Starting phenix.real_space_refine on Thu Jul 2 22:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.map" model { file = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2026/7kjy_22902.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 8 5.49 5 S 56 5.16 5 C 6632 2.51 5 N 1780 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10508 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "D" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 38.026 59.693 54.887 1.00141.59 S ATOM 1158 SG CYS A 153 39.083 56.108 52.991 1.00113.64 S ATOM 747 SG CYS A 97 32.022 48.850 34.077 1.00138.02 S ATOM 766 SG CYS A 100 36.101 49.335 33.968 1.00133.66 S ATOM 793 SG CYS A 103 35.139 47.934 36.928 1.00130.51 S ATOM 851 SG CYS A 111 33.795 51.117 36.047 1.00131.41 S ATOM 2921 SG CYS B 43 75.493 59.543 24.902 1.00140.20 S ATOM 3739 SG CYS B 153 74.435 55.963 26.806 1.00114.33 S ATOM 3328 SG CYS B 97 81.440 48.722 45.750 1.00138.47 S ATOM 3347 SG CYS B 100 77.380 49.199 45.948 1.00133.10 S ATOM 3374 SG CYS B 103 78.378 47.852 42.892 1.00129.21 S ATOM 3432 SG CYS B 111 79.743 50.995 43.754 1.00130.34 S ATOM 5502 SG CYS C 43 75.276 22.259 55.034 1.00141.93 S ATOM 6320 SG CYS C 153 74.244 25.844 53.125 1.00114.20 S ATOM 5909 SG CYS C 97 81.394 32.997 34.191 1.00137.88 S ATOM 5928 SG CYS C 100 77.315 32.593 34.000 1.00133.54 S ATOM 5955 SG CYS C 103 78.332 33.986 37.029 1.00130.48 S ATOM 6013 SG CYS C 111 79.626 30.794 36.172 1.00131.13 S ATOM 8083 SG CYS D 43 37.973 22.298 24.761 1.00140.99 S ATOM 8901 SG CYS D 153 39.015 25.881 26.668 1.00112.42 S ATOM 8490 SG CYS D 97 31.993 33.121 45.633 1.00136.84 S ATOM 8509 SG CYS D 100 36.045 32.650 45.895 1.00131.86 S ATOM 8536 SG CYS D 103 35.028 33.949 42.787 1.00129.36 S ATOM 8594 SG CYS D 111 33.682 30.817 43.630 1.00129.47 S Time building chain proxies: 2.05, per 1000 atoms: 0.20 Number of scatterers: 10508 At special positions: 0 Unit cell: (114.45, 82.95, 80.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 56 16.00 P 8 15.00 O 2024 8.00 N 1780 7.00 C 6632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS B 277 " distance=1.93 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS D 277 " distance=2.14 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: 1.22 Conformation dependent library (CDL) restraints added in 417.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 34.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.560A pdb=" N LEU A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 removed outlier: 3.775A pdb=" N GLU A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 180 through 194 removed outlier: 4.137A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.560A pdb=" N LEU B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 165 Processing helix chain 'B' and resid 180 through 194 removed outlier: 4.137A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 279 through 286 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.560A pdb=" N LEU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 111 Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 165 Processing helix chain 'C' and resid 180 through 194 removed outlier: 4.138A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 279 through 286 Processing helix chain 'C' and resid 297 through 310 Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'D' and resid 43 through 52 removed outlier: 3.560A pdb=" N LEU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 165 Processing helix chain 'D' and resid 180 through 194 removed outlier: 4.138A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 324 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 7.594A pdb=" N GLU A 32 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET A 75 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 73 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER A 40 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU A 67 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 87 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 132 removed outlier: 6.423A pdb=" N VAL A 320 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 220 removed