Starting phenix.real_space_refine on Tue Jun 17 12:11:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b77_44302/06_2025/9b77_44302.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b77_44302/06_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_44302/06_2025/9b77_44302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b77_44302/06_2025/9b77_44302.map" model { file = "/net/cci-nas-00/data/ceres_data/9b77_44302/06_2025/9b77_44302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b77_44302/06_2025/9b77_44302.cif" } resolution = 2.74 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= 0.014 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'ASP: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: C, B, D Time building chain proxies: 12.71, per 1000 atoms: 0.64 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: 5.10 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.75 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: 6.91 Time building geometry restraints manager: 6.21 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: 0.08 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: 6.860 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: 0.370 Extract box with map and model: 0.840 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 46.500 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.710 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.001 0.000 TRP A 41 HIS 0.002 0.001 HIS B 202 PHE 0.009 0.001 PHE C 183 TYR 0.006 0.001 TYR A 166 ARG 0.002 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.24244 ( 552) hydrogen bonds : angle 6.56485 ( 1644) covalent geometry : bond 0.00258 ( 9948) covalent geometry : angle 0.46091 (13476) *********************** 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 : 1.597 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: 2.2196 time to fit residues: 526.0977 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 : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.0060 chunk 112 optimal weight: 1.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- 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 145 ASN D 300 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114856 restraints weight = 30134.548| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.77 r_work: 0.3219 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2144 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= 0.192 Angle : 0.563 5.325 13476 Z= 0.307 Chirality : 0.043 0.146 1584 Planarity : 0.005 0.039 1716 Dihedral : 3.845 12.455 1372 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.76 % Allowed : 7.77 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.23), residues: 1236 helix: 2.34 (0.20), residues: 668 sheet: 1.42 (0.35), residues: 196 loop : -0.50 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 41 HIS 0.002 0.001 HIS D 81 PHE 0.010 0.002 PHE B 285 TYR 0.009 0.002 TYR D 166 ARG 0.003 0.000 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.09107 ( 552) hydrogen bonds : angle 4.97091 ( 1644) covalent geometry : bond 0.00427 ( 9948) covalent geometry : angle 0.56333 (13476) *********************** 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: 8 poor density : 162 time to evaluate : 1.432 Fit side-chains REVERT: A 8 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7854 (mmtp) REVERT: A 64 GLU cc_start: 0.6584 (tt0) cc_final: 0.6241 (tp30) REVERT: A 144 ILE cc_start: 0.7838 (mm) cc_final: 0.7493 (mt) REVERT: A 221 MET cc_start: 0.7862 (mmp) cc_final: 0.6330 (ttt) REVERT: A 238 LEU cc_start: 0.7499 (mp) cc_final: 0.7003 (tp) REVERT: B 8 