Starting phenix.real_space_refine on Thu Sep 18 06:51:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9go5_51491/09_2025/9go5_51491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9go5_51491/09_2025/9go5_51491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9go5_51491/09_2025/9go5_51491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9go5_51491/09_2025/9go5_51491.map" model { file = "/net/cci-nas-00/data/ceres_data/9go5_51491/09_2025/9go5_51491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9go5_51491/09_2025/9go5_51491.cif" } resolution = 2.5 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= 0.001 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 95 5.16 5 C 9205 2.51 5 N 2470 2.21 5 O 3145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 14930 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Time building chain proxies: 3.64, per 1000 atoms: 0.24 Number of scatterers: 14930 At special positions: 0 Unit cell: (77.562, 96.744, 193.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 10 15.00 Mg 5 11.99 O 3145 8.00 N 2470 7.00 C 9205 6.00 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: 1.07 Conformation dependent library (CDL) restraints added in 619.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 51.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.591A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.863A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.572A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.575A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.622A pdb=" N ALA A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.601A pdb=" N VAL A 266 " --> pdb=" O HIS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.001A pdb=" N PHE A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.974A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.625A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.592A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.572A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.576A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.622A pdb=" N ALA B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.601A pdb=" N VAL B 266 " --> pdb=" O HIS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.001A pdb=" N PHE B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.974A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.626A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.592A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.573A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.575A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.621A pdb=" N ALA C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.601A pdb=" N VAL C 266 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.001A pdb=" N PHE C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.974A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.626A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.591A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.572A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.576A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.622A pdb=" N ALA D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.601A pdb=" N VAL D 266 " --> pdb=" O HIS D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.001A pdb=" N PHE D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.974A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.625A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.591A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.572A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.576A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.622A pdb=" N ALA E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.601A pdb=" N VAL E 266 " --> pdb=" O HIS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.001A pdb=" N PHE E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.974A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.626A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.677A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ILE A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.499A pdb=" N ILE A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.677A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ILE B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.498A pdb=" N ILE B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.678A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ILE C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.499A pdb=" N ILE C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.676A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ILE D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.499A pdb=" N ILE D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.677A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ILE E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.500A pdb=" N ILE E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 725 hydrogen bonds defined for protein. 