outlier: 3.552A pdb=" N VAL A 217 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP A 172 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 243 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA A 174 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS A 240 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.594A pdb=" N GLU B 32 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET B 75 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 73 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER B 40 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU B 67 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR B 87 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.423A pdb=" N VAL B 320 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 93 through 95 Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 220 removed outlier: 3.552A pdb=" N VAL B 217 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP B 172 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE B 243 " --> pdb=" O TRP B 172 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 174 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS B 240 " --> pdb=" O ASN B 262 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'C' and resid 128 through 132 removed outlier: 7.594A pdb=" N GLU C 32 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET C 75 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 73 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER C 40 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU C 67 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR C 87 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 132 removed outlier: 6.423A pdb=" N VAL C 320 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB6, first strand: chain 'C' and resid 217 through 220 removed outlier: 3.552A pdb=" N VAL C 217 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP C 172 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE C 243 " --> pdb=" O TRP C 172 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA C 174 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS C 240 " --> pdb=" O ASN C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB8, first strand: chain 'D' and resid 128 through 132 removed outlier: 7.593A pdb=" N GLU D 32 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N MET D 75 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 73 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER D 40 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU D 67 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR D 87 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.424A pdb=" N VAL D 320 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95 Processing sheet with id=AC2, first strand: chain 'D' and resid 217 through 220 removed outlier: 3.552A pdb=" N VAL D 217 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP D 172 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE D 243 " --> pdb=" O TRP D 172 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA D 174 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS D 240 " --> pdb=" O ASN D 262 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1236 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: 1.64 Time building geometry restraints manager: 1.48 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: 3374 1.34 - 1.45: 1857 1.45 - 1.57: 5405 1.57 - 1.69: 16 1.69 - 1.81: 80 Bond restraints: 10732 Sorted by residual: bond pdb=" O3 NAD B 403 " pdb=" PA NAD B 403 " ideal model delta sigma weight residual 1.653 1.597 0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" O3 NAD A 403 " pdb=" PA NAD A 403 " ideal model delta sigma weight residual 1.653 1.597 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" O3 NAD C 403 " pdb=" PA NAD C 403 " ideal model delta sigma weight residual 1.653 1.597 0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" O3 NAD D 403 " pdb=" PA NAD D 403 " ideal model delta sigma weight residual 1.653 1.598 0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" N SER D 96 " pdb=" CA SER D 96 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.60e+00 ... (remaining 10727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 14238 2.01 - 4.01: 281 4.01 - 6.02: 53 6.02 - 8.02: 4 8.02 - 10.02: 4 Bond angle restraints: 14580 Sorted by residual: angle pdb=" CA MET D 98 " pdb=" C MET D 98 " pdb=" O MET D 98 " ideal model delta sigma weight residual 121.54 117.56 3.98 1.16e+00 7.43e-01 1.17e+01 angle pdb=" CA MET C 98 " pdb=" C MET C 98 " pdb=" O MET C 98 " ideal model delta sigma weight residual 121.54 117.59 3.95 1.16e+00 7.43e-01 1.16e+01 angle pdb=" CA SER D 96 " pdb=" C SER D 96 " pdb=" O SER D 96 " ideal model delta sigma weight residual 121.89 117.73 4.16 1.27e+00 6.20e-01 1.07e+01 angle pdb=" CA MET B 98 " pdb=" C MET B 98 " pdb=" O MET B 98 " ideal model delta sigma weight residual 121.54 117.74 3.80 1.16e+00 7.43e-01 1.07e+01 angle pdb=" CA MET A 98 " pdb=" C MET A 98 " pdb=" O MET A 98 " ideal model delta sigma weight residual 121.54 117.79 3.75 1.16e+00 7.43e-01 1.04e+01 ... (remaining 14575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5516 17.41 - 34.82: 520 34.82 - 52.23: 118 52.23 - 69.64: 24 69.64 - 87.05: 20 Dihedral angle restraints: 6198 sinusoidal: 2334 harmonic: 3864 Sorted by residual: dihedral pdb=" CA ASP B 220 " pdb=" CB ASP B 220 " pdb=" CG ASP B 220 " pdb=" OD1 ASP B 220 " ideal model delta sinusoidal sigma weight residual -30.00 -88.57 58.57 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP D 220 " pdb=" CB ASP D 220 " pdb=" CG ASP D 220 " pdb=" OD1 ASP D 220 " ideal model delta sinusoidal sigma weight residual -30.00 -88.57 58.57 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 220 " pdb=" CB ASP A 220 " pdb=" CG ASP A 220 " pdb=" OD1 ASP A 220 " ideal model delta sinusoidal sigma weight residual -30.00 -88.55 58.55 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 6195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1304 0.056 - 0.113: 279 0.113 - 0.169: 26 0.169 - 0.226: 3 0.226 - 0.282: 12 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA CYS D 111 " pdb=" N CYS D 111 " pdb=" C CYS D 111 " pdb=" CB CYS D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA CYS B 111 " pdb=" N CYS B 111 " pdb=" C CYS B 111 " pdb=" CB CYS B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA CYS A 111 " pdb=" N CYS A 111 " pdb=" C CYS A 111 " pdb=" CB CYS A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1621 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 403 " -0.010 2.00e-02 2.50e+03 1.76e-02 6.22e+00 pdb=" C2N NAD A 403 " -0.017 2.00e-02 2.50e+03 pdb=" C3N NAD A 403 " -0.006 2.00e-02 2.50e+03 pdb=" C4N NAD A 403 " -0.025 2.00e-02 2.50e+03 pdb=" C5N NAD A 403 " -0.002 2.00e-02 2.50e+03 pdb=" C6N NAD A 403 " 0.029 2.00e-02 2.50e+03 pdb=" C7N NAD A 403 " 0.023 2.00e-02 2.50e+03 pdb=" N1N NAD A 403 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 403 " 0.010 2.00e-02 2.50e+03 1.75e-02 6.12e+00 pdb=" C2N NAD B 403 " 0.017 2.00e-02 2.50e+03 pdb=" C3N NAD B 403 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD B 403 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD B 403 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAD B 403 " -0.029 2.00e-02 2.50e+03 pdb=" C7N NAD B 403 " -0.023 2.00e-02 2.50e+03 pdb=" N1N NAD B 403 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 403 " -0.010 2.00e-02 2.50e+03 1.75e-02 6.11e+00 pdb=" C2N NAD D 403 " -0.017 2.00e-02 2.50e+03 pdb=" C3N NAD D 403 " -0.006 2.00e-02 2.50e+03 pdb=" C4N NAD D 403 " -0.025 2.00e-02 2.50e+03 pdb=" C5N NAD D 403 " -0.002 2.00e-02 2.50e+03 pdb=" C6N NAD D 403 " 0.029 2.00e-02 2.50e+03 pdb=" C7N NAD D 403 " 0.023 2.00e-02 2.50e+03 pdb=" N1N NAD D 403 " 0.008 2.00e-02 2.50e+03 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 668 2.72 - 3.26: 11528 3.26 - 3.81: 18142 3.81 - 4.35: 22325 4.35 - 4.90: 38107 Nonbonded interactions: 90770 Sorted by model distance: nonbonded pdb=" OD2 ASP B 201 " pdb=" O3B NAD B 403 " model vdw 2.169 3.040 nonbonded pdb=" OD2 ASP D 201 " pdb=" O3B NAD D 403 " model vdw 2.169 3.040 nonbonded pdb=" OD2 ASP C 201 " pdb=" O3B NAD C 403 " model vdw 2.170 3.040 nonbonded pdb=" OD2 ASP A 201 " pdb=" O3B NAD A 403 " model