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7889 (mmtp) REVERT: B 56 GLU cc_start: 0.7791 (tp30) cc_final: 0.7534 (tp30) REVERT: B 64 GLU cc_start: 0.6595 (tt0) cc_final: 0.6256 (tp30) REVERT: B 144 ILE cc_start: 0.7833 (mm) cc_final: 0.7495 (mt) REVERT: B 221 MET cc_start: 0.7922 (mmp) cc_final: 0.6394 (tmm) REVERT: B 238 LEU cc_start: 0.7581 (mp) cc_final: 0.7068 (tp) REVERT: C 8 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7832 (mmtp) REVERT: C 64 GLU cc_start: 0.6583 (tt0) cc_final: 0.6212 (mm-30) REVERT: C 144 ILE cc_start: 0.7870 (mm) cc_final: 0.7520 (mt) REVERT: C 221 MET cc_start: 0.7875 (mmp) cc_final: 0.6366 (ttt) REVERT: C 238 LEU cc_start: 0.7551 (mp) cc_final: 0.7052 (tp) REVERT: D 8 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7801 (mmtp) REVERT: D 64 GLU cc_start: 0.6604 (tt0) cc_final: 0.6242 (tp30) REVERT: D 144 ILE cc_start: 0.7840 (mm) cc_final: 0.7496 (mt) REVERT: D 221 MET cc_start: 0.7912 (mmp) cc_final: 0.6379 (ttt) REVERT: D 238 LEU cc_start: 0.7437 (mp) cc_final: 0.6942 (tp) outliers start: 8 outliers final: 1 residues processed: 167 average time/residue: 2.2629 time to fit residues: 410.7115 Evaluate side-chains 150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.0010 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 = 0.147097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114143 restraints weight = 29867.122| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.79 r_work: 0.3212 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2606 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= 0.154 Angle : 0.513 4.438 13476 Z= 0.273 Chirality : 0.041 0.140 1584 Planarity : 0.005 0.043 1716 Dihedral : 3.836 13.436 1372 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.38 % Allowed : 8.71 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.24), residues: 1236 helix: 2.46 (0.20), residues: 668 sheet: 1.44 (0.34), residues: 204 loop : -0.75 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP D 41 HIS 0.002 0.001 HIS C 202 PHE 0.012 0.001 PHE B 214 TYR 0.006 0.001 TYR B 166 ARG 0.002 0.000 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.07349 ( 552) hydrogen bonds : angle 4.48614 ( 1644) covalent geometry : bond 0.00344 ( 9948) covalent geometry : angle 0.51318 (13476) *********************** 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 161 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 1.532 Fit side-chains REVERT: A 8 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7943 (mmtp) REVERT: A 64 GLU cc_start: 0.6632 (tt0) cc_final: 0.6203 (tp30) REVERT: A 142 LYS cc_start: 0.7540 (mtpt) cc_final: 0.6779 (mttp) REVERT: A 144 ILE cc_start: 0.7842 (mm) cc_final: 0.7469 (mt) REVERT: A 221 MET cc_start: 0.7968 (mmp) cc_final: 0.6430 (ttt) REVERT: A 238 LEU cc_start: 0.7550 (mp) cc_final: 0.7012 (tp) REVERT: B 8 LYS cc_start: 0.8247 (mtpp) cc_final: 0.7966 (mmtp) REVERT: B 64 GLU cc_start: 0.6634 (tt0) cc_final: 0.6252 (tp30) REVERT: B 142 LYS cc_start: 0.7608 (mtpt) cc_final: 0.6848 (mttt) REVERT: B 144 ILE cc_start: 0.7862 (mm) cc_final: 0.7489 (mt) REVERT: B 221 MET cc_start: 0.7976 (mmp) cc_final: 0.6428 (tmm) REVERT: B 238 LEU cc_start: 0.7548 (mp) cc_final: 0.6996 (tp) REVERT: C 8 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7859 (mmtp) REVERT: C 64 GLU cc_start: 0.6642 (tt0) cc_final: 0.6252 (tp30) REVERT: C 142 LYS cc_start: 0.7544 (mtpt) cc_final: 0.7336 (mtpm) REVERT: C 144 ILE cc_start: 0.7846 (mm) cc_final: 0.7468 (mt) REVERT: C 221 MET cc_start: 0.7963 (mmp) cc_final: 0.6431 (tmm) REVERT: C 238 LEU cc_start: 0.7520 (mp) cc_final: 0.6974 (tp) REVERT: D 8 