Starting phenix.real_space_refine on Fri Jun 13 07:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9go5_51491/06_2025/9go5_51491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9go5_51491/06_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_51491/06_2025/9go5_51491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9go5_51491/06_2025/9go5_51491.map" model { file = "/net/cci-nas-00/data/ceres_data/9go5_51491/06_2025/9go5_51491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9go5_51491/06_2025/9go5_51491.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.25, per 1000 atoms: 0.62 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: 3.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.38 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: 5.31 Time building geometry restraints manager: 4.24 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.270 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (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 TRP 0.015 0.003 TRP E 340 HIS 0.004 0.001 HIS A 161 PHE 0.013 0.002 PHE E 255 TYR 0.007 0.001 TYR B 69 ARG 0.003 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.14923 ( 715) hydrogen bonds : angle 6.62995 ( 1860) covalent geometry : bond 0.00412 (14905) covalent geometry : angle 0.71357 (20210) *********************** 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 : 2.528 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: 1.7197 time to fit residues: 397.2831 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 : 1.782 ------------------------------------------------------------------------------- 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 156 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 12 ASN E 121 GLN E 228 GLN E 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101575 restraints weight = 16718.528| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.10 r_work: 0.3109 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14905 Z= 0.148 Angle : 0.585 8.043 20210 Z= 0.283 Chirality : 0.045 0.184 2230 Planarity : 0.005 0.033 2590 Dihedral : 11.502 171.936 2081 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.17 % Allowed : 18.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1840 helix: 0.29 (0.19), residues: 735 sheet: 0.80 (0.28), residues: 335 loop : 1.73 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 340 HIS 0.006 0.001 HIS A 161 PHE 0.008 0.001 PHE C 262 TYR 0.007 0.001 TYR A 69 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 715) hydrogen bonds : angle 4.86699 ( 1860) covalent geometry : bond 0.00345 (14905) covalent geometry : angle 0.58537 (20210) *********************** 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: 50 poor density : 175 time to evaluate : 1.858 Fit side-chains REVERT: A 286 ASP cc_start: 0.8443 (m-30) cc_final: 0.8152 (m-30) REVERT: B 241 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: B 286 ASP cc_start: 0.8293 (m-30) cc_final: 0.8060 (m-30) REVERT: B 311 GLU cc_start: 0.8707 (mp0) cc_final: 0.8415 (mp0) REVERT: C 39 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7911 (mtm110) REVERT: C 286 ASP cc_start: 0.8382 (m-30) cc_final: 0.8029 (m-30) REVERT: D 44 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7421 (mtm) REVERT: D 178 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8160 (mt) REVERT: E 92 ASN cc_start: 0.9051 (m110) cc_final: 0.8778 (m-40) REVERT: E 228 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7169 (mm-40) outliers start: 50 outliers final: 22 residues processed: 208 average time/residue: 1.5811 time to fit residues: 360.2105 Evaluate side-chains 192 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain B residue 45 VAL 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 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 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 47 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 116 optimal weight: 0.0270 overall best weight: 2.0844 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.118035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100180 restraints weight = 16763.784| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.12 r_work: 0.3089 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14905 Z= 0.162 Angle : 0.591 8.051 20210 Z= 0.285 Chirality : 0.046 0.186 2230 Planarity : 0.004 0.033 2590 Dihedral : 11.252 171.890 2070 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.86 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1840 helix: 0.72 (0.19), residues: 735 sheet: 0.83 (0.28), residues: 335 loop : 1.83 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 340 HIS 0.006 0.001 HIS A 161 PHE 0.009 0.001 PHE C 262 TYR 0.006 0.001 TYR D 69 ARG 0.004 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 715) hydrogen bonds : angle 4.70505 ( 1860) covalent geometry : bond 0.00384 (14905) covalent geometry : angle 0.59125 (20210) *********************** 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 215 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 1.839 Fit side-chains REVERT: A 64 