vdw 2.170 3.040 nonbonded pdb=" OD1 ASP B 220 " pdb=" N LYS B 223 " model vdw 2.282 3.120 ... (remaining 90765 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.009 0.283 10762 Z= 0.400 Angle : 0.920 26.250 14608 Z= 0.395 Chirality : 0.051 0.282 1624 Planarity : 0.003 0.030 1856 Dihedral : 15.155 87.055 3768 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.48 % Allowed : 13.62 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.91 (0.17), residues: 1380 helix: -1.72 (0.19), residues: 448 sheet: -3.68 (0.23), residues: 212 loop : -2.85 (0.17), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 257 TYR 0.015 0.001 TYR B 258 PHE 0.007 0.001 PHE C 221 TRP 0.005 0.001 TRP D 92 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.34 (10732) covalent geometry : angle 0.70678 / 0.38 (14580) SS BOND : bond 0.10341 / 5.17 ( 2) SS BOND : angle 3.21162 / 1.74 ( 4) hydrogen bonds : bond 0.15976 / 10.90 ( 424) hydrogen bonds : angle 7.66160 / 5.28 ( 1236) metal coordination : bond 0.11655 / 7.82 ( 28) metal coordination : angle 14.48864 / 8.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8382 (tt) REVERT: A 126 GLN cc_start: 0.9194 (pt0) cc_final: 0.8778 (pt0) REVERT: A 270 MET cc_start: 0.9030 (mtm) cc_final: 0.8825 (mtm) REVERT: B 56 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8241 (tt) REVERT: B 126 GLN cc_start: 0.9188 (pt0) cc_final: 0.8791 (pt0) REVERT: C 126 GLN cc_start: 0.9178 (pt0) cc_final: 0.8659 (pt0) REVERT: D 126 GLN cc_start: 0.9246 (pt0) cc_final: 0.8886 (pt0) REVERT: D 211 ARG cc_start: 0.9071 (mmt90) cc_final: 0.8755 (mmm-85) outliers start: 48 outliers final: 21 residues processed: 134 average time/residue: 0.1297 time to fit residues: 23.1133 Evaluate side-chains 82 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 HIS A 51 HIS ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN B 48 HIS B 51 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN C 48 HIS C 51 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN D 48 HIS D 51 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.061501 restraints weight = 18741.560| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.13 r_work: 0.2628 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10762 Z= 0.115 Angle : 0.601 10.642 14608 Z= 0.268 Chirality : 0.043 0.148 1624 Planarity : 0.004 0.035 1856 Dihedral : 6.267 52.568 1526 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.99 % Allowed : 14.65 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.21), residues: 1380 helix: 0.26 (0.23), residues: 452 sheet: -2.93 (0.25), residues: 232 loop : -1.70 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 340 TYR 0.014 0.001 TYR C 258 PHE 0.011 0.001 PHE A 11 TRP 0.009 0.001 TRP C 82 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10732) covalent geometry : angle 0.54696 / 0.26 (14580) SS BOND : bond 0.00363 / 0.19 ( 2) SS BOND : angle 0.80792 / 0.42 ( 4) hydrogen bonds : bond 0.03087 / 2.09 ( 424) hydrogen bonds : angle 5.41260 / 3.72 ( 1236) metal coordination : bond 0.00587 / 0.37 ( 28) metal coordination : angle 6.18135 / 3.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8930 (t0) cc_final: 0.8611 (p0) REVERT: A 126 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8888 (pt0) REVERT: B 126 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8962 (pt0) REVERT: C 31 ASN cc_start: 0.8937 (t0) cc_final: 0.8670 (p0) REVERT: C 126 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8918 (pt0) REVERT: C 226 ASP cc_start: 0.9379 (t0) cc_final: 0.9118 (t0) REVERT: C 236 ASP cc_start: 0.9238 (t70) cc_final: 0.8880 (t0) REVERT: D 126 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.9068 (pt0) outliers start: 32 outliers final: 22 residues processed: 101 average time/residue: 0.1229 time to fit residues: 17.2490 Evaluate side-chains 72 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 329 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 108 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.059913 restraints weight = 18783.137| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.09 r_work: 0.2584 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10762 