Starting phenix.real_space_refine on Mon Jul 28 18:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kjy_22902/07_2025/7kjy_22902.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjy_22902/07_2025/7kjy_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_22902/07_2025/7kjy_22902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2025/7kjy_22902.map" model { file = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2025/7kjy_22902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjy_22902/07_2025/7kjy_22902.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.23, per 1000 atoms: 0.59 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: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.38 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: 3.53 Time building geometry restraints manager: 3.13 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.360 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 29.310 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- 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 : 14.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP D 92 HIS 0.003 0.001 HIS B 138 PHE 0.007 0.001 PHE C 221 TYR 0.015 0.001 TYR B 258 ARG 0.002 0.000 ARG D 257 Details of bonding type rmsd hydrogen bonds : bond 0.15976 ( 424) hydrogen bonds : angle 7.66160 ( 1236) metal coordination : bond 0.11655 ( 28) metal coordination : angle 14.48864 ( 24) SS BOND : bond 0.10341 ( 2) SS BOND : angle 3.21162 ( 4) covalent geometry : bond 0.00690 (10732) covalent geometry : angle 0.70678 (14580) *********************** 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 : 1.188 Fit side-chains 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: 0.3059 time to fit residues: 54.5315 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 : 1.204 ------------------------------------------------------------------------------- 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 114 optimal weight: 9.9990 chunk 103 optimal weight: 0.0570 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.0060 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1716 ------------------------------------------------------------------------------- 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 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 = 0.3354 r_free = 0.3354 target = 0.089602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.061549 restraints weight = 18664.306| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.13 r_work: 0.2625 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10762 Z= 0.126 Angle : 0.599 10.319 14608 Z= 0.269 Chirality : 0.043 0.146 1624 Planarity : 0.004 0.035 1856 Dihedral : 8.214 71.613 1726 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.08 % Allowed : 14.46 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.21), residues: 1380 helix: 0.27 (0.23), residues: 452 sheet: -2.94 (0.25), residues: 232 loop : -1.67 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS C 48 PHE 0.012 0.001 PHE A 11 TYR 0.015 0.001 TYR C 258 ARG 0.006 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 424) hydrogen bonds : angle 5.36866 ( 1236) metal coordination : bond 0.00569 ( 28) metal coordination : angle 6.11323 ( 24) SS BOND : bond 0.00288 ( 2) SS BOND : angle 0.74795 ( 4) covalent geometry : bond 0.00281 (10732) covalent geometry : angle 0.54621 (14580) *********************** 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: 33 poor density : 73 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8892 (t0) cc_final: 0.8583 (p0) REVERT: A 126 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8899 (pt0) REVERT: B 126 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8959 (pt0) REVERT: C 31 ASN cc_start: 0.8897 (t0) cc_final: 0.8636 (p0) REVERT: C 126 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8932 (pt0) REVERT: C 226 ASP cc_start: 0.9386 (t0) cc_final: 0.9127 (t0) REVERT: C 236 ASP cc_start: 0.9237 (t70) cc_final: 0.8881 (t0) REVERT: D 126 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.9094 (pt0) outliers start: 33 outliers final: 22 residues processed: 102 average time/residue: 0.2682 time to fit residues: 38.5215 Evaluate side-chains 72 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 329 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 36 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 35 optimal weight: 0.0170 chunk 113 optimal weight: 7.9990 overall best weight: 1.1538 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.093439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.065018 restraints weight = 19404.247| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.07 r_work: 0.2624 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10762 Z= 0.120 Angle : 0.569 9.552 14608 Z= 0.257 Chirality : 0.043 0.142 1624 Planarity : 0.003 0.035 1856 Dihedral : 7.572 70.379 1706 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.17 % Allowed : 16.42 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1380 helix: 0.86 (0.24), residues: 456 sheet: -2.56 (0.26), residues: 232 loop : -1.14 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 50 HIS 0.002 0.000 HIS A 138 PHE 0.015 0.001 PHE C 11 TYR 0.014 0.001 TYR D 258 ARG 0.004 0.001 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 424) hydrogen bonds : angle 5.06238 ( 1236) metal coordination : bond 0.00409 ( 28) metal coordination : angle 5.43090 ( 24) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.60823 ( 4) covalent geometry : bond 0.00281 (10732) covalent geometry : angle 