 0.7630 (tppt) REVERT: B 230 PHE cc_start: 0.8363 (m-10) cc_final: 0.8057 (m-10) REVERT: B 300 MET cc_start: 0.7967 (ppp) cc_final: 0.7761 (ppp) REVERT: C 43 LYS cc_start: 0.6441 (tptt) cc_final: 0.5803 (tppt) REVERT: C 47 GLU cc_start: 0.8807 (tp30) cc_final: 0.8206 (tp30) REVERT: D 46 GLN cc_start: 0.7794 (pp30) cc_final: 0.7563 (pp30) REVERT: D 107 PHE cc_start: 0.4569 (p90) cc_final: 0.4354 (p90) REVERT: D 119 ASP cc_start: 0.7316 (t0) cc_final: 0.6840 (t0) REVERT: E 26 GLN cc_start: 0.6468 (mm-40) cc_final: 0.6136 (tm-30) REVERT: E 37 ILE cc_start: 0.6855 (pt) cc_final: 0.6564 (mp) REVERT: F 131 PHE cc_start: 0.3125 (OUTLIER) cc_final: 0.2803 (m-80) outliers start: 59 outliers final: 35 residues processed: 300 average time/residue: 0.1281 time to fit residues: 61.3847 Evaluate side-chains 267 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 131 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 157 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 230 optimal weight: 0.0570 chunk 185 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 HIS ** E 79 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 = 0.4179 r_free = 0.4179 target = 0.139457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097231 restraints weight = 44810.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097196 restraints weight = 28323.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097179 restraints weight = 19947.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098028 restraints weight = 18095.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098090 restraints weight = 16343.504| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19823 Z= 0.118 Angle : 0.564 10.383 26667 Z= 0.281 Chirality : 0.040 0.340 2889 Planarity : 0.003 0.050 3463 Dihedral : 6.372 111.598 2615 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.39 % Allowed : 18.29 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2391 helix: 1.43 (0.14), residues: 1347 sheet: -1.05 (0.42), residues: 148 loop : -0.95 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 869 TYR 0.014 0.001 TYR B 624 PHE 0.019 0.001 PHE D 181 TRP 0.007 0.001 TRP B 438 HIS 0.003 0.001 HIS B 556 Details of bonding type rmsd covalent geometry : bond 0.00257 (19823) covalent geometry : angle 0.56411 (26667) hydrogen bonds : bond 0.03634 ( 1094) hydrogen bonds : angle 4.59365 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8386 (tp30) cc_final: 0.8103 (mm-30) REVERT: A 403 ARG cc_start: 0.8261 (mtm110) cc_final: 0.7765 (mtp85) REVERT: A 785 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.7974 (tp) REVERT: A 800 GLU cc_start: 0.8503 (tp30) cc_final: 0.8251 (tp30) REVERT: A 890 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 43 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7628 (tppt) REVERT: B 230 PHE cc_start: 0.8377 (m-10) cc_final: 0.8046 (m-10) REVERT: B 476 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7638 (tt) REVERT: C 43 LYS cc_start: 0.6411 (tptt) cc_final: 0.5761 (tppt) REVERT: C 47 GLU cc_start: 0.8804 (tp30) cc_final: 0.8474 (tp30) REVERT: D 46 GLN cc_start: 0.7821 (pp30) cc_final: 0.7592 (pp30) REVERT: D 97 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6292 (mmm) REVERT: D 107 PHE cc_start: 0.4493 (p90) cc_final: 0.4197 (p90) REVERT: E 26 GLN cc_start: 0.6442 (mm-40) cc_final: 0.6149 (tm-30) REVERT: F 131 PHE cc_start: 0.3037 (OUTLIER) cc_final: 0.2717 (m-80) outliers start: 71 outliers final: 49 residues processed: 296 average time/residue: 0.1316 time to fit residues: 62.3467 Evaluate side-chains 289 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 131 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 157 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 93 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.135563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092724 restraints weight = 45702.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092587 restraints weight = 29541.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091983 restraints weight = 22309.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092415 restraints weight = 22446.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092389 restraints weight = 21050.970| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 19823 Z= 0.314 Angle : 0.706 10.624 26667 Z= 0.358 Chirality : 0.045 0.244 2889 Planarity : 0.005 0.054 3463 Dihedral : 6.546 111.533 2615 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.87 % Allowed : 19.10 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2391 helix: 1.02 (0.14), residues: 1356 sheet: -1.58 (0.40), residues: 156 loop : -1.05 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 783 TYR 0.033 0.002 TYR A 582 PHE 0.018 0.002 PHE D 181 TRP 0.011 0.002 TRP A 816 HIS 0.006 0.002 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00731 (19823) covalent geometry : angle 0.70598 (26667) hydrogen bonds : bond 0.04343 ( 1094) hydrogen bonds : angle 5.02197 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 230 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 