1860 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: 2.87 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4755 1.34 - 1.46: 3027 1.46 - 1.58: 6938 1.58 - 1.69: 15 1.69 - 1.81: 170 Bond restraints: 14905 Sorted by residual: bond pdb=" C ALA D 257 " pdb=" N PRO D 258 " ideal model delta sigma weight residual 1.337 1.352 -0.016 1.11e-02 8.12e+03 2.01e+00 bond pdb=" N VAL C 163 " pdb=" CA VAL C 163 " ideal model delta sigma weight residual 1.454 1.465 -0.011 7.70e-03 1.69e+04 1.90e+00 bond pdb=" C ALA A 257 " pdb=" N PRO A 258 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.11e-02 8.12e+03 1.87e+00 bond pdb=" C ALA C 257 " pdb=" N PRO C 258 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.11e-02 8.12e+03 1.84e+00 bond pdb=" C ALA E 257 " pdb=" N PRO E 258 " ideal model delta sigma weight residual 1.337 1.351 -0.015 1.11e-02 8.12e+03 1.80e+00 ... (remaining 14900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 19488 1.58 - 3.17: 577 3.17 - 4.75: 89 4.75 - 6.33: 31 6.33 - 7.92: 25 Bond angle restraints: 20210 Sorted by residual: angle pdb=" CB MET D 16 " pdb=" CG MET D 16 " pdb=" SD MET D 16 " ideal model delta sigma weight residual 112.70 120.62 -7.92 3.00e+00 1.11e-01 6.96e+00 angle pdb=" CB MET E 16 " pdb=" CG MET E 16 " pdb=" SD MET E 16 " ideal model delta sigma weight residual 112.70 120.61 -7.91 3.00e+00 1.11e-01 6.96e+00 angle pdb=" CB MET C 16 " pdb=" CG MET C 16 " pdb=" SD MET C 16 " ideal model delta sigma weight residual 112.70 120.59 -7.89 3.00e+00 1.11e-01 6.92e+00 angle pdb=" CB MET B 16 " pdb=" CG MET B 16 " pdb=" SD MET B 16 " ideal model delta sigma weight residual 112.70 120.59 -7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" CB MET A 16 " pdb=" CG MET A 16 " pdb=" SD MET A 16 " ideal model delta sigma weight residual 112.70 120.59 -7.89 3.00e+00 1.11e-01 6.91e+00 ... (remaining 20205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 8305 29.83 - 59.65: 575 59.65 - 89.48: 60 89.48 - 119.30: 5 119.30 - 149.13: 10 Dihedral angle restraints: 8955 sinusoidal: 3630 harmonic: 5325 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.13 -149.13 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.11 -149.12 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.08 -149.08 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 8952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1440 0.042 - 0.083: 545 0.083 - 0.125: 200 0.125 - 0.167: 40 0.167 - 0.208: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CB ILE E 151 " pdb=" CA ILE E 151 " pdb=" CG1 ILE E 151 " pdb=" CG2 ILE E 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2227 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 341 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ILE B 341 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE B 341 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 342 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 341 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C ILE C 341 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE C 341 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY C 342 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 341 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C ILE A 341 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE A 341 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY A 342 " -0.013 2.00e-02 2.50e+03 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 239 2.61 - 3.18: 11535 3.18 - 3.75: 25243 3.75 - 4.33: 37728 4.33 - 4.90: 57657 Nonbonded interactions: 132402 Sorted by model distance: nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.037 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.037 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 2.037 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 2.037 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.037 2.170 ... (remaining 132397 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.010 Find NCS groups from input model: 0.130 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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 : 0.004 0.051 14905 Z= 0.187 Angle : 0.714 7.917 20210 Z= 0.369 Chirality : 0.050 0.208 2230 Planarity : 0.007 0.054 2590 Dihedral : 19.451 149.131 5545 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.10 % Allowed : 20.44 % Favored : 77.46 % 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: 0.07 (0.20), residues: 1840 helix: -1.01 (0.17), residues: 730 sheet: 0.60 (0.28), residues: 335 loop : 1.23 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.007 0.001 TYR B 69 PHE 0.013 0.002 PHE E 255 TRP 0.015 0.003 TRP E 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00412 (14905) covalent geometry : angle 0.71357 (20210) hydrogen bonds : bond 0.14923 ( 715) hydrogen bonds : angle 6.62995 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.608 Fit side-chains REVERT: A 64 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9071 (pp) REVERT: A 286 ASP cc_start: 0.8577 (m-30) cc_final: 0.8257 (m-30) REVERT: B 286 ASP cc_start: 0.8518 (m-30) cc_final: 0.8288 (m-30) REVERT: C 64 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.8776 (pp) REVERT: C 190 MET cc_start: 0.9037 (mtp) cc_final: 0.8826 (mtp) REVERT: C 286 ASP cc_start: 0.8554 (m-30) cc_final: 0.8111 (m-30) REVERT: C 311 GLU cc_start: 0.8851 (mp0) cc_final: 0.8647 (mp0) REVERT: E 92 