Starting phenix.real_space_refine on Thu Sep 18 20:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b77_44302/09_2025/9b77_44302.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b77_44302/09_2025/9b77_44302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b77_44302/09_2025/9b77_44302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b77_44302/09_2025/9b77_44302.map" model { file = "/net/cci-nas-00/data/ceres_data/9b77_44302/09_2025/9b77_44302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b77_44302/09_2025/9b77_44302.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 6256 2.51 5 N 1696 2.21 5 O 1898 1.98 5 H 10008 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19910 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4945 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Restraints were copied for chains: B, C, D Time building chain proxies: 4.72, per 1000 atoms: 0.24 Number of scatterers: 19910 At special positions: 0 Unit cell: (110.55, 110.55, 105.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1898 8.00 N 1696 7.00 C 6256 6.00 H 10008 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 355.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 56.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.567A pdb=" N LEU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.574A pdb=" N THR A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 removed outlier: 3.560A pdb=" N ASN A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.597A pdb=" N TYR A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 262 removed outlier: 3.863A pdb=" N ARG A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 304 removed outlier: 3.503A pdb=" N PHE A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.567A pdb=" N LEU B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.574A pdb=" N THR B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.560A pdb=" N ASN B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.597A pdb=" N TYR B 222 " --> pdb=" O ILE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 262 removed outlier: 3.863A pdb=" N ARG B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 304 removed outlier: 3.503A pdb=" N PHE B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 53 through 64 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 118 removed outlier: 3.567A pdb=" N LEU C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 153 Processing helix chain 'C' and resid 168 through 175 removed outlier: 3.574A pdb=" N THR C 173 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.561A pdb=" N ASN C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.596A pdb=" N TYR C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 262 removed outlier: 3.863A pdb=" N ARG C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 304 removed outlier: 3.503A pdb=" N PHE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 79 through 89 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 109 through 118 removed outlier: 3.567A pdb=" N LEU D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 153 Processing helix chain 'D' and resid 168 through 175 removed outlier: 3.573A pdb=" N THR D 173 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 removed outlier: 3.560A pdb=" N ASN D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.597A pdb=" N TYR D 222 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 262 removed outlier: 3.863A pdb=" N ARG D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 238 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 304 removed outlier: 3.503A pdb=" N PHE D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 200 removed outlier: 6.456A pdb=" N VAL A 123 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE A 198 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 125 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 200 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL A 127 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 164 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ILE A 70 " --> pdb=" O TRP A 41 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 43 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 72 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 45 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 74 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP A 47 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER A 71 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 313 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 73 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 314 removed outlier: 7.080A pdb=" N LEU D 73 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 313 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER D 71 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ILE D 70 " --> pdb=" O TRP D 41 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 43 