Starting phenix.real_space_refine on Wed Mar 4 03:45:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kjy_22902/03_2026/7kjy_22902.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjy_22902/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kjy_22902/03_2026/7kjy_22902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjy_22902/03_2026/7kjy_22902.map" model { file = "/net/cci-nas-00/data/ceres_data/7kjy_22902/03_2026/7kjy_22902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjy_22902/03_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-5986/lib/python3.9/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: 2.54, per 1000 atoms: 0.24 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: 1.03 Conformation dependent library (CDL) restraints added in 640.7 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: 0.46 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: 1.59 Time building geometry restraints manager: 1.38 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: 5644 17.41 - 34.82: 584 34.82 - 52.23: 122 52.23 - 69.64: 24 69.64 - 87.05: 24 Dihedral angle restraints: 6398 sinusoidal: 2534 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 6395 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: 0.03 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: 0.640 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.370 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 15.495 87.055 3968 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 covalent geometry : bond 0.00690 (10732) covalent geometry : angle 0.70678 (14580) SS BOND : bond 0.10341 ( 2) SS BOND : angle 3.21162 ( 4) hydrogen bonds : bond 0.15976 ( 424) hydrogen bonds : angle 7.66160 ( 1236) metal coordination : bond 0.11655 ( 28) metal coordination : angle 14.48864 ( 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 : 0.410 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: 0.1367 time to fit residues: 24.2632 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 : 0.265 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 121 HIS ** 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 = 0.3357 r_free = 0.3357 target = 0.089783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.061889 restraints weight = 18733.960| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.14 r_work: 0.2634 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10762 Z= 0.114 Angle : 0.590 10.245 14608 Z= 0.265 Chirality : 0.043 0.148 1624 Planarity : 0.004 0.035 1856 Dihedral : 8.167 71.229 1726 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.99 % Allowed : 14.37 % Favored : 82.65 % 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: -1.87 (0.21), residues: 1380 helix: 0.33 (0.23), residues: 452 sheet: -2.94 (0.25), residues: 232 loop : -1.66 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 340 TYR 0.015 0.001 TYR C 258 PHE 0.012 0.001 PHE A 11 TRP 0.008 0.001 TRP B 82 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00254 (10732) covalent geometry : angle 0.53797 (14580) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.77501 ( 4) hydrogen bonds : bond 0.02988 ( 424) hydrogen bonds : angle 5.35379 ( 1236) metal coordination : bond 0.00567 ( 28) metal coordination : angle 6.00742 ( 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 106 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8880 (t0) cc_final: 0.8590 (p0) REVERT: A 126 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8896 (pt0) REVERT: B 126 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8966 (pt0) REVERT: C 31 ASN cc_start: 0.8906 (t0) cc_final: 0.8643 (p0) REVERT: C 126 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8935 (pt0) REVERT: C 226 ASP cc_start: 0.9387 (t0) cc_final: 0.9127 (t0) REVERT: C 236 ASP cc_start: 0.9231 (t70) cc_final: 0.8867 (t0) REVERT: D 126 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.9064 (pt0) outliers start: 32 outliers final: 21 residues processed: 102 average time/residue: 0.1206 time to fit residues: 16.9912 Evaluate side-chains 72 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 79 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.3345 r_free = 0.3345 target = 0.089707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.059953 restraints weight = 19043.958| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.20 r_work: 0.2593 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10762 Z= 0.164 Angle : 0.590 9.684 14608 Z= 0.266 Chirality : 0.043 0.139 1624 Planarity : 0.003 0.035 1856 Dihedral : 7.713 72.979 1706 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.54 % Allowed : 15.49 % Favored : 80.97 % 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: -1.16 (0.22), residues: 1380 helix: 0.89 (0.24), residues: 452 sheet: -2.59 (0.26), residues: 232 loop : -1.19 (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 A 258 PHE 0.015 0.001 PHE C 11 TRP 0.006 0.001 TRP B 50 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00376 (10732) covalent geometry : angle 0.54368 (14580) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.55072 ( 4) hydrogen bonds : bond 0.02957 ( 424) hydrogen bonds : angle 5.13930 ( 1236) metal coordination : bond 0.00617 ( 28) metal coordination : angle 5.66123 ( 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 88 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 50 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8885 (t0) cc_final: 0.8461 (p0) REVERT: A 56 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (tt) REVERT: B 56 