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9037 (pp) REVERT: A 286 ASP cc_start: 0.8501 (m-30) cc_final: 0.8165 (m-30) REVERT: B 241 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: B 286 ASP cc_start: 0.8290 (m-30) cc_final: 0.8071 (m-30) REVERT: C 39 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7926 (mtm110) REVERT: C 286 ASP cc_start: 0.8427 (m-30) cc_final: 0.8070 (m-30) REVERT: D 44 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7486 (mtm) REVERT: D 178 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8174 (mt) REVERT: D 179 ASP cc_start: 0.8101 (m-30) cc_final: 0.7893 (m-30) REVERT: D 299 MET cc_start: 0.9190 (mtm) cc_final: 0.8967 (mtp) REVERT: D 359 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7736 (ttmt) REVERT: E 360 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6796 (mp10) outliers start: 45 outliers final: 29 residues processed: 202 average time/residue: 1.6878 time to fit residues: 371.6278 Evaluate side-chains 197 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 2.125 ------------------------------------------------------------------------------- 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 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 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 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 178 ILE Chi-restraints excluded: chain E residue 289 VAL 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 117 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.118114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100263 restraints weight = 16769.081| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.12 r_work: 0.3090 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1593 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= 0.156 Angle : 0.585 8.019 20210 Z= 0.281 Chirality : 0.046 0.190 2230 Planarity : 0.004 0.033 2590 Dihedral : 10.794 178.543 2070 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.37 % Allowed : 18.41 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 1840 helix: 0.93 (0.19), residues: 735 sheet: 0.82 (0.28), residues: 335 loop : 1.87 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.006 0.001 HIS A 161 PHE 0.009 0.001 PHE C 262 TYR 0.007 0.001 TYR D 143 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 715) hydrogen bonds : angle 4.61358 ( 1860) covalent geometry : bond 0.00370 (14905) covalent geometry : angle 0.58463 (20210) *********************** 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: 53 poor density : 166 time to evaluate : 1.815 Fit side-chains REVERT: A 64 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9030 (pp) REVERT: A 286 ASP cc_start: 0.8504 (m-30) cc_final: 0.8174 (m-30) REVERT: B 50 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8227 (mtmt) REVERT: B 241 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: B 286 ASP cc_start: 0.8284 (m-30) cc_final: 0.8067 (m-30) REVERT: C 39 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7946 (mtm110) REVERT: C 64 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8397 (pp) REVERT: C 190 MET cc_start: 0.9242 (mtm) cc_final: 0.8971 (mtp) REVERT: C 286 ASP cc_start: 0.8454 (m-30) cc_final: 0.8093 (m-30) REVERT: D 44 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7495 (mtm) REVERT: D 178 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8179 (mt) REVERT: D 232 GLN cc_start: 0.7681 (mt0) cc_final: 0.7479 (mt0) REVERT: D 299 MET cc_start: 0.9202 (mtm) cc_final: 0.8994 (mtp) REVERT: D 359 LYS cc_start: 0.8083 (tmtt) cc_final: 0.7726 (ttmt) REVERT: E 228 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7163 (mm-40) REVERT: E 241 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: E 360 GLN cc_start: 0.7241 (tm-30) cc_final: 0.6863 (pm20) outliers start: 53 outliers final: 32 residues processed: 206 average time/residue: 1.7008 time to fit residues: 381.4571 Evaluate side-chains 203 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 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 64 ILE 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 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 135 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 241 GLU 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 6 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.119101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.100064 restraints weight = 17075.048| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.23 r_work: 0.3099 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14905 Z= 0.145 Angle : 0.574 7.945 20210 Z= 0.276 Chirality : 0.045 0.187 2230 Planarity : 0.004 0.034 2590 Dihedral : 10.522 177.991 2070 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.24 % Allowed : 18.