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7870 (mmtp) REVERT: D 64 GLU cc_start: 0.6631 (tt0) cc_final: 0.6228 (tp30) REVERT: D 142 LYS cc_start: 0.7500 (mtpt) cc_final: 0.6751 (mttt) REVERT: D 144 ILE cc_start: 0.7832 (mm) cc_final: 0.7456 (mt) REVERT: D 221 MET cc_start: 0.7984 (mmp) cc_final: 0.6436 (tmm) REVERT: D 238 LEU cc_start: 0.7481 (mp) cc_final: 0.6941 (tp) outliers start: 4 outliers final: 0 residues processed: 160 average time/residue: 2.6864 time to fit residues: 468.4412 Evaluate side-chains 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.146055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112781 restraints weight = 30065.909| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.80 r_work: 0.3201 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9948 Z= 0.171 Angle : 0.537 4.548 13476 Z= 0.285 Chirality : 0.042 0.142 1584 Planarity : 0.005 0.044 1716 Dihedral : 3.921 14.106 1372 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.66 % Allowed : 10.04 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.89 (0.24), residues: 1236 helix: 2.31 (0.20), residues: 672 sheet: 1.31 (0.34), residues: 204 loop : -0.89 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 41 HIS 0.002 0.001 HIS B 68 PHE 0.009 0.001 PHE B 285 TYR 0.007 0.001 TYR B 166 ARG 0.002 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.07347 ( 552) hydrogen bonds : angle 4.44887 ( 1644) covalent geometry : bond 0.00401 ( 9948) covalent geometry : angle 0.53674 (13476) *********************** 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 156 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 1.624 Fit side-chains REVERT: A 8 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8105 (mmtp) REVERT: A 64 GLU cc_start: 0.6802 (tt0) cc_final: 0.6401 (tp30) REVERT: A 142 LYS cc_start: 0.7631 (mtpt) cc_final: 0.6867 (mttp) REVERT: A 144 ILE cc_start: 0.7983 (mm) cc_final: 0.7609 (mt) REVERT: A 221 MET cc_start: 0.8065 (mmp) cc_final: 0.6585 (tmm) REVERT: A 238 LEU cc_start: 0.7738 (mp) cc_final: 0.7231 (tp) REVERT: B 8 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (mmtp) REVERT: B 64 GLU cc_start: 0.6834 (tt0) cc_final: 0.6446 (tp30) REVERT: B 142 LYS cc_start: 0.7678 (mtpt) cc_final: 0.6913 (mttt) REVERT: B 144 ILE cc_start: 0.7981 (mm) cc_final: 0.7607 (mt) REVERT: B 221 MET cc_start: 0.8075 (mmp) cc_final: 0.6561 (tmm) REVERT: B 238 LEU cc_start: 0.7686 (mp) cc_final: 0.7179 (tp) REVERT: C 8 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8066 (mmtp) REVERT: C 64 GLU cc_start: 0.6776 (tt0) cc_final: 0.6391 (tp30) REVERT: C 142 LYS cc_start: 0.7633 (mtpt) cc_final: 0.7430 (mtpm) REVERT: C 144 ILE cc_start: 0.7985 (mm) cc_final: 0.7602 (mt) REVERT: C 221 MET cc_start: 0.8070 (mmp) cc_final: 0.6581 (tmm) REVERT: C 238 LEU cc_start: 0.7678 (mp) cc_final: 0.7163 (tp) REVERT: D 8 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8092 (mmtp) REVERT: D 64 GLU cc_start: 0.6826 (tt0) cc_final: 0.6421 (tp30) REVERT: D 144 ILE cc_start: 0.7973 (mm) cc_final: 0.7599 (mt) REVERT: D 221 MET cc_start: 0.8092 (mmp) cc_final: 0.6584 (tmm) REVERT: D 238 LEU cc_start: 0.7681 (mp) cc_final: 0.7174 (tp) outliers start: 7 outliers final: 1 residues processed: 150 average time/residue: 2.5672 time to fit residues: 415.2627 Evaluate side-chains 155 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain D residue 8 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 104 GLN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111952 restraints weight = 30164.970| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.80 r_work: 0.3190 