785 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8209 (tp) REVERT: A 890 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 877 MET cc_start: 0.8523 (tpt) cc_final: 0.8284 (tpp) REVERT: C 186 MET cc_start: 0.8132 (mmm) cc_final: 0.7865 (mmt) REVERT: D 97 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6307 (mmm) REVERT: D 119 ASP cc_start: 0.7063 (t0) cc_final: 0.6778 (t0) REVERT: E 26 GLN cc_start: 0.6438 (mm-40) cc_final: 0.6119 (tm-30) REVERT: E 37 ILE cc_start: 0.6831 (pt) cc_final: 0.6532 (mp) REVERT: E 96 PRO cc_start: 0.6172 (Cg_exo) cc_final: 0.5810 (Cg_endo) outliers start: 81 outliers final: 60 residues processed: 285 average time/residue: 0.1203 time to fit residues: 56.0511 Evaluate side-chains 281 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 131 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 157 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 2 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** E 79 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 = 0.4160 r_free = 0.4160 target = 0.138176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094983 restraints weight = 45869.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.095056 restraints weight = 31126.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094777 restraints weight = 21036.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095082 restraints weight = 20676.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095138 restraints weight = 18093.346| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19823 Z= 0.146 Angle : 0.597 11.789 26667 Z= 0.299 Chirality : 0.041 0.218 2889 Planarity : 0.004 0.052 3463 Dihedral : 6.244 108.374 2615 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.58 % Allowed : 20.11 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2391 helix: 1.19 (0.14), residues: 1359 sheet: -1.27 (0.42), residues: 145 loop : -0.94 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 869 TYR 0.022 0.001 TYR B 833 PHE 0.017 0.001 PHE B 230 TRP 0.012 0.001 TRP A 816 HIS 0.003 0.001 HIS B 556 Details of bonding type rmsd covalent geometry : bond 0.00327 (19823) covalent geometry : angle 0.59741 (26667) hydrogen bonds : bond 0.03765 ( 1094) hydrogen bonds : angle 4.72335 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 241 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8422 (tp30) cc_final: 0.7837 (mm-30) REVERT: A 785 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8119 (tp) REVERT: A 890 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 43 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7665 (tppt) REVERT: B 230 PHE cc_start: 0.8396 (m-10) cc_final: 0.8030 (m-10) REVERT: B 871 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8539 (ttpp) REVERT: B 877 MET cc_start: 0.8607 (tpt) cc_final: 0.8380 (tpp) REVERT: C 43 LYS cc_start: 0.6470 (tptt) cc_final: 0.5906 (tppt) REVERT: C 186 MET cc_start: 0.8233 (mmm) cc_final: 0.7995 (mmt) REVERT: D 97 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6224 (mmm) REVERT: E 26 GLN cc_start: 0.6455 (mm-40) cc_final: 0.6173 (tm-30) REVERT: E 37 ILE cc_start: 0.6770 (pt) cc_final: 0.6495 (mp) outliers start: 75 outliers final: 48 residues processed: 292 average time/residue: 0.1210 time to fit residues: 57.3929 Evaluate side-chains 278 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 871 LYS Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 157 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 79 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN B 454 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.134988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088913 restraints weight = 45877.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090057 restraints weight = 28789.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090458 restraints weight = 20310.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090537 restraints weight = 17485.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090719 restraints weight = 17584.049| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 19823 Z= 0.313 Angle : 0.708 11.364 26667 Z= 0.359 Chirality : 0.045 0.241 2889 Planarity : 0.005 0.055 3463 Dihedral : 6.213 108.671 2610 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.82 % Allowed : 20.34 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2391 helix: 0.90 (0.14), residues: 1363 sheet: -1.67 (0.40), residues: 156 loop : -1.06 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 671 TYR 0.031 0.003 TYR A 582 PHE 0.025 0.002 PHE F 131 TRP 0.014 0.002 TRP A 816 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00727 (19823) covalent geometry : angle 0.70805 (26667) hydrogen bonds : bond 0.04317 ( 1094) hydrogen bonds : angle 5.05669 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 223 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7771 (tt) REVERT: A 374 GLU cc_start: 0.8385 (tp30) cc_final: 0.7856 (mm-30) REVERT: A 785 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8224 (tp) REVERT: A 890 