ASN cc_start: 0.9076 (m110) cc_final: 0.8654 (m-40) outliers start: 33 outliers final: 11 residues processed: 211 average time/residue: 0.7342 time to fit residues: 168.4397 Evaluate side-chains 177 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN C 121 GLN D 121 GLN E 121 GLN E 228 GLN E 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096686 restraints weight = 16801.111| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.23 r_work: 0.3054 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14905 Z= 0.275 Angle : 0.680 9.166 20210 Z= 0.335 Chirality : 0.051 0.198 2230 Planarity : 0.006 0.041 2590 Dihedral : 11.851 176.884 2081 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.62 % Allowed : 17.97 % Favored : 78.41 % 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: 0.83 (0.20), residues: 1840 helix: -0.01 (0.18), residues: 770 sheet: 0.68 (0.27), residues: 335 loop : 1.48 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 95 TYR 0.008 0.002 TYR C 279 PHE 0.011 0.002 PHE C 262 TRP 0.021 0.003 TRP A 340 HIS 0.008 0.002 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00661 (14905) covalent geometry : angle 0.68021 (20210) hydrogen bonds : bond 0.04925 ( 715) hydrogen bonds : angle 5.06891 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.617 Fit side-chains REVERT: A 47 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.5735 (ttt) REVERT: A 64 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9057 (pp) REVERT: A 286 ASP cc_start: 0.8450 (m-30) cc_final: 0.8121 (m-30) REVERT: B 47 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.5663 (ttt) REVERT: B 241 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: B 286 ASP cc_start: 0.8325 (m-30) cc_final: 0.8070 (m-30) REVERT: C 39 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7956 (mtm110) REVERT: D 39 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8196 (mtm110) REVERT: D 44 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7421 (mtm) REVERT: D 178 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8204 (mt) REVERT: D 179 ASP cc_start: 0.8109 (m-30) cc_final: 0.7862 (m-30) REVERT: D 359 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7725 (ttmt) REVERT: E 92 ASN cc_start: 0.9085 (m110) cc_final: 0.8806 (m-40) REVERT: E 228 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7181 (mm-40) outliers start: 57 outliers final: 28 residues processed: 212 average time/residue: 0.7805 time to fit residues: 179.3065 Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099318 restraints weight = 16876.789| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.21 r_work: 0.3092 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14905 Z= 0.179 Angle : 0.604 8.331 20210 Z= 0.293 Chirality : 0.047 0.200 2230 Planarity : 0.005 0.037 2590 Dihedral : 11.177 178.663 2075 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.79 % Allowed : 18.60 % Favored : 78.60 % 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: 1.40 (0.20), residues: 1840 helix: 0.60 (0.19), residues: 735 sheet: 0.75 (0.28), residues: 335 loop : 1.68 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.007 0.001 TYR C 91 PHE 0.010 0.001 PHE C 262 TRP 0.015 0.002 TRP C 340 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00426 (14905) covalent geometry : angle 0.60427 (20210) hydrogen bonds : bond 0.03989 ( 715) hydrogen bonds : angle 4.78586 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.542 Fit side-chains REVERT: A 64 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9059 (pp) REVERT: A 286 ASP cc_start: 0.8530 (m-30) cc_final: 0.8195 (m-30) REVERT: B 47 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5462 (ttt) REVERT: B 50 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8242 (mtmt) REVERT: B 241 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: B 286 ASP cc_start: 0.8255 (m-30) cc_final: 0.8042 (m-30) REVERT: C 39 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7934 (mtm110) REVERT: D 44 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7355 (mtm) REVERT: D 178 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8205 (mt) REVERT: D 179 ASP cc_start: 0.8141 (m-30) cc_final: 0.7920 (m-30) REVERT: D 359 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7733 (ttmt) REVERT: E 228 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7203 (mm-40) outliers start: 44 outliers final: 27 residues processed: 200 average time/residue: 0.7375 time to fit residues: 160.0927 Evaluate side-chains 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.109388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.088691 restraints weight = 16067.226| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.23 r_work: 0.2842 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14905 Z= 0.181 Angle : 0.604 8.291 20210 Z= 0.293 Chirality : 0.047 0.203 2230 Planarity : 0.004 0.036 2590 Dihedral : 10.877 179.791 2074 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.49 % Allowed : 18.10 % Favored : 78.41 % 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: 1.57 (0.20), residues: 1840 helix: 0.80 (0.19), residues: 735 sheet: 0.76 (0.27), residues: 335 loop : 1.74 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.007 