Z= 0.201 Angle : 0.622 9.513 14608 Z= 0.278 Chirality : 0.044 0.138 1624 Planarity : 0.003 0.034 1856 Dihedral : 5.319 48.009 1506 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.54 % Allowed : 16.42 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.22), residues: 1380 helix: 0.81 (0.24), residues: 452 sheet: -2.60 (0.26), residues: 232 loop : -1.24 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 340 TYR 0.015 0.001 TYR D 258 PHE 0.014 0.002 PHE C 11 TRP 0.006 0.001 TRP B 50 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (10732) covalent geometry : angle 0.57457 / 0.27 (14580) SS BOND : bond 0.00283 / 0.14 ( 2) SS BOND : angle 0.60607 / 0.31 ( 4) hydrogen bonds : bond 0.03075 / 2.08 ( 424) hydrogen bonds : angle 5.23898 / 3.60 ( 1236) metal coordination : bond 0.00745 / 0.48 ( 28) metal coordination : angle 5.90030 / 3.77 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 48 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8842 (t0) cc_final: 0.8442 (p0) REVERT: A 56 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8413 (tt) REVERT: A 126 GLN cc_start: 0.9340 (pt0) cc_final: 0.9097 (pt0) REVERT: B 56 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8268 (tt) REVERT: B 332 MET cc_start: 0.9153 (ttm) cc_final: 0.8902 (ptm) REVERT: C 31 ASN cc_start: 0.8853 (t0) cc_final: 0.8506 (p0) REVERT: C 126 GLN cc_start: 0.9376 (pt0) cc_final: 0.9117 (pt0) REVERT: C 226 ASP cc_start: 0.9392 (t0) cc_final: 0.9102 (t0) REVERT: C 236 ASP cc_start: 0.9259 (t70) cc_final: 0.8891 (t0) outliers start: 38 outliers final: 26 residues processed: 81 average time/residue: 0.0838 time to fit residues: 10.6145 Evaluate side-chains 69 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 41 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 329 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 6.9990 chunk 69 optimal weight: 0.0870 chunk 114 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** D 66 HIS ** 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 = 0.3378 r_free = 0.3378 target = 0.091007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062083 restraints weight = 18725.477| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.16 r_work: 0.2618 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10762 Z= 0.113 Angle : 0.524 7.645 14608 Z= 0.244 Chirality : 0.042 0.148 1624 Planarity : 0.003 0.032 1856 Dihedral : 4.841 43.836 1504 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.36 % Allowed : 17.44 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.87 (0.22), residues: 1380 helix: 1.04 (0.24), residues: 468 sheet: -2.57 (0.25), residues: 272 loop : -0.78 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 340 TYR 0.017 0.001 TYR A 258 PHE 0.014 0.001 PHE C 11 TRP 0.006 0.001 TRP D 50 HIS 0.002 0.000 HIS C 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (10732) covalent geometry : angle 0.49022 / 0.24 (14580) SS BOND : bond 0.00192 / 0.10 ( 2) SS BOND : angle 0.26573 / 0.13 ( 4) hydrogen bonds : bond 0.02644 / 1.79 ( 424) hydrogen bonds : angle 4.82164 / 3.31 ( 1236) metal coordination : bond 0.00325 / 0.21 ( 28) metal coordination : angle 4.58732 / 2.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 48 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8816 (t0) cc_final: 0.8442 (p0) REVERT: A 126 GLN cc_start: 0.9348 (pt0) cc_final: 0.9120 (pt0) REVERT: B 56 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8315 (tt) REVERT: B 75 MET cc_start: 0.8566 (ptp) cc_final: 0.8190 (mtm) REVERT: C 31 ASN cc_start: 0.8715 (t0) cc_final: 0.8360 (p0) REVERT: C 46 ASP cc_start: 0.8867 (m-30) cc_final: 0.8169 (m-30) REVERT: C 226 ASP cc_start: 0.9407 (t0) cc_final: 0.9092 (t0) REVERT: C 236 ASP cc_start: 0.9246 (t70) cc_final: 0.8829 (t0) REVERT: D 46 ASP cc_start: 0.8938 (m-30) cc_final: 0.8268 (m-30) outliers start: 36 outliers final: 21 residues processed: 79 average time/residue: 0.0818 time to fit residues: 10.2336 Evaluate side-chains 64 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 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 = 0.3347 r_free = 0.3347 target = 