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 230 PHE cc_start: 0.8487 (m-10) cc_final: 0.8086 (m-10) REVERT: C 43 LYS cc_start: 0.6474 (tptt) cc_final: 0.6237 (tptt) REVERT: C 186 MET cc_start: 0.8221 (mmm) cc_final: 0.7996 (mmt) REVERT: D 97 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6284 (mmm) REVERT: E 26 GLN cc_start: 0.6505 (mm-40) cc_final: 0.6172 (tm-30) REVERT: E 37 ILE cc_start: 0.6725 (pt) cc_final: 0.6486 (mp) outliers start: 80 outliers final: 58 residues processed: 279 average time/residue: 0.1178 time to fit residues: 53.9233 Evaluate side-chains 280 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 175 CYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 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 = 0.4143 r_free = 0.4143 target = 0.136975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092314 restraints weight = 45647.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093051 restraints weight = 29224.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093320 restraints weight = 18546.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093701 restraints weight = 17727.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093775 restraints weight = 16451.824| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19823 Z= 0.175 Angle : 0.636 11.880 26667 Z= 0.318 Chirality : 0.042 0.208 2889 Planarity : 0.004 0.054 3463 Dihedral : 5.935 100.782 2610 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.10 % Allowed : 21.16 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2391 helix: 1.07 (0.14), residues: 1351 sheet: -1.47 (0.41), residues: 155 loop : -0.93 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 869 TYR 0.027 0.002 TYR B 833 PHE 0.015 0.001 PHE A 312 TRP 0.014 0.001 TRP A 816 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00400 (19823) covalent geometry : angle 0.63621 (26667) hydrogen bonds : bond 0.03872 ( 1094) hydrogen bonds : angle 4.83980 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8393 (tp30) cc_final: 0.7915 (mm-30) REVERT: A 690 MET cc_start: 0.8579 (mmm) cc_final: 0.8309 (mmm) REVERT: A 785 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8172 (tp) REVERT: A 890 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8514 (tm-30) REVERT: B 230 PHE cc_start: 0.8452 (m-10) cc_final: 0.8003 (m-10) REVERT: B 232 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8263 (m110) REVERT: B 871 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: C 43 LYS cc_start: 0.6424 (tptt) cc_final: 0.6157 (tptt) REVERT: C 186 MET cc_start: 0.8209 (mmm) cc_final: 0.7979 (mmt) REVERT: D 97 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6271 (mmm) REVERT: D 110 MET cc_start: 0.6132 (mmt) cc_final: 0.5911 (tpp) REVERT: E 26 GLN cc_start: 0.6412 (mm-40) cc_final: 0.6108 (tm-30) REVERT: E 37 ILE cc_start: 0.6676 (pt) cc_final: 0.6449 (mp) outliers start: 65 outliers final: 56 residues processed: 276 average time/residue: 0.1174 time to fit residues: 53.0155 Evaluate side-chains 282 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 871 LYS Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 13 optimal weight: 0.1980 chunk 70 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.138358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096757 restraints weight = 44627.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097498 restraints weight = 27762.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.096996 restraints weight = 18891.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097361 restraints weight = 19317.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097472 restraints weight = 17163.742| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19823 Z= 0.126 Angle : 0.620 12.383 26667 Z= 0.306 Chirality : 0.041 0.214 2889 Planarity : 0.004 0.052 3463 Dihedral : 5.681 91.581 2610 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.96 % Allowed : 21.54 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2391 helix: 1.22 (0.14), residues: 1351 sheet: -1.38 (0.41), residues: 157 loop : -0.85 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 869 TYR 0.028 0.001 TYR B 833 PHE 0.015 0.001 PHE B 230 TRP 0.014 0.001 TRP A 816 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00277 (19823) covalent geometry : angle 0.62009 (26667) hydrogen bonds : bond 0.03597 ( 1094) hydrogen bonds : angle 4.65028 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8356 (tp30) cc_final: 0.7921 (mm-30) REVERT: A 690 MET cc_start: 0.8645 (mmm) cc_final: 0.8397 (mmm) REVERT: A 785 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8191 (tp) REVERT: A 890 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 230 PHE cc_start: 0.8366 (m-10) cc_final: 0.7942 (m-10) REVERT: B 871 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8550 (ttpp) REVERT: C 43 LYS cc_start: 0.6414 (tptt) cc_final: 0.6053 (tptt) REVERT: C 47 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: C 186 MET cc_start: 0.8171 (mmm) cc_final: 0.7945 (mmt) REVERT: D 46 GLN cc_start: 0.7721 (pp30) cc_final: 0.7477 (pp30) REVERT: D 97 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6314 (mmm) REVERT: E 26 GLN cc_start: 0.6365 (mm-40) cc_final: 0.6105 (tm-30) REVERT: E 156 ILE cc_start: 0.7154 (tp) cc_final: 0.6489 (mm) REVERT: F 120 LEU cc_start: 0.8065 (pp) cc_final: 0.7830 (pp) outliers start: 62 outliers final: 47 residues processed: 283 average time/residue: 0.1226 time to fit residues: 56.3343 Evaluate side-chains 280 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 871 LYS Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 195 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 0.3980 chunk 200 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.138316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095969 restraints weight = 44734.