Starting phenix.real_space_refine on Fri May 16 20:00:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9go5_51491/05_2025/9go5_51491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9go5_51491/05_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_51491/05_2025/9go5_51491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9go5_51491/05_2025/9go5_51491.map" model { file = "/net/cci-nas-00/data/ceres_data/9go5_51491/05_2025/9go5_51491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9go5_51491/05_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-5687/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: 8.76, per 1000 atoms: 0.59 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: 3.81 Conformation dependent library (CDL) restraints added in 1.8 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: 2.36 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: 5.47 Time building geometry restraints manager: 4.36 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: 1.620 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.290 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.020 ------------------------------------------------------------------------------- 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 : 1.745 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: 1.4067 time to fit residues: 324.2872 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 : 1.843 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100308 restraints weight = 16718.858| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.21 r_work: 0.3111 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1208 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= 0.149 Angle : 0.586 8.040 20210 Z= 0.283 Chirality : 0.045 0.185 2230 Planarity : 0.005 0.033 2590 Dihedral : 11.501 172.049 2081 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.60 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 0.03818 ( 715) hydrogen bonds : angle 4.86704 ( 1860) covalent geometry : bond 0.00345 (14905) covalent geometry : angle 0.58562 (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 : 1.703 Fit side-chains REVERT: A 286 ASP cc_start: 0.8446 (m-30) cc_final: 0.8156 (m-30) REVERT: B 241 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: B 286 ASP cc_start: 0.8283 (m-30) cc_final: 0.8051 (m-30) REVERT: B 311 GLU cc_start: 0.8711 (mp0) cc_final: 0.8415 (mp0) REVERT: C 39 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7910 (mtm110) REVERT: C 286 ASP cc_start: 0.8385 (m-30) cc_final: 0.8034 (m-30) REVERT: D 44 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7420 (mtm) REVERT: D 178 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8161 (mt) REVERT: E 92 ASN cc_start: 0.9050 (m110) cc_final: 0.8777 (m-40) REVERT: E 228 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7148 (mm-40) outliers start: 50 outliers final: 22 residues processed: 208 average time/residue: 1.4920 time to fit residues: 337.7273 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 : 1.842 ------------------------------------------------------------------------------- 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: 1.9990 chunk 181 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 116 optimal weight: 0.1980 overall best weight: 1.6504 ------------------------------------------------------------------------------- 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 = 0.119001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101168 restraints weight = 16766.853| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.12 r_work: 0.3104 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1447 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= 0.137 Angle : 0.569 7.688 20210 Z= 0.273 Chirality : 0.045 0.178 2230 Planarity : 0.004 0.030 2590 Dihedral : 11.202 176.044 2070 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.79 % Allowed : 19.24 % 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: 1.66 (0.20), residues: 1840 helix: 0.80 (0.19), residues: 735 sheet: 0.86 (0.28), residues: 335 loop : 1.87 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.006 0.001 HIS A 161 PHE 0.008 0.001 PHE C 262 TYR 0.006 0.001 TYR D 69 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 715) hydrogen bonds : angle 4.64625 ( 1860) covalent geometry : bond 0.00321 (14905) covalent geometry : angle 0.56942 (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: 44 poor density : 171 time to evaluate : 1.750 Fit side-chains REVERT: A 64 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9044 (pp) REVERT: A 286 ASP cc_start: 0.8517 (m-30) cc_final: 0.8181 (m-30) REVERT: B 241 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: B 286 ASP cc_start: 0.8275 (m-30) cc_final: 0.8048 (m-30) REVERT: C 286 ASP cc_start: 0.8432 (m-30) cc_final: 0.8077 (m-30) REVERT: D 178 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8139 (mt) REVERT: D 179 ASP cc_start: 0.8082 (m-30) cc_final: 0.7839 (m-30) REVERT: D 359 LYS cc_start: 0.8092 (tmtt) cc_final: 0.7734 (ttmt) REVERT: E 360 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6804 (mp10) outliers start: 44 outliers final: 27 residues processed: 203 average time/residue: 1.3814 time to