0.089952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.059700 restraints weight = 18960.393| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.20 r_work: 0.2587 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10762 Z= 0.169 Angle : 0.559 8.872 14608 Z= 0.257 Chirality : 0.043 0.146 1624 Planarity : 0.003 0.031 1856 Dihedral : 4.672 39.593 1502 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.64 % Allowed : 17.63 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.65 (0.23), residues: 1380 helix: 1.32 (0.24), residues: 456 sheet: -2.45 (0.25), residues: 272 loop : -0.69 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 340 TYR 0.016 0.001 TYR A 258 PHE 0.010 0.001 PHE D 11 TRP 0.008 0.001 TRP A 92 HIS 0.002 0.000 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (10732) covalent geometry : angle 0.52598 / 0.26 (14580) SS BOND : bond 0.00186 / 0.09 ( 2) SS BOND : angle 0.15691 / 0.08 ( 4) hydrogen bonds : bond 0.02810 / 1.91 ( 424) hydrogen bonds : angle 4.81706 / 3.31 ( 1236) metal coordination : bond 0.00607 / 0.38 ( 28) metal coordination : angle 4.72196 / 3.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 43 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8748 (t0) cc_final: 0.8396 (p0) REVERT: A 126 GLN cc_start: 0.9334 (pt0) cc_final: 0.9043 (pt0) REVERT: C 31 ASN cc_start: 0.8719 (t0) cc_final: 0.8388 (p0) REVERT: C 46 ASP cc_start: 0.8798 (m-30) cc_final: 0.8211 (m-30) REVERT: C 226 ASP cc_start: 0.9393 (t0) cc_final: 0.9089 (t0) REVERT: C 236 ASP cc_start: 0.9305 (t70) cc_final: 0.8882 (t0) REVERT: D 46 ASP cc_start: 0.8943 (m-30) cc_final: 0.8336 (m-30) outliers start: 39 outliers final: 30 residues processed: 77 average time/residue: 0.0760 time to fit residues: 9.4943 Evaluate side-chains 72 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 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 = 0.3339 r_free = 0.3339 target = 0.088827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.059867 restraints weight = 19111.941| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.11 r_work: 0.2568 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10762 Z= 0.218 Angle : 0.588 7.825 14608 Z= 0.270 Chirality : 0.044 0.143 1624 Planarity : 0.003 0.030 1856 Dihedral : 4.597 33.707 1502 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.54 % Allowed : 18.66 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.63 (0.23), residues: 1380 helix: 1.30 (0.24), residues: 456 sheet: -2.44 (0.25), residues: 272 loop : -0.64 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 340 TYR 0.015 0.001 TYR C 258 PHE 0.009 0.001 PHE C 11 TRP 0.007 0.001 TRP A 92 HIS 0.003 0.000 HIS D 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (10732) covalent geometry : angle 0.55203 / 0.27 (14580) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 0.21817 / 0.11 ( 4) hydrogen bonds : bond 0.02940 / 1.99 ( 424) hydrogen bonds : angle 4.91452 / 3.36 ( 1236) metal coordination : bond 0.00752 / 0.48 ( 28) metal coordination : angle 5.06428 / 3.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 39 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8785 (t0) cc_final: 0.8407 (p0) REVERT: A 126 GLN cc_start: 0.9212 (pt0) cc_final: 0.8832 (pt0) REVERT: C 31 ASN cc_start: 0.8727 (t0) cc_final: 0.8366 (p0) REVERT: C 46 ASP cc_start: 0.8894 (m-30) cc_final: 0.8330 (m-30) outliers start: 38 outliers final: 30 residues processed: 71 average time/residue: 0.0751 time to fit residues: 8.6730 Evaluate side-chains 69 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 131 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 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 = 0.3308 r_free = 0.3308 target = 0.087415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.058538 restraints weight = 18991.502| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.09 r_work: 0.2543 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 10762 Z= 0.252 Angle : 0.611 8.425 14608 Z= 0.280 Chirality : 0.044 0.138 1624 Planarity : 0.003 0.030 1856 Dihedral : 4.632 33.127 1502 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.92 % Allowed : 18.38 