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9948 Z= 0.189 Angle : 0.559 4.326 13476 Z= 0.296 Chirality : 0.042 0.143 1584 Planarity : 0.006 0.046 1716 Dihedral : 4.043 14.566 1372 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.38 % Allowed : 10.80 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.23), residues: 1236 helix: 2.23 (0.20), residues: 672 sheet: 1.17 (0.34), residues: 204 loop : -1.00 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 41 HIS 0.002 0.001 HIS B 202 PHE 0.009 0.001 PHE A 285 TYR 0.007 0.002 TYR A 315 ARG 0.002 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.07548 ( 552) hydrogen bonds : angle 4.42026 ( 1644) covalent geometry : bond 0.00450 ( 9948) covalent geometry : angle 0.55868 (13476) *********************** 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 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 2.149 Fit side-chains REVERT: A 64 GLU cc_start: 0.6804 (tt0) cc_final: 0.6354 (tp30) REVERT: A 142 LYS cc_start: 0.7528 (mtpt) cc_final: 0.7324 (mtpm) REVERT: A 144 ILE cc_start: 0.7894 (mm) cc_final: 0.7501 (mt) REVERT: A 221 MET cc_start: 0.8004 (mmp) cc_final: 0.6474 (tmm) REVERT: A 238 LEU cc_start: 0.7680 (mp) cc_final: 0.7133 (tp) REVERT: B 8 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8116 (mmtp) REVERT: B 64 GLU cc_start: 0.6792 (tt0) cc_final: 0.6363 (tp30) REVERT: B 142 LYS cc_start: 0.7529 (mtpt) cc_final: 0.6761 (mttp) REVERT: B 144 ILE cc_start: 0.7880 (mm) cc_final: 0.7489 (mt) REVERT: B 221 MET cc_start: 0.8014 (mmp) cc_final: 0.6464 (tmm) REVERT: B 238 LEU cc_start: 0.7685 (mp) cc_final: 0.7132 (tp) REVERT: C 64 GLU cc_start: 0.6773 (tt0) cc_final: 0.6343 (tp30) REVERT: C 142 LYS cc_start: 0.7507 (mtpt) cc_final: 0.7298 (mtpm) REVERT: C 144 ILE cc_start: 0.7906 (mm) cc_final: 0.7510 (mt) REVERT: C 221 MET cc_start: 0.8012 (mmp) cc_final: 0.6477 (tmm) REVERT: C 238 LEU cc_start: 0.7665 (mp) cc_final: 0.7119 (tp) REVERT: D 64 GLU cc_start: 0.6804 (tt0) cc_final: 0.6368 (tp30) REVERT: D 142 LYS cc_start: 0.7507 (mtpt) cc_final: 0.7304 (mtpm) REVERT: D 144 ILE cc_start: 0.7908 (mm) cc_final: 0.7516 (mt) REVERT: D 221 MET cc_start: 0.8040 (mmp) cc_final: 0.6492 (tmm) REVERT: D 238 LEU cc_start: 0.7634 (mp) cc_final: 0.7089 (tp) outliers start: 4 outliers final: 0 residues processed: 150 average time/residue: 2.8922 time to fit residues: 470.8539 Evaluate side-chains 149 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LYS 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 86 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.148124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114878 restraints weight = 30047.028| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.80 r_work: 0.3236 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9948 Z= 0.121 Angle : 0.485 4.239 13476 Z= 0.255 Chirality : 0.040 0.141 1584 Planarity : 0.005 0.042 1716 Dihedral : 3.761 14.467 1372 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.09 % Allowed : 11.65 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.07 (0.24), residues: 1236 helix: 2.57 (0.20), residues: 672 sheet: 1.23 (0.34), residues: 204 loop : -0.96 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 265 HIS 0.001 0.001 HIS D 81 PHE 0.006 0.001 PHE B 285 TYR 0.005 0.001 TYR B 166 ARG 0.001 0.000 ARG D 194 Details of bonding type rmsd hydrogen bonds : bond 0.06072 ( 552) hydrogen bonds : angle 4.33129 ( 1644) covalent geometry : bond 0.00260 ( 9948) covalent geometry : angle 0.48477 (13476) *********************** 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 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.499 