fit residues: 306.7893 Evaluate side-chains 192 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 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 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 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 62 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.118047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100162 restraints weight = 16771.076| |-----------------------------------------------------------------------------| 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: 0.2988 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1578 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= 0.161 Angle : 0.588 7.979 20210 Z= 0.283 Chirality : 0.046 0.192 2230 Planarity : 0.004 0.033 2590 Dihedral : 10.853 175.225 2070 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.11 % Allowed : 18.86 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.20), residues: 1840 helix: 0.94 (0.19), residues: 735 sheet: 0.84 (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 0.006 0.001 TYR A 69 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 715) hydrogen bonds : angle 4.62294 ( 1860) covalent geometry : bond 0.00381 (14905) covalent geometry : angle 0.58774 (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 215 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 1.689 Fit side-chains REVERT: A 64 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9028 (pp) REVERT: A 286 ASP cc_start: 0.8499 (m-30) cc_final: 0.8168 (m-30) REVERT: B 50 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8228 (mtmt) REVERT: B 241 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: B 286 ASP cc_start: 0.8283 (m-30) cc_final: 0.8063 (m-30) REVERT: C 190 MET cc_start: 0.9239 (mtm) cc_final: 0.8975 (mtp) REVERT: C 286 ASP cc_start: 0.8444 (m-30) cc_final: 0.8085 (m-30) REVERT: D 44 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7554 (mtm) REVERT: D 178 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8185 (mt) REVERT: D 179 ASP cc_start: 0.8090 (m-30) cc_final: 0.7851 (m-30) REVERT: D 359 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7732 (ttmt) REVERT: E 228 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7172 (mm-40) outliers start: 49 outliers final: 32 residues processed: 204 average time/residue: 1.3694 time to fit residues: 305.4622 Evaluate side-chains 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100719 restraints weight = 16948.397| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.13 r_work: 0.3096 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1633 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= 0.142 Angle : 0.571 7.873 20210 Z= 0.274 Chirality : 0.045 0.184 2230 Planarity : 0.004 0.034 2590 Dihedral : 10.527 178.801 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 : 2.73 % Allowed : 18.98 % 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: 1.85 (0.20), residues: 1840 helix: 1.08 (0.19), residues: 735 sheet: 0.82 (0.28), residues: 335 loop : 1.91 (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 D 161 PHE 0.008 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 0.03477 ( 715) hydrogen bonds : angle 4.55585 ( 1860) covalent geometry : bond 0.00334 (14905) covalent geometry : angle 0.57099 (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 205 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.680 Fit side-chains REVERT: A 64 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9037 (pp) REVERT: A 286 ASP cc_start: 0.8502 (m-30) cc_final: 0.8177 (m-30) REVERT: B 50 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8237 (mtmt) REVERT: B 241 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: B 286 ASP cc_start: 0.8298 (m-30) cc_final: 0.8080 (m-30) REVERT: C 64 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8395 (pp) REVERT: C 190 MET cc_start: 0.9226 (mtm) cc_final: 0.8962 (mtp) REVERT: C 286 ASP cc_start: 0.8445 (m-30) cc_final: 0.8084 (m-30) REVERT: D 178 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8140 (mt) REVERT: D 359 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7725 (ttmt) REVERT: E 228 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7134 (mm-40) REVERT: E 360 GLN cc_start: 0.7231 (tm-30) cc_final: 0.6878 (pm20) outliers start: 43 outliers final: 34 residues processed: 196 average time/residue: 1.4353 time to fit residues: 307.1502 Evaluate side-chains 198 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 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 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 135 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=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: 3.9990 chunk 20 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.116711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097416 restraints weight = 16889.500| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.24 r_work: 0.3067 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14905 Z= 0.213 Angle : 0.625 8.556 20210 Z= 0.304 Chirality : 0.048 0.201 2230 Planarity : 0.005 0.040 2590 Dihedral : 10.887 179.935 2070 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.43 % Allowed : 18.41 