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.20), residues: 1840 helix: 1.06 (0.19), residues: 735 sheet: 0.82 (0.28), residues: 335 loop : 1.88 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 PHE 0.009 0.001 PHE C 262 TYR 0.007 0.001 TYR D 143 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 715) hydrogen bonds : angle 4.56345 ( 1860) covalent geometry : bond 0.00342 (14905) covalent geometry : angle 0.57449 (20210) *********************** 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 217 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.684 Fit side-chains REVERT: A 64 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 286 ASP cc_start: 0.8437 (m-30) cc_final: 0.8114 (m-30) REVERT: B 50 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8254 (mtmt) REVERT: B 62 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7214 (mtm180) REVERT: B 241 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: B 286 ASP cc_start: 0.8246 (m-30) cc_final: 0.8027 (m-30) REVERT: C 64 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8403 (pp) REVERT: C 190 MET cc_start: 0.9224 (mtm) cc_final: 0.8964 (mtp) REVERT: C 286 ASP cc_start: 0.8402 (m-30) cc_final: 0.8040 (m-30) REVERT: D 178 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8162 (mt) REVERT: D 232 GLN cc_start: 0.7704 (mt0) cc_final: 0.7503 (mt0) REVERT: D 299 MET cc_start: 0.9205 (mtm) cc_final: 0.8997 (mtp) REVERT: D 359 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7772 (ttmt) REVERT: E 228 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7142 (mm-40) REVERT: E 241 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8512 (tt0) REVERT: E 360 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6918 (pm20) outliers start: 51 outliers final: 34 residues processed: 206 average time/residue: 2.0671 time to fit residues: 465.6775 Evaluate side-chains 202 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 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 62 ARG 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 45 VAL Chi-restraints excluded: chain C residue 47 MET 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 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 110 MET Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 241 GLU 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 161 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.117937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098868 restraints weight = 16988.182| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.22 r_work: 0.3078 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14905 Z= 0.191 Angle : 0.611 8.352 20210 Z= 0.296 Chirality : 0.047 0.202 2230 Planarity : 0.004 0.039 2590 Dihedral : 10.788 179.392 2070 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.30 % Allowed : 18.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1840 helix: 0.97 (0.19), residues: 735 sheet: 0.75 (0.27), residues: 335 loop : 1.81 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.006 0.001 HIS A 161 PHE 0.010 0.001 PHE C 262 TYR 0.007 0.001 TYR A 69 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 715) hydrogen bonds : angle 4.65806 ( 1860) covalent geometry : bond 0.00460 (14905) covalent geometry : angle 0.61056 (20210) *********************** 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 216 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.640 Fit side-chains REVERT: A 64 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9047 (pp) REVERT: A 286 ASP cc_start: 0.8495 (m-30) cc_final: 0.8132 (m-30) REVERT: B 50 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8281 (mtmt) REVERT: B 241 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: B 286 ASP cc_start: 0.8271 (m-30) cc_final: 0.8043 (m-30) REVERT: C 190 MET cc_start: 0.9232 (mtm) cc_final: 0.8973 (mtp) REVERT: C 286 ASP cc_start: 0.8433 (m-30) cc_final: 0.8086 (m-30) REVERT: D 178 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8159 (mt) REVERT: D 359 LYS cc_start: 0.8083 (tmtt) cc_final: 0.7739 (ttmt) REVERT: E 50 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8256 (mtmt) REVERT: E 228 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7128 (mm-40) REVERT: E 241 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: E 360 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6864 (pm20) outliers start: 52 outliers final: 37 residues processed: 205 average time/residue: 1.4966 time to fit residues: 334.0967 Evaluate side-chains 205 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 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 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 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 241 GLU 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 126 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 151 optimal weight: 0.4980 chunk 129 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN D 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102285 restraints weight = 16855.306| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.11 r_work: 0.3126 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 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 : 0.002 0.030 14905 Z= 0.106 Angle : 0.546 7.603 20210 Z= 0.260 Chirality : 0.044 0.171 2230 Planarity : 0.004 0.034 2590 Dihedral : 9.966 172.993 2070 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.41 % Allowed : 19.