0.52514 (14580) *********************** 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 84 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 50 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.8862 (t0) cc_final: 0.8462 (p0) REVERT: A 56 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 56 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8380 (tt) REVERT: B 75 MET cc_start: 0.8834 (ptp) cc_final: 0.8255 (mtm) REVERT: B 126 GLN cc_start: 0.9256 (pt0) cc_final: 0.8992 (pm20) REVERT: B 332 MET cc_start: 0.9123 (ttm) cc_final: 0.8905 (ptm) REVERT: C 31 ASN cc_start: 0.8825 (t0) cc_final: 0.8494 (p0) REVERT: C 46 ASP cc_start: 0.8788 (m-30) cc_final: 0.8114 (m-30) REVERT: C 226 ASP cc_start: 0.9405 (t0) cc_final: 0.9105 (t0) REVERT: C 236 ASP cc_start: 0.9227 (t70) cc_final: 0.8849 (t0) REVERT: D 44 HIS cc_start: 0.8027 (m170) cc_final: 0.7765 (m170) REVERT: D 46 ASP cc_start: 0.8920 (m-30) cc_final: 0.8255 (m-30) outliers start: 34 outliers final: 23 residues processed: 79 average time/residue: 0.2472 time to fit residues: 30.3791 Evaluate side-chains 67 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 259 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 294 TYR 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 132 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 107 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.058834 restraints weight = 18851.951| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.07 r_work: 0.2554 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2083 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= 0.247 Angle : 0.619 8.773 14608 Z= 0.281 Chirality : 0.044 0.141 1624 Planarity : 0.003 0.033 1856 Dihedral : 7.809 75.350 1705 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1380 helix: 1.03 (0.24), residues: 452 sheet: -2.71 (0.24), residues: 272 loop : -0.90 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 92 HIS 0.002 0.000 HIS C 138 PHE 0.010 0.001 PHE C 11 TYR 0.015 0.001 TYR A 258 ARG 0.004 0.001 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 424) hydrogen bonds : angle 5.12154 ( 1236) metal coordination : bond 0.00912 ( 28) metal coordination : angle 5.89151 ( 24) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.39778 ( 4) covalent geometry : bond 0.00554 (10732) covalent geometry : angle 0.57161 (14580) *********************** 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 : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9275 (pt0) cc_final: 0.8996 (pt0) REVERT: B 332 MET cc_start: 0.9171 (ttm) cc_final: 0.8921 (ptm) REVERT: C 31 ASN cc_start: 0.8722 (t0) cc_final: 0.8437 (p0) REVERT: C 135 GLN cc_start: 0.9351 (mm-40) cc_final: 0.9131 (mm110) outliers start: 38 outliers final: 27 residues processed: 72 average time/residue: 0.2748 time to fit residues: 31.3061 Evaluate side-chains 63 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 36 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 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 325 LEU 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 Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 107 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.059010 restraints weight = 18825.675| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.07 r_work: 0.2558 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2247 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= 0.238 Angle : 0.596 8.004 14608 Z= 0.275 Chirality : 0.044 0.141 1624 Planarity : 0.003 0.032 1856 Dihedral : 7.589 71.016 1705 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.64 % Allowed : 18.47 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1380 helix: 1.09 (0.24), residues: 456 sheet: -2.60 (0.25), residues: 272 loop : -0.83 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 92 HIS 0.003 0.000 HIS B 138 PHE 0.010 0.001 PHE C 11 TYR 0.016 0.001 TYR C 258 ARG 0.003 0.000 ARG C 340 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 424) hydrogen bonds : angle 5.04433 ( 1236) metal coordination : bond 0.00800 ( 28) metal coordination : angle 5.20580 ( 24) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.19142 ( 4) covalent geometry : bond 0.00538 (10732) covalent geometry : angle 0.55833 (14580) *********************** 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 76 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 37 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8868 (pt0) REVERT: C 270 MET cc_start: 0.9076 (mtm) cc_final: 0.8810 (mtm) outliers start: 39 outliers final: 30 residues processed: 71 average time/residue: 0.2315 time to fit residues: 25.7802 Evaluate side-chains 67 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 36 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 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 63 VAL Chi-restraints excluded: chain B residue 126 GLN 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 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 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 315 SER Chi-restraints excluded: chain D residue 329 TYR 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 112 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 0.0470 chunk 49 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 283 GLN C 31 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062453 restraints weight = 18485.241| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.08 r_work: 0.2634 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10762 Z= 0.089 Angle : 0.497 6.906 14608 Z= 0.238 Chirality : 0.043 0.147 1624 Planarity : 0.003 0.031 1856 Dihedral : 7.007 64.520 1703 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.71 % Allowed : 19.