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8407 (tt) REVERT: B 75 MET cc_start: 0.8842 (ptp) cc_final: 0.8202 (mtm) REVERT: B 126 GLN cc_start: 0.9279 (pt0) cc_final: 0.9032 (pm20) REVERT: B 332 MET cc_start: 0.9145 (ttm) cc_final: 0.8925 (ptm) REVERT: C 31 ASN cc_start: 0.8840 (t0) cc_final: 0.8498 (p0) REVERT: C 226 ASP cc_start: 0.9405 (t0) cc_final: 0.9102 (t0) REVERT: C 236 ASP cc_start: 0.9241 (t70) cc_final: 0.8877 (t0) outliers start: 38 outliers final: 28 residues processed: 83 average time/residue: 0.0860 time to fit residues: 10.9995 Evaluate side-chains 71 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 41 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 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 325 LEU Chi-restraints excluded: chain D residue 329 TYR Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 126 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.058555 restraints weight = 19218.334| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.10 r_work: 0.2549 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2108 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= 0.253 Angle : 0.624 8.647 14608 Z= 0.285 Chirality : 0.044 0.140 1624 Planarity : 0.003 0.033 1856 Dihedral : 7.789 76.008 1705 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.54 % Allowed : 17.16 % Favored : 79.29 % 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: -1.06 (0.22), residues: 1380 helix: 1.00 (0.24), residues: 452 sheet: -2.72 (0.24), residues: 272 loop : -0.92 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 340 TYR 0.016 0.001 TYR C 258 PHE 0.011 0.002 PHE C 11 TRP 0.007 0.001 TRP C 92 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00570 (10732) covalent geometry : angle 0.57846 (14580) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.40617 ( 4) hydrogen bonds : bond 0.03116 ( 424) hydrogen bonds : angle 5.15180 ( 1236) metal coordination : bond 0.00904 ( 28) metal coordination : angle 5.80886 ( 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 75 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 37 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9299 (pt0) cc_final: 0.9038 (pt0) REVERT: B 332 MET cc_start: 0.9162 (ttm) cc_final: 0.8914 (ptm) REVERT: C 31 ASN cc_start: 0.8756 (t0) cc_final: 0.8415 (p0) outliers start: 38 outliers final: 25 residues processed: 73 average time/residue: 0.0699 time to fit residues: 8.3443 Evaluate side-chains 60 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 259 VAL Chi-restraints excluded: chain A residue 289 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 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 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 329 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 49 optimal weight: 0.0470 chunk 100 optimal weight: 9.9990 chunk 94 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.061355 restraints weight = 18689.306| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.09 r_work: 0.2594 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10762 Z= 0.136 Angle : 0.537 7.367 14608 Z= 0.250 Chirality : 0.043 0.146 1624 Planarity : 0.003 0.032 1856 Dihedral : 7.302 68.107 1705 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.54 % Allowed : 17.91 % Favored : 78.54 % 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: 1.25 (0.24), residues: 456 sheet: -2.51 (0.25), residues: 272 loop : -0.75 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 340 TYR 0.016 0.001 TYR C 258 PHE 0.012 0.001 PHE C 11 TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00310 (10732) covalent geometry : angle 0.50406 (14580) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.20382 ( 4) hydrogen bonds : bond 0.02757 ( 424) hydrogen bonds : angle 4.87877 ( 1236) metal coordination : bond 0.00429 ( 28) metal coordination : angle 4.59390 ( 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 77 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 39 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9281 (pt0) cc_final: 0.8993 (pt0) REVERT: C 31 ASN cc_start: 0.8719 (t0) cc_final: 0.8366 (p0) REVERT: C 135 GLN cc_start: 0.9298 (mm-40) cc_final: 0.9067 (mm110) REVERT: D 46 ASP cc_start: 0.8958 (m-30) cc_final: 0.8318 (m-30) outliers start: 38 outliers final: 26 residues processed: 72 average time/residue: 0.0881 time to fit residues: 10.0485 Evaluate side-chains 63 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 37 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.3328 r_free = 0.3328 target = 0.088161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.059309 restraints weight = 19211.861| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.12 r_work: 0.2558 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10762 Z= 0.242 Angle : 0.609 8.487 14608 Z= 0.279 Chirality : 0.044 0.139 1624 Planarity : 0.003 0.031 1856 Dihedral : 7.584 73.635 1702 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.45 % Allowed : 19.03 % 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: -0.74 (0.22), residues: 1380 helix: 1.18 (0.24), residues: 456 sheet: -2.47 (0.26), residues: 272 loop : -0.70 (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 C 258 PHE 0.009 0.001 PHE C 11 TRP 0.010 0.001 TRP A 92 HIS 0.003 0.001 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00547 (10732) covalent geometry : angle 0.57204 (14580) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.16521 ( 4) hydrogen bonds : bond 0.03056 ( 424) hydrogen bonds : angle 5.00428 ( 1236) metal coordination : bond 0.00843 ( 28) metal coordination : angle 5.18179 ( 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 71 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 34 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9269 (pt0) cc_final: 0.8880 (pt0) outliers start: 37 outliers final: 32 residues processed: 66 average time/residue: 0.0823 time to fit residues: 8.7507 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 : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 58 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 332 MET 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 256 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 18 LEU 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: 7.9990 chunk 71 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 135 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 135 GLN ** 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 = 0.3299 r_free = 0.3299 target = 0.087302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.057463 restraints weight = 19437.096| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.13 r_work: 0.2529 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 10762 Z= 0.304 Angle : 0.645 8.629 14608 Z= 0.296 Chirality : 0.045 0.137 1624 Planarity : 0.003 0.031 1856 Dihedral : 7.765 74.619 1702 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.92 % Allowed : 18.94 % Favored : 77.15 % 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: -0.92 (0.22), residues: 1380 helix: 1.16 (0.24), residues: 452 sheet: -2.55 (0.25), residues: 280 loop : -0.89 (0.25), residues: 648 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 0.009 0.001 TRP A 92 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00684 (10732) covalent geometry : angle 0.60403 (14580) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.11482 ( 4) hydrogen bonds : bond 0.03177 ( 424) hydrogen bonds : angle 5.15490 ( 1236) metal coordination : bond 0.01040 ( 28) metal coordination : angle 5.60338 ( 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 76 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 34 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9200 (pt0) cc_final: 0.8790 (pt0) outliers start: 42 outliers final: 32 residues processed: 71 average time/residue: 0.0742 time to fit residues: 8.5972 Evaluate side-chains 63 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 31 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 332 MET Chi-restraints excluded: chain A residue 336 GLN 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 256 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 18 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 113 optimal weight: 0.0050 chunk 70 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 283 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** 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 = 0.3355 r_free = 0.3355 target = 0.090344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.060086 restraints weight = 19465.477| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.20 r_work: 0.2606 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10762 Z= 0.091 Angle : 0.497 5.715 14608 Z= 0.239 Chirality : 0.043 0.146 1624 Planarity : 0.003 0.032 1856 Dihedral : 7.055 62.662 1701 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.80 % Allowed : 19.68 % 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: -0.37 (0.23), residues: 1380 helix: 1.58 (0.24), residues: 456 sheet: -2.31 (0.26), residues: 276 loop : -0.52 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 340 TYR 0.016 0.001 TYR C 258 PHE 0.011 0.001 PHE D 11 TRP 0.011 0.001 TRP C 82 HIS 0.002 0.000 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00208 (10732) covalent geometry : angle 0.47596 (14580) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.09738 ( 4) hydrogen bonds : bond 0.02548 ( 424) hydrogen bonds : angle 4.66331 ( 1236) metal coordination : bond 0.00178 ( 28) metal coordination : angle 3.56600 ( 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 85 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9299 (pt0) cc_final: 0.8939 (pt0) REVERT: B 226 ASP cc_start: 0.9362 (t0) cc_final: 0.9109 (t0) REVERT: C 31 ASN cc_start: 0.8816 (t0) cc_final: 0.8456 (p0) REVERT: C 46 ASP cc_start: 0.8782 (m-30) cc_final: 0.8249 (m-30) REVERT: D 226 ASP cc_start: 0.9349 (t0) cc_final: 0.9103 (t0) REVERT: D 347 LYS cc_start: 0.9291 (mmmt) cc_final: 0.9004 (mtmt) outliers start: 30 outliers final: 26 residues processed: 81 average time/residue: 0.0874 time to fit residues: 10.7841 Evaluate side-chains 71 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 117 SER 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 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 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 18 LEU 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 336 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 111 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 121 HIS ** 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** B 283 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 135 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.059649 restraints weight = 19144.270| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.10 r_work: 0.2562 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10762 Z= 0.175 Angle : 0.540 7.844 14608 Z= 0.256 Chirality : 0.044 0.155 1624 Planarity : 0.003 0.030 1856 Dihedral : 7.300 70.125 1700 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.17 % Allowed : 19.12 % 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: -0.39 (0.23), residues: 1380 helix: 1.53 (0.23), residues: 456 sheet: -2.28 (0.26), residues: 276 loop : -0.53 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 257 TYR 0.016 0.001 TYR C 258 PHE 0.009 0.001 PHE D 11 TRP 0.007 0.001 TRP C 50 HIS 0.002 0.000 HIS C 138 Details of bonding type rmsd covalent geometry : bond 0.00398 (10732) covalent geometry : angle 0.51418 (14580) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.08586 ( 4) hydrogen bonds : bond 0.02816 ( 424) hydrogen bonds : angle 4.74597 ( 1236) metal coordination : bond 0.00577 ( 28) metal coordination : angle 4.10506 ( 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 79 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 45 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9301 (pt0) cc_final: 0.8955 (pt0) REVERT: B 244 ASN cc_start: 0.9154 (m-40) cc_final: 0.8908 (m-40) REVERT: C 46 ASP cc_start: 0.8813 (m-30) cc_final: 0.8267 (m-30) REVERT: C 236 ASP cc_start: 0.9322 (t70) cc_final: 0.8872 (t0) REVERT: D 347 LYS cc_start: 0.9276 (mmmt) cc_final: 0.9010 (mtmt) outliers start: 34 outliers final: 30 residues processed: 75 average time/residue: 0.0814 time to fit residues: 9.7355 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 : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 117 SER 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 58 THR Chi-restraints excluded: chain B residue 259 VAL 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 9 VAL 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 18 LEU 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 336 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 121 HIS B 262 ASN B 283 GLN ** C 66 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.061915 restraints weight = 18656.134| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.09 r_work: 0.2636 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10762 Z= 0.088 Angle : 0.488 8.023 14608 Z= 0.238 Chirality : 0.043 0.145 1624 Planarity : 0.003 0.030 1856 Dihedral : 6.982 65.220 1700 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.71 % Allowed : 20.06 % Favored : 77.24 % 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: -0.20 (0.23), residues: 1380 helix: 1.79 (0.24), residues: 456 sheet: -2.11 (0.26), residues: 276 loop : -0.53 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 257 TYR 0.017 0.001 TYR C 258 PHE 0.011 0.001 PHE D 11 TRP 0.011 0.001 TRP B 92 HIS 0.002 0.000 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00204 (10732) covalent geometry : angle 0.47137 (14580) SS BOND : bond 0.00059 ( 2) SS BOND : angle 0.09216 ( 4) hydrogen bonds : bond 0.02489 ( 424) hydrogen bonds : angle 4.52070 ( 1236) metal coordination : bond 0.00201 ( 28) metal coordination : angle 3.14767 ( 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 90 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8821 (m-30) cc_final: 0.8065 (m-30) REVERT: B 94 ASN cc_start: 0.9156 (t0) cc_final: 0.8813 (t0) REVERT: B 126 GLN cc_start: 0.9282 (pt0) cc_final: 0.9011 (pt0) REVERT: B 226 ASP cc_start: 0.9373 (t0) cc_final: 0.9124 (t0) REVERT: B 347 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8723 (tttp) REVERT: C 31 ASN cc_start: 0.8757 (t0) cc_final: 0.8512 (p0) REVERT: C 46 ASP cc_start: 0.8661 (m-30) cc_final: 0.8098 (m-30) REVERT: C 226 ASP cc_start: 0.9359 (t0) cc_final: 0.9096 (t0) REVERT: C 236 ASP cc_start: 0.9271 (t70) cc_final: 0.8800 (t0) REVERT: D 46 ASP cc_start: 0.8808 (m-30) cc_final: 0.8096 (m-30) REVERT: D 226 ASP cc_start: 0.9368 (t0) cc_final: 0.9114 (t0) outliers start: 29 outliers final: 24 residues processed: 85 average time/residue: 0.0790 time to fit residues: 10.7943 Evaluate side-chains 80 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 117 SER 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 259 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 256 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 78 ASN 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 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: 4.9990 chunk 97 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 121 HIS ** 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 283 GLN ** C 66 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.057021 restraints weight = 19703.076| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.13 r_work: 0.2536 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2708 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= 0.241 Angle : 0.588 8.413 14608 Z= 0.279 Chirality : 0.044 0.143 1624 Planarity : 0.003 0.030 1856 Dihedral : 7.581 75.214 1700 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.08 % Allowed : 19.87 % Favored : 77.05 % 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: -0.44 (0.23), residues: 1380 helix: 1.62 (0.24), residues: 456 sheet: -2.28 (0.25), residues: 284 loop : -0.65 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 257 TYR 0.015 0.001 TYR C 258 PHE 0.009 0.001 PHE C 281 TRP 0.009 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00545 (10732) covalent geometry : angle 0.56425 (14580) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.08318 ( 4) hydrogen bonds : bond 0.03042 ( 424) hydrogen bonds : angle 4.80609 ( 1236) metal coordination : bond 0.00841 ( 28) metal coordination : angle 4.12371 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1851.32 seconds wall clock time: 32 minutes 44.51 seconds (1964.51 seconds total)