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE D 72 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 45 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU D 74 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP D 47 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 164 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 123 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE D 198 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY D 125 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 200 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL D 127 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 200 removed outlier: 6.456A pdb=" N VAL B 123 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE B 198 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY B 125 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL B 200 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 127 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 164 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE B 70 " --> pdb=" O TRP B 41 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 43 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE B 72 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 45 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU B 74 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP B 47 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER B 71 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 313 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 73 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.456A pdb=" N VAL C 123 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE C 198 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY C 125 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 200 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL C 127 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 164 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE C 70 " --> pdb=" O TRP C 41 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 43 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE C 72 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 45 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU C 74 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASP C 47 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER C 71 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL D 313 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU C 73 " --> pdb=" O GLN D 311 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1644 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: 4.75 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9992 1.03 - 1.22: 16 1.22 - 1.42: 4048 1.42 - 1.61: 5812 1.61 - 1.81: 88 Bond restraints: 19956 Sorted by residual: bond pdb=" C THR D 231 " pdb=" O THR D 231 " ideal model delta sigma weight residual 1.244 1.237 0.006 9.80e-03 1.04e+04 4.24e-01 bond pdb=" C THR B 231 " pdb=" O THR B 231 " ideal model delta sigma weight residual 1.244 1.237 0.006 9.80e-03 1.04e+04 4.07e-01 bond pdb=" CA ILE B 184 " pdb=" CB ILE B 184 " ideal model delta sigma weight residual 1.539 1.536 0.003 5.40e-03 3.43e+04 3.97e-01 bond pdb=" CG PRO D 15 " pdb=" CD PRO D 15 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.92e-01 bond pdb=" CG PRO A 15 " pdb=" CD PRO A 15 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.92e-01 ... (remaining 19951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 32727 0.89 - 1.78: 3195 1.78 - 2.68: 138 2.68 - 3.57: 48 3.57 - 4.46: 16 Bond angle restraints: 36124 Sorted by residual: angle pdb=" C THR C 230 " pdb=" N THR C 231 " pdb=" CA THR C 231 " ideal model delta sigma weight residual 120.09 123.87 -3.78 1.25e+00 6.40e-01 9.16e+00 angle pdb=" C THR D 230 " pdb=" N THR D 231 " pdb=" CA THR D 231 " ideal model delta sigma weight residual 120.09 123.82 -3.73 1.25e+00 6.40e-01 8.89e+00 angle pdb=" C THR A 230 " pdb=" N THR A 231 " pdb=" CA THR A 231 " ideal model delta sigma weight residual 120.09 123.81 -3.72 1.25e+00 6.40e-01 8.86e+00 angle pdb=" C THR B 230 " pdb=" N THR B 231 " pdb=" CA THR B 231 " ideal model delta sigma weight residual 120.09 123.79 -3.70 1.25e+00 6.40e-01 8.77e+00 angle pdb=" N ASP A 52 " pdb=" CA ASP A 52 " pdb=" C ASP A 52 " ideal model delta sigma weight residual 110.88 112.74 -1.86 1.28e+00 6.10e-01 2.11e+00 ... (remaining 36119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 8637 16.30 - 32.60: 422 32.60 - 48.89: 141 48.89 - 65.19: 104 65.19 - 81.49: 16 Dihedral angle restraints: 9320 sinusoidal: 5152 harmonic: 4168 Sorted by residual: dihedral pdb=" CA ILE A 46 " pdb=" CB ILE A 46 " pdb=" CG1 ILE A 46 " pdb=" CD1 ILE A 46 " ideal model delta sinusoidal sigma weight residual 60.00 115.46 -55.46 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA ILE B 46 " pdb=" CB ILE B 46 " pdb=" CG1 ILE B 46 " pdb=" CD1 ILE B 46 " ideal model