Fit side-chains REVERT: A 64 GLU cc_start: 0.6709 (tt0) cc_final: 0.6262 (tp30) REVERT: A 94 ASP cc_start: 0.8557 (m-30) cc_final: 0.8062 (m-30) REVERT: A 142 LYS cc_start: 0.7532 (mtpt) cc_final: 0.7328 (mtpm) REVERT: A 144 ILE cc_start: 0.7926 (mm) cc_final: 0.7538 (mt) REVERT: A 221 MET cc_start: 0.8001 (mmp) cc_final: 0.6456 (tmm) REVERT: A 238 LEU cc_start: 0.7520 (mp) cc_final: 0.6979 (tp) REVERT: A 300 ASN cc_start: 0.8214 (m110) cc_final: 0.7874 (t0) REVERT: B 56 GLU cc_start: 0.7692 (tp30) cc_final: 0.7324 (tp30) REVERT: B 64 GLU cc_start: 0.6694 (tt0) cc_final: 0.6235 (tp30) REVERT: B 142 LYS cc_start: 0.7536 (mtpt) cc_final: 0.6781 (mttp) REVERT: B 144 ILE cc_start: 0.7896 (mm) cc_final: 0.7508 (mt) REVERT: B 221 MET cc_start: 0.8010 (mmp) cc_final: 0.6446 (tmm) REVERT: B 222 TYR cc_start: 0.8472 (m-80) cc_final: 0.8250 (m-80) REVERT: B 238 LEU cc_start: 0.7537 (mp) cc_final: 0.6983 (tp) REVERT: B 300 ASN cc_start: 0.8168 (m-40) cc_final: 0.7830 (t0) REVERT: C 64 GLU cc_start: 0.6707 (tt0) cc_final: 0.6249 (tp30) REVERT: C 144 ILE cc_start: 0.7926 (mm) cc_final: 0.7536 (mt) REVERT: C 221 MET cc_start: 0.7994 (mmp) cc_final: 0.6437 (tmm) REVERT: C 222 TYR cc_start: 0.8464 (m-80) cc_final: 0.8244 (m-80) REVERT: C 238 LEU cc_start: 0.7506 (mp) cc_final: 0.6957 (tp) REVERT: C 300 ASN cc_start: 0.8240 (m110) cc_final: 0.7901 (t0) REVERT: D 64 GLU cc_start: 0.6683 (tt0) cc_final: 0.6239 (tp30) REVERT: D 142 LYS cc_start: 0.7514 (mtpt) cc_final: 0.6740 (mttp) REVERT: D 144 ILE cc_start: 0.7922 (mm) cc_final: 0.7534 (mt) REVERT: D 221 MET cc_start: 0.8018 (mmp) cc_final: 0.6459 (tmm) REVERT: D 238 LEU cc_start: 0.7490 (mp) cc_final: 0.6944 (tp) REVERT: D 300 ASN cc_start: 0.8222 (m110) cc_final: 0.7883 (t0) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 2.5415 time to fit residues: 411.2787 Evaluate side-chains 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.146964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113729 restraints weight = 30122.047| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.81 r_work: 0.3212 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3210 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= 0.150 Angle : 0.516 4.215 13476 Z= 0.271 Chirality : 0.041 0.145 1584 Planarity : 0.005 0.044 1716 Dihedral : 3.841 14.555 1372 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 12.31 % 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 (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: 2.01 (0.24), residues: 1236 helix: 2.54 (0.20), residues: 668 sheet: 1.18 (0.34), residues: 204 loop : -0.96 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 41 HIS 0.002 0.001 HIS A 202 PHE 0.007 0.001 PHE B 285 TYR 0.006 0.001 TYR B 166 ARG 0.001 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.06613 ( 552) hydrogen bonds : angle 4.30178 ( 1644) covalent geometry : bond 0.00346 ( 9948) covalent geometry : angle 0.51598 (13476) *********************** 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 150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.594 Fit side-chains REVERT: A 64 GLU cc_start: 0.6748 (tt0) cc_final: 0.6318 (tp30) REVERT: A 94 ASP cc_start: 0.8583 (m-30) cc_final: 0.8380 (m-30) REVERT: A 142 LYS cc_start: 0.7530 (mtpt) cc_final: 0.7326 (mtpm) REVERT: A 144 ILE cc_start: 0.7957 (mm) cc_final: 0.7562 (mt) REVERT: A 221 MET cc_start: 0.8009 (mmp) cc_final: 0.6474 (tmm) REVERT: A 238 LEU cc_start: 0.7651 (mp) cc_final: 0.7106 (tp) REVERT: A 300 ASN cc_start: 0.8263 (m110) cc_final: 0.7901 (t0) REVERT: B 56 GLU cc_start: 0.7717 (tp30) cc_final: 0.7317 (tp30) REVERT: B 64 GLU cc_start: 0.6725 (tt0) cc_final: 0.6296 (tp30) REVERT: B 142 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6772 (mttp) REVERT: B 144 ILE cc_start: 0.7951 (mm) cc_final: 0.7556 (mt) REVERT: B 221 MET cc_start: 0.8038 (mmp) cc_final: 0.6473 (tmm) REVERT: B 222 TYR cc_start: 0.8504 (m-80) cc_final: 0.8268 (m-80) REVERT: B 238 LEU cc_start: 0.7650 (mp) cc_final: 0.7094 (tp) REVERT: B 300 ASN cc_start: 0.8210 (m-40) cc_final: 0.7845 (t0) REVERT: C 64 GLU cc_start: 0.6746 (tt0) cc_final: 0.6323 (tp30) REVERT: C 144 ILE cc_start: 0.7945 (mm) cc_final: 0.7543 (mt) REVERT: C 221 MET cc_start: 0.8013 (mmp) cc_final: 0.6466 (tmm) REVERT: C 222 TYR cc_start: 0.8502 (m-80) cc_final: 0.8269 (m-80) REVERT: C 238 LEU cc_start: 0.7616 (mp) cc_final: 0.7066 (tp) REVERT: C 300 ASN cc_start: 0.8284 (m110) cc_final: 0.7922 (t0) REVERT: D 64 GLU cc_start: 0.6745 (tt0) cc_final: 0.6316 (tp30) REVERT: D 142 LYS cc_start: 0.7524 (mtpt) cc_final: 0.6759 (mttp) REVERT: D 144 ILE cc_start: 0.7931 (mm) cc_final: 0.7532 (mt) REVERT: D 221 MET cc_start: 0.8030 (mmp) cc_final: 0.6469 (tmm) REVERT: D 238 LEU cc_start: 0.7604 (mp) cc_final: 0.7059 (tp) REVERT: D 300 ASN cc_start: 0.8256 (m110) cc_final: 0.7889 (t0) outliers start: 0 outliers final: 2 residues processed: 150 average time/residue: 2.6627 time to fit residues: 431.2761 Evaluate side-chains 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 255 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.0070 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.148398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115150 restraints weight = 30057.641| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.81 r_work: 0.3236 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9948 Z= 0.118 Angle : 0.478 4.426 13476 Z= 0.250 Chirality : 0.040 0.142 1584 Planarity : 0.005 0.041 1716 Dihedral : 3.695 14.474 1372 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.09 % Allowed : 12.31 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.24), residues: 1236 helix: 2.74 (0.20), residues: 668 sheet: 1.32 (0.36), residues: 196 loop : -0.96 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 265 HIS 0.002 0.001 HIS B 202 PHE 0.006 0.001 PHE B 285 TYR 0.005 0.001 TYR D 166 ARG 0.001 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.05855 ( 552) hydrogen bonds : angle 4.26487 ( 1644) covalent geometry : bond 0.00251 ( 9948) covalent geometry : angle 0.47763 (13476) *********************** 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 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 3.732 Fit side-chains REVERT: A 64 GLU cc_start: 0.6752 (tt0) cc_final: 0.6352 (tp30) REVERT: A 94 ASP cc_start: 0.8568 (m-30) cc_final: 0.8044 (m-30) REVERT: A 144 ILE cc_start: 0.8046 (mm) cc_final: 0.7658 (mt) REVERT: A 221 MET cc_start: 0.8070 (mmp) cc_final: 0.6565 (tmm) REVERT: A 238 LEU cc_start: 0.7668 (mp) cc_final: 0.7156 (tp) REVERT: A 300 ASN cc_start: 0.8219 (m110) cc_final: 0.7927 (t0) REVERT: B 56 GLU cc_start: 0.7759 (tp30) cc_final: 0.7403 (tp30) REVERT: B 60 LYS cc_start: 0.7516 (ttpt) cc_final: 0.6856 (ttpp) REVERT: B 64 GLU cc_start: 0.6712 (tt0) cc_final: 0.6331 (tp30) REVERT: B 144 ILE cc_start: 0.8041 (mm) cc_final: 0.7662 (mt) REVERT: B 222 TYR cc_start: 0.8532 (m-80) cc_final: 0.8325 (m-80) REVERT: B 238 LEU cc_start: 0.7650 (mp) cc_final: 0.7124 (tp) REVERT: B 300 ASN cc_start: 0.8171 (m-40) cc_final: 0.7862 (t0) REVERT: C 64 GLU cc_start: 0.6732 (tt0) cc_final: 0.6344 (tp30) REVERT: C 144 ILE cc_start: 0.8032 (mm) cc_final: 0.7639 (mt) REVERT: C 221 MET cc_start: 0.8094 (mmp) cc_final: 