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.75 (0.22), residues: 1380 helix: 1.30 (0.24), residues: 456 sheet: -2.51 (0.25), residues: 280 loop : -0.76 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 340 TYR 0.015 0.001 TYR C 258 PHE 0.008 0.001 PHE C 11 TRP 0.007 0.001 TRP A 92 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 (10732) covalent geometry : angle 0.57432 / 0.28 (14580) SS BOND : bond 0.00083 / 0.04 ( 2) SS BOND : angle 0.11726 / 0.06 ( 4) hydrogen bonds : bond 0.03027 / 2.04 ( 424) hydrogen bonds : angle 4.99165 / 3.42 ( 1236) metal coordination : bond 0.00851 / 0.54 ( 28) metal coordination : angle 5.15975 / 3.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 36 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.9213 (pt0) cc_final: 0.8798 (pt0) REVERT: C 332 MET cc_start: 0.8958 (ppp) cc_final: 0.8728 (ppp) outliers start: 42 outliers final: 32 residues processed: 72 average time/residue: 0.0820 time to fit residues: 9.5415 Evaluate side-chains 67 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 35 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 70 optimal weight: 0.0770 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 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 = 0.3369 r_free = 0.3369 target = 0.090692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.061511 restraints weight = 18614.854| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.13 r_work: 0.2622 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10762 Z= 0.129 Angle : 0.521 6.686 14608 Z= 0.245 Chirality : 0.043 0.144 1624 Planarity : 0.003 0.030 1856 Dihedral : 4.520 34.494 1502 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.08 % Allowed : 19.31 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.45 (0.23), residues: 1380 helix: 1.37 (0.24), residues: 468 sheet: -2.30 (0.26), residues: 272 loop : -0.53 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 340 TYR 0.016 0.001 TYR A 258 PHE 0.010 0.001 PHE C 11 TRP 0.006 0.001 TRP B 82 HIS 0.002 0.000 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10732) covalent geometry : angle 0.49376 / 0.24 (14580) SS BOND : bond 0.00111 / 0.06 ( 2) SS BOND : angle 0.11075 / 0.06 ( 4) hydrogen bonds : bond 0.02693 / 1.82 ( 424) hydrogen bonds : angle 4.74275 / 3.25 ( 1236) metal coordination : bond 0.00368 / 0.23 ( 28) metal coordination : angle 4.15173 / 2.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 45 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8859 (m-30) cc_final: 0.8195 (m-30) REVERT: A 126 GLN cc_start: 0.9184 (pt0) cc_final: 0.8776 (pt0) REVERT: C 46 ASP cc_start: 0.8826 (m-30) cc_final: 0.8248 (m-30) REVERT: C 236 ASP cc_start: 0.9316 (t70) cc_final: 0.8866 (t0) REVERT: C 332 MET cc_start: 0.8958 (ppp) cc_final: 0.8720 (ppp) REVERT: D 347 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8957 (mtmt) outliers start: 33 outliers final: 29 residues processed: 72 average time/residue: 0.0971 time to fit residues: 10.5523 Evaluate side-chains 70 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 41 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 111 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 283 GLN C 31 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.059751 restraints weight = 19370.452| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.19 r_work: 0.2596 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10762 Z= 0.101 Angle : 0.499 7.521 14608 Z= 0.236 Chirality : 0.043 0.144 1624 Planarity : 0.003 0.029 1856 Dihedral : 4.342 33.655 1500 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 19.40 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.24 (0.23), residues: 1380 helix: 1.63 (0.24), residues: 468 sheet: -2.21 (0.26), residues: 276 loop : -0.45 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 257 TYR 0.017 0.001 TYR A 258 PHE 0.010 0.001 PHE C 11 TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (10732) covalent geometry : angle 0.47557 / 0.24 (14580) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 0.10187 / 0.05 ( 4) hydrogen bonds : bond 0.02495 / 1.69 ( 424) hydrogen bonds : angle 4.54284 / 3.12 ( 1236) metal coordination : bond 0.00260 / 0.16 ( 28) metal coordination : angle 3.75054 / 2.