0.001 TYR A 69 PHE 0.010 0.001 PHE C 262 TRP 0.015 0.002 TRP C 340 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00432 (14905) covalent geometry : angle 0.60397 (20210) hydrogen bonds : bond 0.03935 ( 715) hydrogen bonds : angle 4.71124 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 0.618 Fit side-chains REVERT: A 286 ASP cc_start: 0.8496 (m-30) cc_final: 0.8110 (m-30) REVERT: B 47 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5386 (ttt) REVERT: B 50 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8238 (mtmt) REVERT: B 241 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: B 286 ASP cc_start: 0.8268 (m-30) cc_final: 0.8021 (m-30) REVERT: C 39 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7876 (mtm110) REVERT: C 50 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8244 (mttt) REVERT: C 64 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8285 (pp) REVERT: D 178 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8163 (mt) REVERT: D 299 MET cc_start: 0.9247 (mtm) cc_final: 0.9037 (mtp) REVERT: D 359 LYS cc_start: 0.8024 (tmtt) cc_final: 0.7594 (ttmt) REVERT: E 50 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8309 (mtmt) REVERT: E 228 GLN cc_start: 0.7379 (mm-40) cc_final: 0.7147 (mm110) outliers start: 55 outliers final: 34 residues processed: 206 average time/residue: 0.7347 time to fit residues: 164.4596 Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.108765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.087981 restraints weight = 16216.229| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.23 r_work: 0.2830 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14905 Z= 0.208 Angle : 0.626 8.458 20210 Z= 0.305 Chirality : 0.048 0.204 2230 Planarity : 0.005 0.038 2590 Dihedral : 10.928 179.628 2072 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.37 % Allowed : 18.54 % Favored : 78.10 % 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: 1.44 (0.20), residues: 1840 helix: 0.71 (0.19), residues: 765 sheet: 0.71 (0.27), residues: 335 loop : 1.68 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.007 0.001 TYR A 53 PHE 0.012 0.001 PHE C 262 TRP 0.017 0.003 TRP C 340 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00500 (14905) covalent geometry : angle 0.62606 (20210) hydrogen bonds : bond 0.04166 ( 715) hydrogen bonds : angle 4.75167 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.590 Fit side-chains REVERT: A 64 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8979 (pp) REVERT: A 286 ASP cc_start: 0.8509 (m-30) cc_final: 0.8120 (m-30) REVERT: B 47 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5411 (ttt) REVERT: B 50 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8254 (mtmt) REVERT: B 241 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: B 286 ASP cc_start: 0.8257 (m-30) cc_final: 0.7979 (m-30) REVERT: C 39 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7873 (mtm110) REVERT: D 178 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8173 (mt) REVERT: D 232 GLN cc_start: 0.7659 (mt0) cc_final: 0.7362 (mt0) REVERT: D 359 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7599 (ttmt) REVERT: E 50 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8306 (mtmt) REVERT: E 228 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7124 (mm110) outliers start: 53 outliers final: 37 residues processed: 203 average time/residue: 0.7619 time to fit residues: 167.6586 Evaluate side-chains 204 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 162 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.118277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099454 restraints weight = 16726.346| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.20 r_work: 0.3095 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14905 Z= 0.164 Angle : 0.592 8.096 20210 Z= 0.286 Chirality : 0.046 0.196 2230 Planarity : 0.004 0.037 2590 Dihedral : 10.682 178.546 2072 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.17 % Allowed : 18.67 % Favored : 78.16 % 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: 1.68 (0.20), residues: 1840 helix: 0.96 (0.19), residues: 735 sheet: 0.73 (0.27), residues: 335 loop : 1.77 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.007 0.001 TYR D 143 PHE 0.010 0.001 PHE C 262 TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00389 (14905) covalent geometry : angle 0.59214 (20210) hydrogen bonds : bond 0.03736 ( 715) hydrogen bonds : angle 4.64409 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.630 Fit side-chains REVERT: A 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9038 (pp) REVERT: A 286 ASP cc_start: 0.8521 (m-30) cc_final: 0.8158 (m-30) REVERT: A 291 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8700 (tttt) REVERT: B 47 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.5376 (ttt) REVERT: B 50 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8263 (mtmt) REVERT: B 241 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: B 286 ASP cc_start: 0.8257 (m-30) cc_final: 0.8016 (m-30) REVERT: C 39 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7952 (mtm110) REVERT: C 50 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8015 (mtmm) REVERT: C 286 ASP cc_start: 0.8413 (m-30) cc_final: 0.8066 (m-30) REVERT: D 178 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8199 (mt) REVERT: D 232 GLN cc_start: 0.7663 (mt0) cc_final: 0.7431 (mt0) REVERT: D 299 MET cc_start: 0.9243 (mtm) cc_final: 0.9035 (mtp) REVERT: D 359 LYS cc_start: 0.8100 (tmtt) cc_final: 0.7714 (ttmt) REVERT: E 50 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8376 (mtmt) REVERT: E 228 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7202 (mm110) outliers start: 50 outliers final: 32 residues processed: 198 average time/residue: 0.8062 time to fit residues: 172.8526 Evaluate side-chains 198 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 123 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.118339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099555 restraints weight = 16660.205| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.20 r_work: 0.3095 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14905 Z= 0.164 Angle : 0.593 8.066 20210 Z= 0.286 Chirality : 0.046 0.197 2230 Planarity : 0.004 0.039 2590 Dihedral : 10.640 177.711 2072 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.37 % Allowed : 18.48 % Favored : 78.16 % 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: 1.70 (0.20), residues: 1840 helix: 1.00 (0.19), residues: 735 sheet: 0.72 (0.27), residues: 335 loop : 1.78 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.007 0.001 TYR D 143 PHE 0.010 0.001 PHE C 262 TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00390 (14905) covalent geometry : angle 0.59292 (20210) hydrogen bonds : bond 0.03745 ( 715) hydrogen bonds : angle 4.62455 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.618 Fit side-chains REVERT: A 64 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9039 (pp) REVERT: A 286 ASP cc_start: 0.8525 (m-30) cc_final: 0.8159 (m-30) REVERT: A 291 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8704 (tttt) REVERT: B 47 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5355 (ttt) REVERT: B 50 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8271 (mtmt) REVERT: B 241 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: B 286 ASP cc_start: 0.8237 (m-30) cc_final: 0.7996 (m-30) REVERT: C 39 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7952 (mtm110) REVERT: C 50 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8034 (mtmm) REVERT: C 286 ASP cc_start: 0.8413 (m-30) cc_final: 0.8069 (m-30) REVERT: D 178 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8192 (mt) REVERT: D 232 GLN cc_start: 0.7669 (mt0) cc_final: 0.7403 (mt0) REVERT: D 359 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7729 (ttmt) REVERT: E 50 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8382 (mtmt) outliers start: 53 outliers final: 31 residues processed: 200 average time/residue: 0.7731 time to fit residues: 167.9385 Evaluate side-chains 197 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099008 restraints weight = 16746.739| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.19 r_work: 0.3068 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14905 Z= 0.191 Angle : 0.614 8.274 20210 Z= 0.298 Chirality : 0.047 0.202 2230 Planarity : 0.004 0.042 2590 Dihedral : 10.789 178.938 2072 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.05 % Allowed : 18.67 % Favored : 78.29 % 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: 1.62 (0.20), residues: 1840 helix: 0.94 (0.19), residues: 735 sheet: 0.66 (0.27), residues: 335 loop : 1.73 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.007 0.001 TYR A 69 PHE 0.011 0.001 PHE C 262 TRP 0.016 0.002 TRP C 340 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00459 (14905) covalent geometry : angle 0.61436 (20210) hydrogen bonds : bond 0.03990 ( 715) hydrogen bonds : angle 4.67983 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.622 Fit side-chains REVERT: A 64 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9038 (pp) REVERT: A 286 ASP cc_start: 0.8522 (m-30) cc_final: 0.8154 (m-30) REVERT: A 291 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8713 (tttt) REVERT: B 47 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.5350 (ttt) REVERT: B 50 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8291 (mtmt) REVERT: B 241 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: B 286 ASP cc_start: 0.8231 (m-30) cc_final: 0.7992 (m-30) REVERT: C 39 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7950 (mtm110) REVERT: C 50 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8040 (mtmm) REVERT: C 286 ASP cc_start: 0.8408 (m-30) cc_final: 0.8081 (m-30) REVERT: D 178 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8188 (mt) REVERT: D 232 GLN cc_start: 0.7674 (mt0) cc_final: 0.7409 (mt0) REVERT: D 359 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7730 (ttmt) REVERT: E 50 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8397 (mtmt) REVERT: E 228 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7271 (mm-40) outliers start: 48 outliers final: 36 residues processed: 195 average time/residue: 0.7935 time to fit residues: 167.7149 Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 