delta sinusoidal sigma weight residual 60.00 115.46 -55.46 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA ILE D 46 " pdb=" CB ILE D 46 " pdb=" CG1 ILE D 46 " pdb=" CD1 ILE D 46 " ideal model delta sinusoidal sigma weight residual 60.00 115.43 -55.43 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 9317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 976 0.025 - 0.051: 352 0.051 - 0.076: 136 0.076 - 0.101: 52 0.101 - 0.127: 68 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE A 70 " pdb=" N ILE A 70 " pdb=" C ILE A 70 " pdb=" CB ILE A 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE B 70 " pdb=" N ILE B 70 " pdb=" C ILE B 70 " pdb=" CB ILE B 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1581 not shown) Planarity restraints: 2908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 106 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 107 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 106 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO D 107 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 107 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 107 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 106 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO C 107 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 107 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 107 " 0.018 5.00e-02 4.00e+02 ... (remaining 2905 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 1550 2.23 - 2.82: 43245 2.82 - 3.41: 49373 3.41 - 4.01: 69610 4.01 - 4.60: 108165 Nonbonded interactions: 271943 Sorted by model distance: nonbonded pdb="HH21 ARG A 297 " pdb=" OD1 ASP D 223 " model vdw 1.635 2.450 nonbonded pdb=" OD1 ASP B 223 " pdb="HH21 ARG C 297 " model vdw 1.649 2.450 nonbonded pdb=" OD1 ASP A 223 " pdb="HH21 ARG B 297 " model vdw 1.653 2.450 nonbonded pdb=" O ILE C 148 " pdb=" HG1 THR C 152 " model vdw 1.675 2.450 nonbonded pdb=" O ILE D 148 " pdb=" HG1 THR D 152 " model vdw 1.675 2.450 ... (remaining 271938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.700 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: 0.140 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.400 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.003 0.022 9948 Z= 0.107 Angle : 0.461 4.461 13476 Z= 0.257 Chirality : 0.039 0.127 1584 Planarity : 0.004 0.032 1716 Dihedral : 10.863 81.490 3684 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.24), residues: 1236 helix: 2.53 (0.21), residues: 660 sheet: 1.74 (0.37), residues: 196 loop : -0.20 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 194 TYR 0.006 0.001 TYR A 166 PHE 0.009 0.001 PHE C 183 TRP 0.001 0.000 TRP A 41 HIS 0.002 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9948) covalent geometry : angle 0.46091 (13476) hydrogen bonds : bond 0.24244 ( 552) hydrogen bonds : angle 6.56485 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.559 Fit side-chains REVERT: A 221 MET cc_start: 0.7649 (mmp) cc_final: 0.6287 (tmm) REVERT: A 238 LEU cc_start: 0.8096 (mp) cc_final: 0.7704 (tp) REVERT: B 144 ILE cc_start: 0.7825 (mm) cc_final: 0.7549 (mt) REVERT: B 221 MET cc_start: 0.7697 (mmp) cc_final: 0.6318 (tmm) REVERT: B 238 LEU cc_start: 0.8140 (mp) cc_final: 0.7734 (tp) REVERT: C 94 ASP cc_start: 0.8713 (m-30) cc_final: 0.8493 (m-30) REVERT: C 144 ILE cc_start: 0.7896 (mm) cc_final: 0.7610 (mt) REVERT: C 221 MET cc_start: 0.7676 (mmp) cc_final: 0.6327 (tmm) REVERT: C 238 LEU cc_start: 0.8121 (mp) cc_final: 0.7727 (tp) REVERT: D 144 ILE cc_start: 0.7887 (mm) cc_final: 0.7608 (mt) REVERT: D 221 MET cc_start: 0.7660 (mmp) cc_final: 0.6304 (tmm) REVERT: D 238 LEU cc_start: 0.8023 (mp) cc_final: 0.7660 (tp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 1.2146 time to fit residues: 285.4216 Evaluate side-chains 178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 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 77 ASN A 145 ASN A 300 ASN B 145 ASN B 300 ASN C 77 ASN C 145 ASN C 300 ASN D 77 ASN D 145 ASN D 300 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115734 restraints weight = 30172.862| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.79 r_work: 0.3232 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9948 Z= 0.175 Angle : 0.548 5.124 13476 Z= 0.297 Chirality : 0.042 0.142 1584 Planarity : 0.005 0.038 1716 Dihedral : 3.773 12.525 1372 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.66 % Allowed : 7.77 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.23), residues: 1236 helix: 2.38 (0.20), residues: 668 sheet: 1.44 (0.35), residues: 196 loop : -0.47 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 76 TYR 0.008 0.001 TYR C 166 PHE 0.010 0.002 PHE B 285 TRP 0.002 0.001 TRP C 265 HIS 0.002 0.001 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9948) covalent geometry : angle 0.54803 (13476) hydrogen bonds : bond 0.08686 ( 552) hydrogen bonds : angle 4.91157 