0.6569 (tmm) REVERT: C 222 TYR cc_start: 0.8515 (m-80) cc_final: 0.8315 (m-80) REVERT: C 238 LEU cc_start: 0.7628 (mp) cc_final: 0.7111 (tp) REVERT: C 300 ASN cc_start: 0.8237 (m110) cc_final: 0.7936 (t0) REVERT: D 64 GLU cc_start: 0.6740 (tt0) cc_final: 0.6344 (tp30) REVERT: D 144 ILE cc_start: 0.8023 (mm) cc_final: 0.7637 (mt) REVERT: D 221 MET cc_start: 0.8116 (mmp) cc_final: 0.6595 (tmm) REVERT: D 222 TYR cc_start: 0.8545 (m-80) cc_final: 0.8309 (m-80) REVERT: D 238 LEU cc_start: 0.7603 (mp) cc_final: 0.7086 (tp) REVERT: D 300 ASN cc_start: 0.8211 (m110) cc_final: 0.7915 (t0) outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 2.9199 time to fit residues: 458.5222 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 0.9980 chunk 30 optimal weight: 0.0060 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.4554 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.150432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117243 restraints weight = 29942.985| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.81 r_work: 0.3268 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9948 Z= 0.103 Angle : 0.449 4.517 13476 Z= 0.235 Chirality : 0.040 0.142 1584 Planarity : 0.004 0.040 1716 Dihedral : 3.507 14.378 1372 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.24), residues: 1236 helix: 2.87 (0.20), residues: 680 sheet: 1.39 (0.36), residues: 196 loop : -0.77 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 41 HIS 0.001 0.001 HIS D 202 PHE 0.005 0.001 PHE B 285 TYR 0.005 0.001 TYR D 166 ARG 0.001 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 552) hydrogen bonds : angle 4.15078 ( 1644) covalent geometry : bond 0.00213 ( 9948) covalent geometry : angle 0.44914 (13476) *********************** 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 147 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.477 Fit side-chains REVERT: A 60 LYS cc_start: 0.7545 (ttpt) cc_final: 0.6900 (ttpp) REVERT: A 64 GLU cc_start: 0.6741 (tt0) cc_final: 0.6358 (tp30) REVERT: A 94 ASP cc_start: 0.8514 (m-30) cc_final: 0.7965 (m-30) REVERT: A 144 ILE cc_start: 0.8042 (mm) cc_final: 0.7654 (mt) REVERT: A 221 MET cc_start: 0.8089 (mmp) cc_final: 0.6602 (tmm) REVERT: A 238 LEU cc_start: 0.7660 (mp) cc_final: 0.7160 (tp) REVERT: B 56 GLU cc_start: 0.7757 (tp30) cc_final: 0.7418 (tp30) REVERT: B 60 LYS cc_start: 0.7505 (ttpt) cc_final: 0.6857 (ttpp) REVERT: B 64 GLU cc_start: 0.6704 (tt0) cc_final: 0.6338 (tp30) REVERT: B 144 ILE cc_start: 0.8035 (mm) cc_final: 0.7638 (mt) REVERT: B 221 MET cc_start: 0.8160 (mmp) cc_final: 0.6678 (tmt) REVERT: B 222 TYR cc_start: 0.8514 (m-80) cc_final: 0.8291 (m-80) REVERT: B 238 LEU cc_start: 0.7651 (mp) cc_final: 0.7136 (tp) REVERT: B 300 ASN cc_start: 0.8061 (m-40) cc_final: 0.7853 (t0) REVERT: C 64 GLU cc_start: 0.6732 (tt0) cc_final: 0.6357 (tp30) REVERT: C 144 ILE cc_start: 0.8047 (mm) cc_final: 0.7648 (mt) REVERT: C 221 MET cc_start: 0.8159 (mmp) cc_final: 0.6690 (tmt) REVERT: C 222 TYR cc_start: 0.8504 (m-80) cc_final: 0.8286 (m-80) REVERT: D 60 LYS cc_start: 0.7530 (ttpt) cc_final: 0.6892 (ttpp) REVERT: D 64 GLU cc_start: 0.6729 (tt0) cc_final: 0.6366 (tp30) REVERT: D 144 ILE cc_start: 0.8032 (mm) cc_final: 0.7637 (mt) REVERT: D 221 MET cc_start: 0.8179 (mmp) cc_final: 0.6729 (tmt) REVERT: D 222 TYR cc_start: 0.8545 (m-80) cc_final: 0.8309 (m-80) outliers start: 0 outliers final: 1 residues processed: 147 average time/residue: 2.6374 time to fit residues: 417.9361 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.146581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113380 restraints weight = 30108.012| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.80 r_work: 0.3205 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9948 Z= 0.172 Angle : 0.531 5.422 13476 Z= 0.279 Chirality : 0.042 0.150 1584 Planarity : 0.005 0.042 1716 Dihedral : 3.838 14.808 1372 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 13.26 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.24), residues: 1236 helix: 2.66 (0.20), residues: 672 sheet: 1.60 (0.37), residues: 176 loop : -1.00 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 41 HIS 0.002 0.001 HIS C 81 PHE 0.007 0.001 PHE B 285 TYR 0.007 0.001 TYR A 315 ARG 0.002 0.000 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.06736 ( 552) hydrogen bonds : angle 4.24516 ( 1644) covalent geometry : bond 0.00410 ( 9948) covalent geometry : angle 0.53140 (13476) ********************** 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 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.745 Fit side-chains REVERT: A 60 LYS cc_start: 0.7585 (ttpt) cc_final: 0.6899 (ttpp) REVERT: A 64 GLU cc_start: 0.6858 (tt0) cc_final: 0.6454 (tp30) REVERT: A 94 ASP cc_start: 0.8644 (m-30) cc_final: 0.8434 (m-30) REVERT: A 144 ILE cc_start: 0.8072 (mm) cc_final: 0.7675 (mt) REVERT: A 221 MET cc_start: 0.8043 (mmp) cc_final: 0.6563 (tmm) REVERT: A 238 LEU cc_start: 0.7758 (mp) cc_final: 0.7249 (tp) REVERT: B 56 GLU cc_start: 0.7805 (tp30) cc_final: 0.7395 (tp30) REVERT: B 60 LYS cc_start: 0.7528 (ttpt) cc_final: 0.6853 (ttpp) REVERT: B 64 GLU cc_start: 0.6804 (tt0) cc_final: 0.6408 (tp30) REVERT: B 144 ILE cc_start: 0.8062 (mm) cc_final: 0.7668 (mt) REVERT: B 221 MET cc_start: 0.8099 (mmp) cc_final: 0.6597 (tmm) REVERT: B 238 LEU cc_start: 0.7768 (mp) cc_final: 0.7249 (tp) REVERT: B 300 ASN cc_start: 0.8266 (m-40) cc_final: 0.7911 (t0) REVERT: C 64 GLU cc_start: 0.6850 (tt0) cc_final: 0.6435 (tp30) REVERT: C 144 ILE cc_start: 0.8040 (mm) cc_final: 0.7642 (mt) REVERT: C 221 MET cc_start: 0.8109 (mmp) cc_final: 0.6613 (tmm) REVERT: C 238 LEU cc_start: 0.7751 (mp) cc_final: 0.7235 (tp) REVERT: D 60 LYS cc_start: 0.7566 (ttpt) cc_final: 0.6876 (ttpp) REVERT: D 64 GLU cc_start: 0.6844 (tt0) cc_final: 0.6449 (tp30) REVERT: D 144 ILE cc_start: 0.8049 (mm) cc_final: 0.7649 (mt) REVERT: D 221 MET cc_start: 0.8137 (mmp) cc_final: 0.6636 (tmm) REVERT: D 238 LEU cc_start: 0.7726 (mp) cc_final: 0.7216 (tp) outliers start: 0 outliers final: 1 residues processed: 145 average time/residue: 2.6536 time to fit residues: 414.6685 Evaluate side-chains 146 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.147181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113865 restraints weight = 30162.127| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.82 r_work: 0.3208 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9948 Z= 0.145 Angle : 0.509 5.079 13476 Z= 0.267 Chirality : 0.041 0.146 1584 Planarity : 0.005 0.043 1716 Dihedral : 3.795 14.901 1372 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 12.97 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.24), residues: 1236 helix: 2.67 (0.20), residues: 668 sheet: 1.24 (0.35), residues: 196 loop : -0.97 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 41 HIS 0.002 0.001 HIS B 202 PHE 0.007 0.001 PHE C 285 TYR 0.006 0.001 TYR D 166 ARG 0.001 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.06381 ( 552) hydrogen bonds : angle 4.28680 ( 1644) covalent geometry : bond 0.00331 ( 9948) covalent geometry : angle 0.50936 (13476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16293.18 seconds wall clock time: 286 minutes 36.23 seconds (17196.23 seconds total)