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 1840 helix: 1.28 (0.19), residues: 735 sheet: 0.82 (0.28), residues: 335 loop : 1.96 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.007 0.001 PHE C 262 TYR 0.009 0.001 TYR D 143 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 715) hydrogen bonds : angle 4.43913 ( 1860) covalent geometry : bond 0.00242 (14905) covalent geometry : angle 0.54586 (20210) *********************** 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 203 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.503 Fit side-chains REVERT: A 64 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9003 (pp) REVERT: A 286 ASP cc_start: 0.8460 (m-30) cc_final: 0.8091 (m-30) REVERT: B 50 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8187 (mtmt) REVERT: B 241 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: B 286 ASP cc_start: 0.8255 (m-30) cc_final: 0.8051 (m-30) REVERT: C 190 MET cc_start: 0.9185 (mtm) cc_final: 0.8935 (mtp) REVERT: C 286 ASP cc_start: 0.8419 (m-30) cc_final: 0.8049 (m-30) REVERT: D 178 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8084 (mt) REVERT: D 299 MET cc_start: 0.9214 (mtm) cc_final: 0.8973 (mtp) REVERT: D 359 LYS cc_start: 0.8095 (tmtt) cc_final: 0.7720 (tttt) REVERT: E 50 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8231 (mtmt) REVERT: E 228 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7144 (mm-40) outliers start: 38 outliers final: 27 residues processed: 193 average time/residue: 1.8799 time to fit residues: 396.5223 Evaluate side-chains 190 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 199 SER 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 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 110 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 88 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096693 restraints weight = 16815.771| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.23 r_work: 0.3057 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14905 Z= 0.261 Angle : 0.661 9.020 20210 Z= 0.323 Chirality : 0.050 0.205 2230 Planarity : 0.005 0.045 2590 Dihedral : 10.975 179.741 2070 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.98 % Allowed : 18.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.20), residues: 1840 helix: 0.79 (0.19), residues: 765 sheet: 0.68 (0.27), residues: 335 loop : 1.71 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 340 HIS 0.007 0.002 HIS A 161 PHE 0.012 0.002 PHE C 262 TYR 0.009 0.002 TYR A 69 ARG 0.006 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 715) hydrogen bonds : angle 4.74394 ( 1860) covalent geometry : bond 0.00634 (14905) covalent geometry : angle 0.66092 (20210) *********************** 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: 47 poor density : 159 time to evaluate : 4.264 Fit side-chains REVERT: A 47 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.5653 (ttt) REVERT: A 64 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9072 (pp) REVERT: A 286 ASP cc_start: 0.8540 (m-30) cc_final: 0.8173 (m-30) REVERT: B 47 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5406 (ttt) REVERT: B 50 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8349 (mtmt) REVERT: B 241 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: B 286 ASP cc_start: 0.8314 (m-30) cc_final: 0.8061 (m-30) REVERT: C 50 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8042 (mtmm) REVERT: C 64 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8369 (pp) REVERT: C 190 MET cc_start: 0.9243 (mtm) cc_final: 0.8961 (mtp) REVERT: C 286 ASP cc_start: 0.8471 (m-30) cc_final: 0.8131 (m-30) REVERT: D 178 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8173 (mt) REVERT: D 179 ASP cc_start: 0.8123 (m-30) cc_final: 0.7905 (m-30) REVERT: D 359 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7730 (ttmt) REVERT: E 50 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8278 (mtmt) REVERT: E 228 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7219 (mm110) REVERT: E 360 GLN cc_start: 0.7272 (tm-30) cc_final: 0.6877 (pm20) outliers start: 47 outliers final: 28 residues processed: 195 average time/residue: 1.5748 time to fit residues: 335.0184 Evaluate side-chains 194 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 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 241 GLU Chi-restraints excluded: chain B residue 289 VAL 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 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 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 140 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.120230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101338 restraints weight = 16754.835| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.24 r_work: 0.3137 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14905 Z= 0.099 Angle : 0.546 7.413 20210 Z= 0.259 Chirality : 0.044 0.168 2230 Planarity : 0.004 0.034 2590 Dihedral : 9.818 173.379 2070 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.29 % Allowed : 19.87 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 1840 helix: 1.32 (0.19), residues: 735 sheet: 0.78 (0.27), residues: 335 loop : 1.90 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS C 161 PHE 0.006 0.001 PHE C 262 TYR 0.010 0.001 TYR D 143 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 715) hydrogen bonds : angle 4.41368 ( 1860) covalent geometry : bond 0.00221 (14905) covalent geometry : angle 0.54630 (20210) *********************** 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 : 2.014 Fit side-chains REVERT: A 64 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9010 (pp) REVERT: A 286 ASP cc_start: 0.8459 (m-30) cc_final: 0.8084 (m-30) REVERT: B 50 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8192 (mtmt) REVERT: B 241 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: B 286 ASP cc_start: 0.8274 (m-30) cc_final: 0.8067 (m-30) REVERT: C 50 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: C 190 MET cc_start: 0.9184 (mtm) cc_final: 0.8931 (mtp) REVERT: C 286 ASP cc_start: 0.8431 (m-30) cc_final: 0.8058 (m-30) REVERT: D 178 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8065 (mt) REVERT: D 299 MET cc_start: 0.9216 (mtm) cc_final: 0.8982 (mtp) REVERT: D 359 LYS cc_start: 0.8104 (tmtt) cc_final: 0.7713 (tttt) REVERT: E 50 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8233 (mtmt) REVERT: E 228 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7170 (mm110) outliers start: 36 outliers final: 26 residues processed: 189 average time/residue: 1.5560 time to fit residues: 320.3783 Evaluate side-chains 189 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 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 199 SER Chi-restraints excluded: chain B residue 241 GLU 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 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 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 0.0170 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100241 restraints weight = 16876.939| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.29 r_work: 0.3110 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14905 Z= 0.119 Angle : 0.557 7.352 20210 Z= 0.265 Chirality : 0.044 0.176 2230 Planarity : 0.004 0.035 2590 Dihedral : 9.376 179.915 2070 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.16 % Allowed : 19.87 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.20), residues: 1840 helix: 1.35 (0.19), residues: 735 sheet: 0.81 (0.28), residues: 335 loop : 1.94 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS D 372 PHE 0.007 0.001 PHE C 262 TYR 0.009 0.001 TYR D 143 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 715) hydrogen bonds : angle 4.42573 ( 1860) covalent geometry : bond 0.00276 (14905) covalent geometry : angle 0.55722 (20210) ********************** 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 193 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.574 Fit side-chains REVERT: A 64 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9012 (pp) REVERT: A 286 ASP cc_start: 0.8509 (m-30) cc_final: 0.8145 (m-30) REVERT: B 50 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8228 (mtmt) REVERT: B 241 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: B 286 ASP cc_start: 0.8283 (m-30) cc_final: 0.8073 (m-30) REVERT: C 190 MET cc_start: 0.9192 (mtm) cc_final: 0.8935 (mtp) REVERT: C 286 ASP cc_start: 0.8450 (m-30) cc_final: 0.8090 (m-30) REVERT: D 178 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8129 (mt) REVERT: D 299 MET cc_start: 0.9226 (mtm) cc_final: 0.8996 (mtp) REVERT: D 359 LYS cc_start: 0.8088 (tmtt) cc_final: 0.7682 (ttmt) REVERT: E 50 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8231 (mtmt) REVERT: E 228 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7209 (mm110) outliers start: 34 outliers final: 27 residues processed: 185 average time/residue: 1.4901 time to fit residues: 300.5485 Evaluate side-chains 188 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 199 SER Chi-restraints excluded: chain B residue 241 GLU 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 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 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 142 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099475 restraints weight = 16718.995| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.29 r_work: 0.3097 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14905 Z= 0.135 Angle : 0.573 7.817 20210 Z= 0.274 Chirality : 0.045 0.186 2230 Planarity : 0.004 0.037 2590 Dihedral : 9.038 169.618 2070 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.03 % Allowed : 20.25 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.20), residues: 1840 helix: 1.29 (0.19), residues: 735 sheet: 0.76 (0.27), residues: 335 loop : 1.93 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.005 0.001 HIS D 161 PHE 0.008 0.001 PHE C 262 TYR 0.007 0.001 TYR D 143 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 715) hydrogen bonds : angle 4.47124 ( 1860) covalent geometry : bond 0.00319 (14905) covalent geometry : angle 0.57293 (20210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11796.70 seconds wall clock time: 210 minutes 14.04 seconds (12614.04 seconds total)