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.560 Fit side-chains REVERT: A 8 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7854 (mmtp) REVERT: A 64 GLU cc_start: 0.6568 (tt0) cc_final: 0.6222 (tp30) REVERT: A 142 LYS cc_start: 0.7584 (mtpt) cc_final: 0.6825 (mttt) REVERT: A 144 ILE cc_start: 0.7824 (mm) cc_final: 0.7478 (mt) REVERT: A 221 MET cc_start: 0.7872 (mmp) cc_final: 0.6333 (ttt) REVERT: A 238 LEU cc_start: 0.7460 (mp) cc_final: 0.6961 (tp) REVERT: B 8 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7872 (mmtp) REVERT: B 56 GLU cc_start: 0.7774 (tp30) cc_final: 0.7537 (tp30) REVERT: B 64 GLU cc_start: 0.6632 (tt0) cc_final: 0.6267 (tp30) REVERT: B 142 LYS cc_start: 0.7632 (mtpt) cc_final: 0.6874 (mttt) REVERT: B 144 ILE cc_start: 0.7819 (mm) cc_final: 0.7482 (mt) REVERT: B 221 MET cc_start: 0.7909 (mmp) cc_final: 0.6378 (tmm) REVERT: B 238 LEU cc_start: 0.7540 (mp) cc_final: 0.7021 (tp) REVERT: C 8 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7795 (mmtp) REVERT: C 64 GLU cc_start: 0.6569 (tt0) cc_final: 0.6216 (mm-30) REVERT: C 142 LYS cc_start: 0.7573 (mtpt) cc_final: 0.6803 (mttt) REVERT: C 144 ILE cc_start: 0.7869 (mm) cc_final: 0.7521 (mt) REVERT: C 221 MET cc_start: 0.7880 (mmp) cc_final: 0.6368 (ttt) REVERT: C 238 LEU cc_start: 0.7476 (mp) cc_final: 0.6969 (tp) REVERT: D 8 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7784 (mmtp) REVERT: D 64 GLU cc_start: 0.6569 (tt0) cc_final: 0.6211 (tp30) REVERT: D 142 LYS cc_start: 0.7527 (mtpt) cc_final: 0.6767 (mttt) REVERT: D 144 ILE cc_start: 0.7827 (mm) cc_final: 0.7485 (mt) REVERT: D 221 MET cc_start: 0.7909 (mmp) cc_final: 0.6364 (ttt) REVERT: D 238 LEU cc_start: 0.7385 (mp) cc_final: 0.6886 (tp) outliers start: 7 outliers final: 1 residues processed: 168 average time/residue: 1.2071 time to fit residues: 219.3867 Evaluate side-chains 148 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116762 restraints weight = 29882.349| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.79 r_work: 0.3253 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 9948 Z= 0.124 Angle : 0.470 4.298 13476 Z= 0.250 Chirality : 0.040 0.136 1584 Planarity : 0.005 0.039 1716 Dihedral : 3.604 13.424 1372 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.38 % Allowed : 7.77 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.24), residues: 1236 helix: 2.54 (0.20), residues: 680 sheet: 1.48 (0.34), residues: 204 loop : -0.50 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.006 0.001 TYR D 17 PHE 0.012 0.001 PHE B 214 TRP 0.001 0.000 TRP D 41 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9948) covalent geometry : angle 0.46974 (13476) hydrogen bonds : bond 0.06598 ( 552) hydrogen bonds : angle 4.42792 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.553 Fit side-chains REVERT: A 8 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7875 (mmtp) REVERT: A 64 GLU cc_start: 0.6689 (tt0) cc_final: 0.6312 (tp30) REVERT: A 144 ILE cc_start: 0.7930 (mm) cc_final: 0.7566 (mt) REVERT: A 221 MET cc_start: 0.8056 (mmp) cc_final: 0.6557 (ttt) REVERT: B 8 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7874 (mmtp) REVERT: B 56 GLU cc_start: 0.7868 (tp30) cc_final: 0.7583 (tp30) REVERT: B 64 GLU cc_start: 0.6692 (tt0) cc_final: 0.6318 (tp30) REVERT: B 142 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7011 (mttt) REVERT: B 144 ILE cc_start: 0.7974 (mm) cc_final: 0.7609 (mt) REVERT: B 221 MET cc_start: 0.8051 (mmp) cc_final: 0.6553 (tmm) REVERT: C 8 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7832 (mmtp) REVERT: C 64 GLU cc_start: 0.6657 (tt0) cc_final: 0.6300 (tp30) REVERT: C 144 ILE cc_start: 0.7966 (mm) cc_final: 0.7593 (mt) REVERT: C 221 MET cc_start: 0.8040 (mmp) cc_final: 0.6566 (tmm) REVERT: D 8 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7857 (mmtp) REVERT: D 64 GLU cc_start: 0.6675 (tt0) cc_final: 0.6295 (tp30) REVERT: D 144 ILE cc_start: 0.7943 (mm) cc_final: 0.7578 (mt) REVERT: D 221 MET cc_start: 0.8074 (mmp) cc_final: 0.6561 (tmm) outliers start: 4 outliers final: 0 residues processed: 164 average time/residue: 1.2747 time to fit residues: 224.7766 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 0.0670 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116676 restraints weight = 29872.584| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.83 r_work: 0.3261 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9948 Z= 0.115 Angle : 0.453 4.188 13476 Z= 0.240 Chirality : 0.040 0.137 1584 Planarity : 0.004 0.039 1716 Dihedral : 3.516 13.649 1372 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.28 % Allowed : 9.19 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.24), residues: 1236 helix: 2.75 (0.20), residues: 676 sheet: 1.51 (0.36), residues: 196 loop : -0.53 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.006 0.001 TYR C 166 PHE 0.007 0.001 PHE B 214 TRP 0.001 