131 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.120628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102015 restraints weight = 16735.954| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.20 r_work: 0.3138 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14905 Z= 0.107 Angle : 0.550 7.383 20210 Z= 0.263 Chirality : 0.044 0.171 2230 Planarity : 0.004 0.034 2590 Dihedral : 9.934 172.198 2072 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.29 % Allowed : 19.43 % Favored : 78.29 % 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: 1.96 (0.20), residues: 1840 helix: 1.27 (0.19), residues: 735 sheet: 0.78 (0.28), residues: 335 loop : 1.91 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.009 0.001 TYR D 143 PHE 0.007 0.001 PHE C 262 TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS D 372 Details of bonding type rmsd covalent geometry : bond 0.00242 (14905) covalent geometry : angle 0.55018 (20210) hydrogen bonds : bond 0.03102 ( 715) hydrogen bonds : angle 4.45150 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.675 Fit side-chains REVERT: A 64 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9007 (pp) REVERT: A 286 ASP cc_start: 0.8514 (m-30) cc_final: 0.8146 (m-30) REVERT: B 50 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8235 (mtmt) REVERT: B 241 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: B 286 ASP cc_start: 0.8232 (m-30) cc_final: 0.8005 (m-30) REVERT: C 286 ASP cc_start: 0.8369 (m-30) cc_final: 0.8019 (m-30) REVERT: D 178 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8116 (mt) REVERT: D 232 GLN cc_start: 0.7708 (mt0) cc_final: 0.7460 (mt0) REVERT: D 299 MET cc_start: 0.9211 (mtm) cc_final: 0.8977 (mtp) REVERT: D 359 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7719 (ttmt) REVERT: E 50 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8370 (mtmt) REVERT: E 228 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7217 (mm-40) outliers start: 36 outliers final: 23 residues processed: 189 average time/residue: 0.8037 time to fit residues: 164.6404 Evaluate side-chains 184 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 21 optimal weight: 6.9990 chunk 110 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106958 restraints weight = 16830.976| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.20 r_work: 0.3219 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14905 Z= 0.080 Angle : 0.518 7.509 20210 Z= 0.243 Chirality : 0.043 0.141 2230 Planarity : 0.004 0.035 2590 Dihedral : 7.746 163.001 2071 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.21 % Allowed : 20.44 % Favored : 78.35 % 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: 2.26 (0.20), residues: 1840 helix: 1.56 (0.20), residues: 740 sheet: 1.00 (0.29), residues: 325 loop : 1.97 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.011 0.001 TYR C 143 PHE 0.006 0.001 PHE D 306 TRP 0.012 0.001 TRP C 79 HIS 0.004 0.000 HIS D 372 Details of bonding type rmsd covalent geometry : bond 0.00169 (14905) covalent geometry : angle 0.51758 (20210) hydrogen bonds : bond 0.02546 ( 715) hydrogen bonds : angle 4.26353 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.640 Fit side-chains REVERT: A 64 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8992 (pp) REVERT: A 286 ASP cc_start: 0.8450 (m-30) cc_final: 0.8110 (m-30) REVERT: B 50 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8143 (mtmt) REVERT: B 241 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: B 350 THR cc_start: 0.8846 (p) cc_final: 0.8631 (m) REVERT: C 286 ASP cc_start: 0.8274 (m-30) cc_final: 0.7889 (m-30) REVERT: D 178 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8048 (mt) REVERT: D 359 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7697 (tttt) REVERT: E 228 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7104 (mm-40) REVERT: E 232 GLN cc_start: 0.7409 (mt0) cc_final: 0.7194 (mt0) outliers start: 19 outliers final: 10 residues processed: 188 average time/residue: 0.7754 time to fit residues: 158.4791 Evaluate side-chains 176 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 GLN D 232 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101012 restraints weight = 16701.309| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.20 r_work: 0.3119 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14905 Z= 0.150 Angle : 0.590 7.857 20210 Z= 0.282 Chirality : 0.046 0.181 2230 Planarity : 0.004 0.038 2590 Dihedral : 8.293 156.658 2066 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.08 % Allowed : 20.83 % Favored : 78.10 % 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: 2.04 (0.20), residues: 1840 helix: 1.33 (0.19), residues: 735 sheet: 0.83 (0.28), residues: 335 loop : 1.96 (0.25), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.007 0.001 TYR D 143 PHE 0.009 0.001 PHE C 262 TRP 0.014 0.002 TRP A 340 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00355 (14905) covalent geometry : angle 0.59011 (20210) hydrogen bonds : bond 0.03523 ( 715) hydrogen bonds : angle 4.48881 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5638.94 seconds wall clock time: 97 minutes 1.03 seconds (5821.03 seconds total)