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.20), residues: 1840 helix: 0.92 (0.19), residues: 735 sheet: 0.75 (0.27), residues: 335 loop : 1.78 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.007 0.001 HIS A 161 PHE 0.011 0.001 PHE C 262 TYR 0.008 0.001 TYR A 69 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 715) hydrogen bonds : angle 4.69777 ( 1860) covalent geometry : bond 0.00514 (14905) covalent geometry : angle 0.62526 (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 217 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 1.656 Fit side-chains REVERT: A 64 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9075 (pp) REVERT: A 286 ASP cc_start: 0.8534 (m-30) cc_final: 0.8168 (m-30) REVERT: B 50 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8280 (mtmt) REVERT: B 241 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: B 286 ASP cc_start: 0.8314 (m-30) cc_final: 0.8089 (m-30) REVERT: C 64 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8375 (pp) REVERT: C 190 MET cc_start: 0.9238 (mtm) cc_final: 0.8974 (mtp) REVERT: C 286 ASP cc_start: 0.8474 (m-30) cc_final: 0.8118 (m-30) REVERT: D 178 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8174 (mt) REVERT: D 179 ASP cc_start: 0.8143 (m-30) cc_final: 0.7933 (m-30) REVERT: D 359 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7710 (ttmt) REVERT: E 50 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8255 (mtmt) REVERT: E 228 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7149 (mm-40) REVERT: E 360 GLN cc_start: 0.7232 (tm-30) cc_final: 0.6838 (pm20) outliers start: 54 outliers final: 34 residues processed: 207 average time/residue: 1.4093 time to fit residues: 318.0046 Evaluate side-chains 199 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 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 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 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 129 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.118934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101186 restraints weight = 16857.950| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.12 r_work: 0.3107 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14905 Z= 0.124 Angle : 0.560 7.720 20210 Z= 0.268 Chirality : 0.045 0.183 2230 Planarity : 0.004 0.035 2590 Dihedral : 10.303 178.710 2070 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.73 % Allowed : 19.37 % Favored : 77.90 % 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: 1.90 (0.20), residues: 1840 helix: 1.19 (0.19), residues: 735 sheet: 0.79 (0.27), residues: 335 loop : 1.88 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.008 0.001 PHE C 262 TYR 0.008 0.001 TYR D 143 ARG 0.006 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 715) hydrogen bonds : angle 4.49890 ( 1860) covalent geometry : bond 0.00287 (14905) covalent geometry : angle 0.56029 (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 201 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 2.656 Fit side-chains REVERT: A 64 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9030 (pp) REVERT: A 286 ASP cc_start: 0.8496 (m-30) cc_final: 0.8157 (m-30) REVERT: B 50 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8262 (mtmt) REVERT: B 241 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: B 286 ASP cc_start: 0.8261 (m-30) cc_final: 0.8050 (m-30) REVERT: C 190 MET cc_start: 0.9213 (mtm) cc_final: 0.8949 (mtp) REVERT: C 286 ASP cc_start: 0.8446 (m-30) cc_final: 0.8077 (m-30) REVERT: D 178 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8132 (mt) REVERT: D 359 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7730 (ttmt) REVERT: E 50 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8241 (mtmt) REVERT: E 228 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7129 (mm-40) outliers start: 43 outliers final: 34 residues processed: 193 average time/residue: 1.4549 time to fit residues: 307.5544 Evaluate side-chains 193 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 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 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 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 88 optimal weight: 6.9990 chunk 161 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.117832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098334 restraints weight = 16758.024| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.29 r_work: 0.3078 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14905 Z= 0.161 Angle : 0.587 8.345 20210 Z= 0.283 Chirality : 0.046 0.192 2230 Planarity : 0.004 0.038 2590 Dihedral : 10.346 174.986 2070 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.67 % Allowed : 19.43 % Favored : 77.90 % 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: 1.82 (0.20), residues: 1840 helix: 1.12 (0.19), residues: 735 sheet: 0.74 (0.27), residues: 335 loop : 1.85 (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 A 69 ARG 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 715) hydrogen bonds : angle 4.56176 ( 1860) covalent geometry : bond 0.00384 (14905) covalent geometry : angle 0.58721 (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 200 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.794 