0.000 TRP D 41 HIS 0.001 0.001 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9948) covalent geometry : angle 0.45332 (13476) hydrogen bonds : bond 0.05834 ( 552) hydrogen bonds : angle 4.29147 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 0.589 Fit side-chains REVERT: A 8 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7985 (mmtp) REVERT: A 64 GLU cc_start: 0.6683 (tt0) cc_final: 0.6279 (tp30) REVERT: A 142 LYS cc_start: 0.7658 (mtpt) cc_final: 0.6910 (mttp) REVERT: A 144 ILE cc_start: 0.7974 (mm) cc_final: 0.7597 (mt) REVERT: A 221 MET cc_start: 0.8044 (mmp) cc_final: 0.6544 (ttt) REVERT: A 300 ASN cc_start: 0.8264 (m110) cc_final: 0.7964 (t0) REVERT: B 8 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7983 (mmtp) REVERT: B 56 GLU cc_start: 0.7860 (tp30) cc_final: 0.7570 (tp30) REVERT: B 64 GLU cc_start: 0.6698 (tt0) cc_final: 0.6284 (tp30) REVERT: B 142 LYS cc_start: 0.7713 (mtpt) cc_final: 0.6984 (mttp) REVERT: B 144 ILE cc_start: 0.7951 (mm) cc_final: 0.7577 (mt) REVERT: B 221 MET cc_start: 0.8066 (mmp) cc_final: 0.6559 (tmm) REVERT: B 300 ASN cc_start: 0.8181 (m-40) cc_final: 0.7898 (t0) REVERT: C 8 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7846 (mmtp) REVERT: C 64 GLU cc_start: 0.6665 (tt0) cc_final: 0.6260 (tp30) REVERT: C 144 ILE cc_start: 0.8007 (mm) cc_final: 0.7632 (mt) REVERT: C 221 MET cc_start: 0.8066 (mmp) cc_final: 0.6575 (tmm) REVERT: C 300 ASN cc_start: 0.8283 (m-40) cc_final: 0.8000 (t0) REVERT: D 8 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7998 (mmtp) REVERT: D 64 GLU cc_start: 0.6696 (tt0) cc_final: 0.6259 (tp30) REVERT: D 144 ILE cc_start: 0.8012 (mm) cc_final: 0.7642 (mt) REVERT: D 221 MET cc_start: 0.8084 (mmp) cc_final: 0.6575 (tmm) REVERT: D 300 ASN cc_start: 0.8251 (m110) cc_final: 0.7943 (t0) outliers start: 3 outliers final: 1 residues processed: 159 average time/residue: 1.3388 time to fit residues: 228.5783 Evaluate side-chains 157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN C 104 GLN D 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113864 restraints weight = 29704.832| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.80 r_work: 0.3213 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9948 Z= 0.152 Angle : 0.507 4.009 13476 Z= 0.269 Chirality : 0.041 0.141 1584 Planarity : 0.005 0.042 1716 Dihedral : 3.760 14.253 1372 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.47 % Allowed : 9.75 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.24), residues: 1236 helix: 2.65 (0.20), residues: 668 sheet: 1.42 (0.35), residues: 196 loop : -0.79 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 176 TYR 0.007 0.001 TYR B 166 PHE 0.008 0.001 PHE B 285 TRP 0.004 0.001 TRP D 41 HIS 0.002 0.001 HIS D 202 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9948) covalent geometry : angle 0.50715 (13476) hydrogen bonds : bond 0.06722 ( 552) hydrogen bonds : angle 4.28376 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.553 Fit side-chains REVERT: A 8 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7994 (mmtp) REVERT: A 64 GLU cc_start: 0.6690 (tt0) cc_final: 0.6259 (tp30) REVERT: A 142 LYS cc_start: 0.7544 (mtpt) cc_final: 0.6781 (mttp) REVERT: A 144 ILE cc_start: 0.7892 (mm) cc_final: 0.7499 (mt) REVERT: A 221 MET cc_start: 0.7959 (mmp) cc_final: 0.6427 (tmm) REVERT: A 238 LEU cc_start: 0.7598 (mp) cc_final: 0.7054 (tp) REVERT: A 300 ASN cc_start: 0.8266 (m110) cc_final: 0.7905 (t0) REVERT: B 8 LYS cc_start: 0.8247 (mtpp) cc_final: 0.8023 (mmtp) REVERT: B 56 GLU cc_start: 0.7736 (tp30) cc_final: 0.7387 (tp30) REVERT: B 64 GLU cc_start: 0.6689 (tt0) cc_final: 0.6249 (tp30) REVERT: B 142 LYS cc_start: 0.7584 (mtpt) cc_final: 0.6838 (mttp) REVERT: B 144 ILE cc_start: 0.7883 (mm) cc_final: 0.7494 (mt) REVERT: B 221 MET cc_start: 0.7972 (mmp) cc_final: 0.6424 (tmm) REVERT: B 238 LEU cc_start: 0.7626 (mp) cc_final: 0.7069 (tp) REVERT: B 300 ASN cc_start: 0.8216 (m-40) cc_final: 0.7851 (t0) REVERT: C 8 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7927 (mmtp) REVERT: C 64 GLU cc_start: 0.6658 (tt0) cc_final: 0.6209 (tp30) REVERT: C 144 ILE cc_start: 0.7924 (mm) cc_final: 0.7528 (mt) REVERT: C 221 MET cc_start: 0.7974 (mmp) cc_final: 0.6444 (tmm) REVERT: C 238 LEU cc_start: 0.7580 (mp) cc_final: 0.7027 (tp) REVERT: C 300 ASN cc_start: 0.8305 (m-40) cc_final: 0.7944 (t0) REVERT: D 8 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7961 (mmtp) REVERT: D 64 GLU cc_start: 0.6667 (tt0) cc_final: 0.6218 (tp30) REVERT: D 142 LYS cc_start: 0.7528 (mtpt) cc_final: 0.6754 (mttp) REVERT: D 144 ILE cc_start: 0.7903 (mm) cc_final: 0.7510 (mt) REVERT: D 221 MET cc_start: 0.8004 (mmp) cc_final: 0.6451 (tmm) REVERT: D 238 LEU cc_start: 0.7538 (mp) cc_final: 0.6986 (tp) REVERT: D 300 ASN cc_start: 0.8268 (m110) cc_final: 0.7908 (t0) outliers start: 5 outliers final: 4 residues processed: 162 average time/residue: 