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1380 helix: 1.34 (0.24), residues: 468 sheet: -2.43 (0.26), residues: 276 loop : -0.57 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.002 0.000 HIS A 138 PHE 0.012 0.001 PHE C 11 TYR 0.017 0.001 TYR A 258 ARG 0.002 0.000 ARG D 257 Details of bonding type rmsd hydrogen bonds : bond 0.02547 ( 424) hydrogen bonds : angle 4.66162 ( 1236) metal coordination : bond 0.00171 ( 28) metal coordination : angle 3.74821 ( 24) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.11738 ( 4) covalent geometry : bond 0.00203 (10732) covalent geometry : angle 0.47360 (14580) *********************** 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 80 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8908 (m-30) cc_final: 0.8234 (m-30) REVERT: B 46 ASP cc_start: 0.8876 (m-30) cc_final: 0.8202 (m-30) REVERT: B 126 GLN cc_start: 0.9247 (pt0) cc_final: 0.8909 (pt0) REVERT: B 226 ASP cc_start: 0.9368 (t0) cc_final: 0.9115 (t0) REVERT: C 31 ASN cc_start: 0.8751 (t0) cc_final: 0.8493 (p0) REVERT: C 226 ASP cc_start: 0.9373 (t0) cc_final: 0.9080 (t0) REVERT: D 226 ASP cc_start: 0.9370 (t0) cc_final: 0.9091 (t0) outliers start: 29 outliers final: 21 residues processed: 76 average time/residue: 0.2479 time to fit residues: 29.2628 Evaluate side-chains 66 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 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 259 VAL Chi-restraints excluded: chain B residue 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 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 55 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 283 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 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.058440 restraints weight = 19264.438| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.10 r_work: 0.2546 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 10762 Z= 0.277 Angle : 0.620 8.575 14608 Z= 0.288 Chirality : 0.045 0.138 1624 Planarity : 0.003 0.030 1856 Dihedral : 7.625 75.922 1700 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.45 % Allowed : 18.56 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1380 helix: 1.28 (0.24), residues: 456 sheet: -2.72 (0.29), residues: 216 loop : -0.64 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.003 0.001 HIS C 138 PHE 0.008 0.001 PHE A 281 TYR 0.016 0.001 TYR C 258 ARG 0.005 0.001 ARG C 257 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 424) hydrogen bonds : angle 4.98718 ( 1236) metal coordination : bond 0.00984 ( 28) metal coordination : angle 5.15185 ( 24) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.06629 ( 4) covalent geometry : bond 0.00625 (10732) covalent geometry : angle 0.58465 (14580) *********************** 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 73 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 36 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8772 (pt0) REVERT: C 135 GLN cc_start: 0.9396 (mm-40) cc_final: 0.9114 (mm110) outliers start: 37 outliers final: 32 residues processed: 68 average time/residue: 0.2583 time to fit residues: 27.3021 Evaluate side-chains 68 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 35 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 126 GLN 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 101 optimal weight: 9.9990 chunk 135 optimal weight: 0.0010 chunk 5 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.089549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.059156 restraints weight = 19362.780| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.17 r_work: 0.2586 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10762 Z= 0.104 Angle : 0.507 7.819 14608 Z= 0.242 Chirality : 0.043 0.146 1624 Planarity : 0.003 0.030 1856 Dihedral : 7.115 67.628 1700 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1380 helix: 1.38 (0.24), residues: 468 sheet: -2.33 (0.26), residues: 276 loop : -0.48 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 82 HIS 0.002 0.000 HIS C 138 PHE 0.011 0.001 PHE C 11 TYR 0.017 0.001 TYR A 258 ARG 0.004 0.000 ARG C 257 Details of bonding type rmsd hydrogen bonds : bond 0.02658 ( 424) hydrogen bonds : angle 4.68249 ( 1236) metal coordination : bond 0.00243 ( 28) metal coordination : angle 3.83696 ( 24) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.12916 ( 4) covalent geometry : bond 0.00242 (10732) covalent geometry : angle 0.48269 (14580) *********************** 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 77 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8808 (m-30) cc_final: 0.8223 (m-30) REVERT: B 126 GLN cc_start: 0.9165 (pt0) cc_final: 0.8881 (pt0) REVERT: B 226 ASP cc_start: 0.9377 (t0) cc_final: 0.9113 (t0) REVERT: C 31 ASN cc_start: 0.8826 (t0) cc_final: 0.8521 (p0) REVERT: C 46 ASP cc_start: 0.8876 (m-30) cc_final: 0.8185 (m-30) REVERT: D 226 ASP cc_start: 0.9350 (t0) cc_final: 0.9089 (t0) REVERT: D 347 LYS cc_start: 0.9267 (mmmt) cc_final: 0.8981 (mtmt) outliers start: 30 outliers final: 26 residues processed: 72 average time/residue: 0.2052 time to fit residues: 22.7456 Evaluate side-chains 69 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 58 THR 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 58 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER 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 