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 49 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8693 (m-30) cc_final: 0.8264 (m-30) REVERT: A 126 GLN cc_start: 0.9260 (pt0) cc_final: 0.8936 (pt0) REVERT: A 332 MET cc_start: 0.8907 (ppp) cc_final: 0.8697 (ppp) REVERT: B 226 ASP cc_start: 0.9363 (t0) cc_final: 0.9090 (t0) REVERT: C 46 ASP cc_start: 0.8769 (m-30) cc_final: 0.8163 (m-30) REVERT: C 236 ASP cc_start: 0.9295 (t70) cc_final: 0.8835 (t0) REVERT: C 332 MET cc_start: 0.8983 (ppp) cc_final: 0.8742 (ppp) REVERT: D 226 ASP cc_start: 0.9371 (t0) cc_final: 0.9089 (t0) outliers start: 32 outliers final: 27 residues processed: 76 average time/residue: 0.0829 time to fit residues: 10.0284 Evaluate side-chains 69 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 42 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 70 optimal weight: 0.0000 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 62 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.061096 restraints weight = 18582.369| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.09 r_work: 0.2605 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10762 Z= 0.106 Angle : 0.509 8.521 14608 Z= 0.241 Chirality : 0.043 0.148 1624 Planarity : 0.003 0.029 1856 Dihedral : 4.323 32.930 1500 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.89 % Allowed : 19.40 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.17 (0.23), residues: 1380 helix: 1.69 (0.24), residues: 468 sheet: -2.11 (0.26), residues: 276 loop : -0.44 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 257 TYR 0.017 0.001 TYR A 258 PHE 0.010 0.001 PHE D 11 TRP 0.007 0.001 TRP A 50 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10732) covalent geometry : angle 0.48634 / 0.24 (14580) SS BOND : bond 0.00086 / 0.04 ( 2) SS BOND : angle 0.05045 / 0.02 ( 4) hydrogen bonds : bond 0.02504 / 1.70 ( 424) hydrogen bonds : angle 4.51528 / 3.10 ( 1236) metal coordination : bond 0.00302 / 0.19 ( 28) metal coordination : angle 3.71003 / 2.31 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 48 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8690 (m-30) cc_final: 0.8250 (m-30) REVERT: A 126 GLN cc_start: 0.9256 (pt0) cc_final: 0.8943 (pt0) REVERT: B 226 ASP cc_start: 0.9372 (t0) cc_final: 0.9104 (t0) REVERT: C 46 ASP cc_start: 0.8776 (m-30) cc_final: 0.8171 (m-30) REVERT: C 226 ASP cc_start: 0.9362 (t0) cc_final: 0.9078 (t0) REVERT: C 236 ASP cc_start: 0.9285 (t70) cc_final: 0.8823 (t0) REVERT: C 332 MET cc_start: 0.8972 (ppp) cc_final: 0.8753 (ppp) REVERT: D 46 ASP cc_start: 0.8870 (m-30) cc_final: 0.8165 (m-30) REVERT: D 226 ASP cc_start: 0.9373 (t0) cc_final: 0.9092 (t0) outliers start: 31 outliers final: 26 residues processed: 73 average time/residue: 0.0732 time to fit residues: 8.6902 Evaluate side-chains 74 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.057296 restraints weight = 19750.089| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.16 r_work: 0.2586 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10762 Z= 0.239 Angle : 0.606 11.333 14608 Z= 0.284 Chirality : 0.045 0.237 1624 Planarity : 0.003 0.029 1856 Dihedral : 4.457 31.382 1500 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.36 % Allowed : 19.12 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.41 (0.23), residues: 1380 helix: 1.63 (0.24), residues: 456 sheet: -2.25 (0.26), residues: 280 loop : -0.64 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 257 TYR 0.015 0.001 TYR A 258 PHE 0.008 0.001 PHE D 11 TRP 0.006 0.001 TRP A 50 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (10732) covalent geometry : angle 0.57256 / 0.28 (14580) SS BOND : bond 0.01684 / 0.89 ( 2) SS BOND : angle 3.68857 / 1.96 ( 4) hydrogen bonds : bond 0.02933 / 1.99 ( 424) hydrogen bonds : angle 4.81311 / 3.29 ( 1236) metal coordination : bond 0.00827 / 0.52 ( 28) metal coordination : angle 4.66190 / 2.94 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.12 seconds wall clock time: 34 minutes 14.10 seconds (2054.10 seconds total)