1.2713 time to fit residues: 221.7280 Evaluate side-chains 163 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114378 restraints weight = 29945.758| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.80 r_work: 0.3225 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9948 Z= 0.139 Angle : 0.491 4.189 13476 Z= 0.259 Chirality : 0.041 0.143 1584 Planarity : 0.005 0.043 1716 Dihedral : 3.726 14.430 1372 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.57 % Allowed : 10.80 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.24), residues: 1236 helix: 2.70 (0.20), residues: 668 sheet: 1.40 (0.35), residues: 196 loop : -0.80 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 76 TYR 0.006 0.001 TYR A 166 PHE 0.007 0.001 PHE A 285 TRP 0.002 0.001 TRP B 41 HIS 0.002 0.001 HIS D 202 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9948) covalent geometry : angle 0.49149 (13476) hydrogen bonds : bond 0.06344 ( 552) hydrogen bonds : angle 4.26437 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.401 Fit side-chains REVERT: A 64 GLU cc_start: 0.6691 (tt0) cc_final: 0.6268 (tp30) REVERT: A 142 LYS cc_start: 0.7530 (mtpt) cc_final: 0.6770 (mttp) REVERT: A 144 ILE cc_start: 0.7882 (mm) cc_final: 0.7491 (mt) REVERT: A 221 MET cc_start: 0.7963 (mmp) cc_final: 0.6425 (tmm) REVERT: A 238 LEU cc_start: 0.7573 (mp) cc_final: 0.7034 (tp) REVERT: A 300 ASN cc_start: 0.8230 (m110) cc_final: 0.7898 (t0) REVERT: B 56 GLU cc_start: 0.7740 (tp30) cc_final: 0.7379 (tp30) REVERT: B 64 GLU cc_start: 0.6656 (tt0) cc_final: 0.6235 (tp30) REVERT: B 142 LYS cc_start: 0.7554 (mtpt) cc_final: 0.6797 (mttp) REVERT: B 144 ILE cc_start: 0.7883 (mm) cc_final: 0.7491 (mt) REVERT: B 221 MET cc_start: 0.7986 (mmp) cc_final: 0.6438 (tmm) REVERT: B 222 TYR cc_start: 0.8496 (m-80) cc_final: 0.8289 (m-80) REVERT: B 238 LEU cc_start: 0.7563 (mp) cc_final: 0.7014 (tp) REVERT: B 300 ASN cc_start: 0.8191 (m-40) cc_final: 0.7854 (t0) REVERT: C 8 LYS cc_start: 0.8230 (mtpp) cc_final: 0.8029 (mmtp) REVERT: C 64 GLU cc_start: 0.6662 (tt0) cc_final: 0.6241 (tp30) REVERT: C 144 ILE cc_start: 0.7924 (mm) cc_final: 0.7527 (mt) REVERT: C 221 MET cc_start: 0.7973 (mmp) cc_final: 0.6441 (tmm) REVERT: C 222 TYR cc_start: 0.8483 (m-80) cc_final: 0.8273 (m-80) REVERT: C 238 LEU cc_start: 0.7538 (mp) cc_final: 0.6990 (tp) REVERT: C 300 ASN cc_start: 0.8259 (m-40) cc_final: 0.7923 (t0) REVERT: D 64 GLU cc_start: 0.6692 (tt0) cc_final: 0.6253 (tp30) REVERT: D 142 LYS cc_start: 0.7526 (mtpt) cc_final: 0.6760 (mttp) REVERT: D 144 ILE cc_start: 0.7913 (mm) cc_final: 0.7520 (mt) REVERT: D 221 MET cc_start: 0.8013 (mmp) cc_final: 0.6461 (tmm) REVERT: D 222 TYR cc_start: 0.8503 (m-80) cc_final: 0.8296 (m-80) REVERT: D 238 LEU cc_start: 0.7516 (mp) cc_final: 0.6971 (tp) REVERT: D 300 ASN cc_start: 0.8221 (m110) cc_final: 0.7885 (t0) outliers start: 6 outliers final: 3 residues processed: 162 average time/residue: 1.2409 time to fit residues: 216.3502 Evaluate side-chains 162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114105 restraints weight = 30113.989| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.80 r_work: 0.3220 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9948 Z= 0.149 Angle : 0.506 4.210 13476 Z= 0.267 Chirality : 0.041 0.144 1584 Planarity : 0.005 0.043 1716 Dihedral : 3.778 14.527 1372 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.57 % Allowed : 11.08 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.24), residues: 1236 helix: 2.65 (0.20), residues: 668 sheet: 1.30 (0.35), residues: 196 loop : -0.86 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 176 TYR 0.007 0.001 TYR A 166 PHE 0.007 0.001 PHE B 285 TRP 0.003 0.001 TRP D 41 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9948) covalent geometry : angle 0.50599 (13476) hydrogen bonds : bond 0.06509 ( 552) hydrogen bonds : angle 4.26463 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.469 Fit side-chains REVERT: A 64 GLU cc_start: 0.6734 (tt0) cc_final: 0.6305 (tp30) REVERT: A 144 ILE cc_start: 0.7923 (mm) cc_final: 0.7526 (mt) REVERT: A 221 MET cc_start: 0.7968 (mmp) cc_final: 0.6429 (tmm) REVERT: A 238 LEU cc_start: 0.7616 (mp) cc_final: 0.7076 (tp) REVERT: A 300 ASN cc_start: 0.8253 (m110) cc_final: 0.7905 (t0) REVERT: B 56 GLU cc_start: 0.7697 (tp30) cc_final: 0.7328 (tp30) REVERT: B 64 GLU cc_start: 0.6704 (tt0) cc_final: 0.6282 (tp30) REVERT: B 144 ILE cc_start: 0.7920 (mm) cc_final: 0.7518 (mt) REVERT: B 221 MET cc_start: 0.8002 (mmp) cc_final: 0.6480 (tmm) REVERT: B 238 LEU cc_start: 0.7627 (mp) cc_final: 0.7077 (tp) REVERT: B 300 ASN cc_start: 0.8193 (m-40) cc_final: 0.7845 (t0) REVERT: C 8 LYS cc_start: 0.8254 (mtpp) cc_final: 0.8052 (mmtp) REVERT: C 64 GLU cc_start: 0.6716 (tt0) cc_final: 0.6302 (tp30) REVERT: C 142 LYS cc_start: 0.7520 (mtpt) cc_final: 0.6754 (mttt) REVERT: C 144 ILE cc_start: 0.7897 (mm) cc_final: 0.7488 (mt) REVERT: C 221 MET cc_start: 0.8004 (mmp) cc_final: 0.6462 (tmm) REVERT: C 238 LEU cc_start: 0.7567 (mp) cc_final: 0.7017 (tp) REVERT: C 300 ASN cc_start: 0.8268 (m-40) cc_final: 0.7930 (t0) REVERT: D 64 GLU cc_start: 0.6723 (tt0) cc_final: 0.6309 (tp30) REVERT: D 142 LYS cc_start: 0.7538 (mtpt) cc_final: 0.6772 (mttp) REVERT: D 144 ILE cc_start: 0.7901 (mm) cc_final: 0.7499 (mt) REVERT: D 221 MET cc_start: 0.8029 (mmp) cc_final: 0.6490 (tmm) REVERT: D 222 TYR cc_start: 0.8517 (m-80) cc_final: 0.8310 (m-80) REVERT: D 238 LEU cc_start: 0.7581 (mp) cc_final: 0.7033 (tp) REVERT: D 300 ASN cc_start: 0.8238 (m110) cc_final: 0.7884 (t0) outliers start: 6 outliers final: 5 residues processed: 162 average time/residue: 1.2023 time to fit residues: 209.8872 Evaluate side-chains 163 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115010 restraints weight = 30068.336| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.81 r_work: 0.3231 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9948 Z= 0.128 Angle : 0.488 4.328 13476 Z= 0.256 Chirality : 0.040 0.143 1584 Planarity : 0.005 0.043 1716 Dihedral : 3.692 14.540 1372 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.57 % Allowed : 11.46 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.24), residues: 1236 helix: 2.76 (0.20), residues: 668 sheet: 1.27 (0.35), residues: 196 loop : -0.83 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 76 TYR 0.005 0.001 TYR B 166 PHE 0.006 0.001 PHE A 285 TRP 0.001 0.000 TRP D 41 HIS 0.002 0.001 HIS D 202 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9948) covalent geometry : angle 0.48754 (13476) hydrogen bonds : bond 0.06038 ( 552) hydrogen bonds : angle 4.25717 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.535 Fit side-chains REVERT: A 64 GLU cc_start: 0.6666 (tt0) cc_final: 0.6254 (tp30) REVERT: A 142 LYS cc_start: 0.7537 (mtpt) cc_final: 0.6772 (mttt) REVERT: A 144 ILE cc_start: 0.7911 (mm) cc_final: 0.7510 (mt) REVERT: A 221 MET cc_start: 0.7978 (mmp) cc_final: 0.6431 (ttt) REVERT: A 238 LEU cc_start: 0.7589 (mp) cc_final: 0.7043 (tp) REVERT: A 300 ASN cc_start: 0.8190 (m110) cc_final: 0.7885 (t0) REVERT: B 56 GLU cc_start: 0.7670 (tp30) cc_final: 0.7294 (tp30) REVERT: B 64 GLU cc_start: 0.6641 (tt0) cc_final: 0.6230 (tp30) REVERT: B 142 LYS cc_start: 0.7510 (mtpt) cc_final: 0.6747 (mttt) REVERT: B 144 ILE cc_start: 0.7944 (mm) cc_final: 0.7556 (mt) REVERT: B 238 LEU cc_start: 0.7592 (mp) cc_final: 0.7043 (tp) REVERT: B 300 ASN cc_start: 0.8138 (m-40) cc_final: 0.7829 (t0) REVERT: C 64 GLU cc_start: 0.6667 (tt0) cc_final: 0.6256 (tp30) REVERT: C 142 LYS cc_start: 0.7528 (mtpt) cc_final: 0.6757 (mttt) REVERT: C 144 ILE cc_start: 0.7893 (mm) cc_final: 0.7492 (mt) REVERT: C 221 MET cc_start: 0.8003 (mmp) cc_final: 0.6464 (tmm) REVERT: C 222 TYR cc_start: 0.8455 (m-80) cc_final: 0.8244 (m-80) REVERT: C 238 LEU cc_start: 0.7536 (mp) cc_final: 0.6977 (tp) REVERT: C 300 ASN cc_start: 0.8232 (m-40) cc_final: 0.7920 (t0) REVERT: D 64 GLU cc_start: 0.6678 (tt0) cc_final: 0.6252 (tp30) REVERT: D 142 LYS cc_start: 0.7535 (mtpt) cc_final: 0.6769 (mttp) REVERT: D 144 ILE cc_start: 0.7874 (mm) cc_final: 0.7483 (mt) REVERT: D 238 LEU cc_start: 0.7518 (mp) cc_final: 0.6964 (tp) REVERT: D 300 ASN cc_start: 0.8180 (m110) cc_final: 0.7872 (t0) outliers start: 6 outliers final: 5 residues processed: 161 average time/residue: 1.2248 time to fit residues: 212.6443 Evaluate side-chains 163 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114407 restraints weight = 29881.508| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.80 r_work: 0.3223 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9948 Z= 0.144 Angle : 0.507 4.474 13476 Z= 0.265 Chirality : 0.041 0.145 1584 Planarity : 0.005 0.043 1716 Dihedral : 3.746 14.538 1372 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.47 % Allowed : 11.84 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.24), residues: 1236 helix: 2.66 (0.20), residues: 672 sheet: 1.54 (0.37), residues: 176 loop : -0.90 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 176 TYR 0.006 0.001 TYR D 166 PHE 0.007 0.001 PHE A 285 TRP 0.002 0.001 TRP D 41 HIS 0.002 0.001 HIS D 202 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9948) covalent geometry : angle 0.50683 (13476) hydrogen bonds : bond 0.06334 ( 552) hydrogen bonds : angle 4.27260 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.527 Fit side-chains REVERT: A 64 GLU cc_start: 0.6729 (tt0) cc_final: 0.6307 (tp30) REVERT: A 142 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6763 (mttt) REVERT: A 144 ILE cc_start: 0.7910 (mm) cc_final: 0.7508 (mt) REVERT: A 221 MET cc_start: 0.7954 (mmp) cc_final: 0.6413 (tmm) REVERT: A 238 LEU cc_start: 0.7638 (mp) cc_final: 0.7083 (tp) REVERT: A 300 ASN cc_start: 0.8234 (m110) cc_final: 0.7904 (t0) REVERT: B 56 GLU cc_start: 0.7696 (tp30) cc_final: 0.7321 (tp30) REVERT: B 60 LYS