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096115 restraints weight = 27815.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096137 restraints weight = 18891.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096553 restraints weight = 18578.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096678 restraints weight = 16610.726| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19823 Z= 0.130 Angle : 0.627 12.687 26667 Z= 0.307 Chirality : 0.041 0.291 2889 Planarity : 0.004 0.052 3463 Dihedral : 5.576 89.673 2610 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.87 % Allowed : 21.39 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2391 helix: 1.24 (0.14), residues: 1352 sheet: -1.27 (0.43), residues: 153 loop : -0.85 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 869 TYR 0.041 0.001 TYR B 833 PHE 0.013 0.001 PHE A 312 TRP 0.016 0.001 TRP A 816 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00290 (19823) covalent geometry : angle 0.62708 (26667) hydrogen bonds : bond 0.03584 ( 1094) hydrogen bonds : angle 4.62690 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4782 Ramachandran restraints generated. 2391 Oldfield, 0 Emsley, 2391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8312 (tp30) cc_final: 0.7863 (mm-30) REVERT: A 531 MET cc_start: 0.8560 (mtt) cc_final: 0.8223 (mtt) REVERT: A 690 MET cc_start: 0.8676 (mmm) cc_final: 0.8429 (mmm) REVERT: A 785 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8169 (tp) REVERT: A 890 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8456 (tm-30) REVERT: B 43 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7548 (tppt) REVERT: B 230 PHE cc_start: 0.8417 (m-10) cc_final: 0.7995 (m-10) REVERT: B 871 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8552 (ttpp) REVERT: C 43 LYS cc_start: 0.6374 (tptt) cc_final: 0.6002 (tptt) REVERT: C 47 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: C 186 MET cc_start: 0.8153 (mmm) cc_final: 0.7934 (mmt) REVERT: D 46 GLN cc_start: 0.7735 (pp30) cc_final: 0.7494 (pp30) REVERT: D 97 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6316 (mmm) REVERT: E 26 GLN cc_start: 0.6354 (mm-40) cc_final: 0.6105 (tm-30) REVERT: E 37 ILE cc_start: 0.6864 (pt) cc_final: 0.6536 (mp) REVERT: F 120 LEU cc_start: 0.7982 (pp) cc_final: 0.7722 (pp) outliers start: 60 outliers final: 50 residues processed: 280 average time/residue: 0.1199 time to fit residues: 55.1335 Evaluate side-chains 288 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 869 ARG Chi-restraints excluded: chain B residue 15 TYR Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 312 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 871 LYS Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 184 HIS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 206 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 0.0010 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 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 = 0.4180 r_free = 0.4180 target = 0.139555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095774 restraints weight = 45829.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096749 restraints weight = 27670.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.097034 restraints weight = 18543.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097447 restraints weight = 16468.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097509 restraints weight = 15268.857| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19823 Z= 0.119 Angle : 0.622 12.749 26667 Z= 0.305 Chirality : 0.041 0.259 2889 Planarity : 0.004 0.051 3463 Dihedral : 5.395 84.145 2610 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.82 % Allowed : 21.59 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2391 helix: 1.37 (0.14), residues: 1342 sheet: -1.34 (0.42), residues: 159 loop : -0.76 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 869 TYR 0.039 0.001 TYR B 833 PHE 0.011 0.001 PHE B 230 TRP 0.017 0.001 TRP A 816 HIS 0.006 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00260 (19823) covalent geometry : angle 0.62237 (26667) hydrogen bonds : bond 0.03497 ( 1094) hydrogen bonds : angle 4.52538 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3652.41 seconds wall clock time: 64 minutes 2.88 seconds (3842.88 seconds total)