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 102 optimal weight: 20.0000 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 283 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.089026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061137 restraints weight = 18863.486| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.00 r_work: 0.2606 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10762 Z= 0.106 Angle : 0.495 7.248 14608 Z= 0.236 Chirality : 0.042 0.144 1624 Planarity : 0.003 0.029 1856 Dihedral : 7.077 68.443 1700 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.89 % Allowed : 19.40 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1380 helix: 1.55 (0.24), residues: 468 sheet: -2.23 (0.26), residues: 276 loop : -0.44 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 92 HIS 0.002 0.000 HIS B 138 PHE 0.011 0.001 PHE C 11 TYR 0.017 0.001 TYR A 258 ARG 0.004 0.000 ARG C 257 Details of bonding type rmsd hydrogen bonds : bond 0.02600 ( 424) hydrogen bonds : angle 4.56423 ( 1236) metal coordination : bond 0.00314 ( 28) metal coordination : angle 3.73267 ( 24) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.06697 ( 4) covalent geometry : bond 0.00245 (10732) covalent geometry : angle 0.47167 (14580) *********************** 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: 31 poor density : 48 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8701 (m-30) cc_final: 0.8120 (m-30) REVERT: B 126 GLN cc_start: 0.9174 (pt0) cc_final: 0.8886 (pt0) REVERT: B 226 ASP cc_start: 0.9372 (t0) cc_final: 0.9100 (t0) REVERT: C 31 ASN cc_start: 0.8845 (t0) cc_final: 0.8602 (p0) REVERT: C 46 ASP cc_start: 0.8825 (m-30) cc_final: 0.8116 (m-30) REVERT: C 226 ASP cc_start: 0.9362 (t0) cc_final: 0.9083 (t0) REVERT: C 236 ASP cc_start: 0.9281 (t70) cc_final: 0.8809 (t0) REVERT: D 226 ASP cc_start: 0.9367 (t0) cc_final: 0.9088 (t0) outliers start: 31 outliers final: 26 residues processed: 75 average time/residue: 0.1998 time to fit residues: 23.1626 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 : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 329 TYR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 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 315 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.089721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.059388 restraints weight = 19540.601| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.19 r_work: 0.2589 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10762 Z= 0.118 Angle : 0.506 8.405 14608 Z= 0.241 Chirality : 0.043 0.143 1624 Planarity : 0.003 0.029 1856 Dihedral : 7.126 69.866 1700 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.89 % Allowed : 19.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1380 helix: 1.59 (0.24), residues: 468 sheet: -2.15 (0.26), residues: 276 loop : -0.45 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 92 HIS 0.002 0.000 HIS C 138 PHE 0.010 0.001 PHE D 11 TYR 0.017 0.001 TYR A 258 ARG 0.004 0.000 ARG C 257 Details of bonding type rmsd hydrogen bonds : bond 0.02603 ( 424) hydrogen bonds : angle 4.54973 ( 1236) metal coordination : bond 0.00372 ( 28) metal coordination : angle 3.76178 ( 24) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.03028 ( 4) covalent geometry : bond 0.00275 (10732) covalent geometry : angle 0.48323 (14580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 48 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8685 (m-30) cc_final: 0.8250 (m-30) REVERT: B 126 GLN cc_start: 0.9176 (pt0) cc_final: 0.8888 (pt0) REVERT: B 226 ASP cc_start: 0.9383 (t0) cc_final: 0.9117 (t0) REVERT: B 347 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8770 (tttp) REVERT: C 46 ASP cc_start: 0.8807 (m-30) cc_final: 0.8099 (m-30) REVERT: C 135 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8966 (mm110) REVERT: C 226 ASP cc_start: 0.9380 (t0) cc_final: 0.9102 (t0) REVERT: C 236 ASP cc_start: 0.9295 (t70) cc_final: 0.8847 (t0) REVERT: D 226 ASP cc_start: 0.9372 (t0) cc_final: 0.9088 (t0) outliers start: 31 outliers final: 28 residues processed: 75 average time/residue: 0.2044 time to fit residues: 23.6817 Evaluate side-chains 75 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 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 329 TYR Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 329 TYR Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.058134 restraints weight = 19563.550| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.15 r_work: 0.2616 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10762 Z= 0.180 Angle : 0.556 11.812 14608 Z= 0.265 Chirality : 0.044 0.252 1624 Planarity : 0.003 0.029 1856 Dihedral : 7.296 72.324 1700 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.89 % Allowed : 19.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1380 helix: 1.53 (0.24), residues: 468 sheet: -2.15 (0.26), residues: 276 loop : -0.46 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 92 HIS 0.002 0.000 HIS C 138 PHE 0.007 0.001 PHE B 11 TYR 0.016 0.001 TYR A 258 ARG 0.004 0.000 ARG C 257 Details of bonding type rmsd hydrogen bonds : bond 0.02761 ( 424) hydrogen bonds : angle 4.65101 ( 1236) metal coordination : bond 0.00621 ( 28) metal coordination : angle 4.08201 ( 24) SS BOND : bond 0.01814 ( 2) SS BOND : angle 4.20943 ( 4) covalent geometry : bond 0.00415 (10732) covalent geometry : angle 0.52655 (14580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4470.51 seconds wall clock time: 82 minutes 48.30 seconds (4968.30 seconds total)