cc_start: 0.7453 (ttpt) cc_final: 0.6752 (ttpp) REVERT: B 64 GLU cc_start: 0.6703 (tt0) cc_final: 0.6270 (tp30) REVERT: B 142 LYS cc_start: 0.7521 (mtpt) cc_final: 0.6750 (mttt) REVERT: B 144 ILE cc_start: 0.7958 (mm) cc_final: 0.7558 (mt) REVERT: B 221 MET cc_start: 0.8023 (mmp) cc_final: 0.6474 (tmm) REVERT: B 222 TYR cc_start: 0.8492 (m-80) cc_final: 0.8276 (m-80) REVERT: B 238 LEU cc_start: 0.7641 (mp) cc_final: 0.7085 (tp) REVERT: B 300 ASN cc_start: 0.8175 (m-40) cc_final: 0.7854 (t0) REVERT: C 64 GLU cc_start: 0.6721 (tt0) cc_final: 0.6290 (tp30) REVERT: C 142 LYS cc_start: 0.7532 (mtpt) cc_final: 0.6765 (mttt) REVERT: C 144 ILE cc_start: 0.7900 (mm) cc_final: 0.7495 (mt) REVERT: C 221 MET cc_start: 0.8024 (mmp) cc_final: 0.6477 (tmm) REVERT: C 238 LEU cc_start: 0.7586 (mp) cc_final: 0.7032 (tp) REVERT: C 300 ASN cc_start: 0.8248 (m-40) cc_final: 0.7922 (t0) REVERT: D 64 GLU cc_start: 0.6727 (tt0) cc_final: 0.6304 (tp30) REVERT: D 144 ILE cc_start: 0.7876 (mm) cc_final: 0.7473 (mt) REVERT: D 221 MET cc_start: 0.8026 (mmp) cc_final: 0.6450 (tmm) REVERT: D 238 LEU cc_start: 0.7594 (mp) cc_final: 0.7040 (tp) REVERT: D 300 ASN cc_start: 0.8214 (m110) cc_final: 0.7878 (t0) outliers start: 5 outliers final: 3 residues processed: 160 average time/residue: 1.2803 time to fit residues: 220.3586 Evaluate side-chains 158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.145768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112409 restraints weight = 30200.567| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.82 r_work: 0.3191 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9948 Z= 0.185 Angle : 0.562 5.238 13476 Z= 0.295 Chirality : 0.042 0.150 1584 Planarity : 0.005 0.045 1716 Dihedral : 3.947 14.809 1372 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.28 % Allowed : 12.41 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.23), residues: 1236 helix: 2.48 (0.20), residues: 672 sheet: 1.10 (0.33), residues: 204 loop : -0.94 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 176 TYR 0.007 0.001 TYR A 315 PHE 0.008 0.001 PHE A 285 TRP 0.004 0.001 TRP D 41 HIS 0.002 0.001 HIS D 202 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 9948) covalent geometry : angle 0.56166 (13476) hydrogen bonds : bond 0.07142 ( 552) hydrogen bonds : angle 4.34463 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.461 Fit side-chains REVERT: A 64 GLU cc_start: 0.6855 (tt0) cc_final: 0.6462 (tp30) REVERT: A 142 LYS cc_start: 0.7607 (mtpt) cc_final: 0.6849 (mttt) REVERT: A 144 ILE cc_start: 0.8023 (mm) cc_final: 0.7622 (mt) REVERT: A 221 MET cc_start: 0.8067 (mmp) cc_final: 0.6584 (ttt) REVERT: A 238 LEU cc_start: 0.7808 (mp) cc_final: 0.7299 (tp) REVERT: B 60 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7192 (mttt) REVERT: B 64 GLU cc_start: 0.6823 (tt0) cc_final: 0.6431 (tp30) REVERT: B 142 LYS cc_start: 0.7607 (mtpt) cc_final: 0.6843 (mttt) REVERT: B 144 ILE cc_start: 0.8074 (mm) cc_final: 0.7676 (mt) REVERT: B 221 MET cc_start: 0.8101 (mmp) cc_final: 0.6621 (tmm) REVERT: B 238 LEU cc_start: 0.7805 (mp) cc_final: 0.7289 (tp) REVERT: C 64 GLU cc_start: 0.6852 (tt0) cc_final: 0.6461 (tp30) REVERT: C 142 LYS cc_start: 0.7631 (mtpt) cc_final: 0.6852 (mttt) REVERT: C 144 ILE cc_start: 0.8023 (mm) cc_final: 0.7618 (mt) REVERT: C 221 MET cc_start: 0.8109 (mmp) cc_final: 0.6625 (tmm) REVERT: C 238 LEU cc_start: 0.7775 (mp) cc_final: 0.7258 (tp) REVERT: D 64 GLU cc_start: 0.6845 (tt0) cc_final: 0.6454 (tp30) REVERT: D 142 LYS cc_start: 0.7621 (mtpt) cc_final: 0.6848 (mttt) REVERT: D 144 ILE cc_start: 0.7987 (mm) cc_final: 0.7583 (mt) REVERT: D 221 MET cc_start: 0.8125 (mmp) cc_final: 0.6625 (tmm) REVERT: D 238 LEU cc_start: 0.7780 (mp) cc_final: 0.7262 (tp) outliers start: 3 outliers final: 5 residues processed: 155 average time/residue: 1.1992 time to fit residues: 200.2715 Evaluate side-chains 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114482 restraints weight = 30257.408| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.82 r_work: 0.3219 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9948 Z= 0.129 Angle : 0.499 4.786 13476 Z= 0.261 Chirality : 0.040 0.144 1584 Planarity : 0.005 0.042 1716 Dihedral : 3.761 14.833 1372 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.28 % Allowed : 12.41 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.24), residues: 1236 helix: 2.70 (0.20), residues: 668 sheet: 1.22 (0.35), residues: 196 loop : -0.93 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 76 TYR 0.006 0.001 TYR B 166 PHE 0.007 0.001 PHE A 285 TRP 0.002 0.000 TRP C 265 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9948) covalent geometry : angle 0.49893 (13476) hydrogen bonds : bond 0.06116 ( 552) hydrogen bonds : angle 4.29384 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7043.93 seconds wall clock time: 119 minutes 39.84 seconds (7179.84 seconds total)