Fit side-chains REVERT: A 64 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9047 (pp) REVERT: A 286 ASP cc_start: 0.8531 (m-30) cc_final: 0.8161 (m-30) REVERT: B 50 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8270 (mtmt) REVERT: B 241 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: B 286 ASP cc_start: 0.8300 (m-30) cc_final: 0.8082 (m-30) REVERT: C 190 MET cc_start: 0.9239 (mtm) cc_final: 0.8965 (mtp) REVERT: C 286 ASP cc_start: 0.8468 (m-30) cc_final: 0.8108 (m-30) REVERT: D 178 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8188 (mt) REVERT: D 359 LYS cc_start: 0.8095 (tmtt) cc_final: 0.7707 (ttmt) REVERT: E 50 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8245 (mtmt) REVERT: E 228 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7221 (mm110) outliers start: 42 outliers final: 35 residues processed: 192 average time/residue: 1.3989 time to fit residues: 293.4476 Evaluate side-chains 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 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 47 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 135 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 140 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.117178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097997 restraints weight = 16762.635| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.23 r_work: 0.3076 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14905 Z= 0.187 Angle : 0.611 8.683 20210 Z= 0.295 Chirality : 0.047 0.199 2230 Planarity : 0.004 0.042 2590 Dihedral : 10.545 174.755 2070 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.67 % Allowed : 19.49 % 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: 1.73 (0.20), residues: 1840 helix: 1.03 (0.19), residues: 735 sheet: 0.71 (0.27), residues: 335 loop : 1.80 (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 0.007 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 715) hydrogen bonds : angle 4.62985 ( 1860) covalent geometry : bond 0.00449 (14905) covalent geometry : angle 0.61064 (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 200 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.648 Fit side-chains REVERT: A 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9042 (pp) REVERT: A 286 ASP cc_start: 0.8516 (m-30) cc_final: 0.8149 (m-30) REVERT: B 50 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8286 (mtmt) REVERT: B 241 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: B 286 ASP cc_start: 0.8293 (m-30) cc_final: 0.8070 (m-30) REVERT: C 50 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8052 (mtmm) REVERT: C 190 MET cc_start: 0.9235 (mtm) cc_final: 0.8950 (mtp) REVERT: C 286 ASP cc_start: 0.8460 (m-30) cc_final: 0.8104 (m-30) REVERT: D 178 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8187 (mt) REVERT: D 359 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7716 (ttmt) REVERT: E 50 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8271 (mtmt) REVERT: E 228 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7240 (mm110) outliers start: 42 outliers final: 34 residues processed: 192 average time/residue: 1.3885 time to fit residues: 291.3275 Evaluate side-chains 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 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 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 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 289 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 168 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.120471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102890 restraints weight = 16871.716| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.12 r_work: 0.3137 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14905 Z= 0.099 Angle : 0.542 7.335 20210 Z= 0.257 Chirality : 0.044 0.168 2230 Planarity : 0.004 0.034 2590 Dihedral : 9.402 175.179 2070 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.16 % Allowed : 20.19 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1840 helix: 1.37 (0.19), residues: 735 sheet: 0.79 (0.27), 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 D 372 PHE 0.007 0.001 PHE C 262 TYR 0.009 0.001 TYR D 143 ARG 0.008 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 715) hydrogen bonds : angle 4.40003 ( 1860) covalent geometry : bond 0.00224 (14905) covalent geometry : angle 0.54247 (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 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.920 Fit side-chains REVERT: A 64 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9001 (pp) REVERT: A 286 ASP cc_start: 0.8483 (m-30) cc_final: 0.8115 (m-30) REVERT: B 50 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8211 (mtmt) REVERT: B 241 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: B 286 ASP cc_start: 0.8253 (m-30) cc_final: 0.8045 (m-30) REVERT: C 50 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8032 (mtmm) REVERT: C 190 MET cc_start: 0.9181 (mtm) cc_final: 0.8921 (mtp) REVERT: C 286 ASP cc_start: 0.8404 (m-30) cc_final: 0.8032 (m-30) REVERT: D 178 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8114 (mt) REVERT: D 232 GLN cc_start: 0.7601 (mt0) cc_final: 0.7364 (mt0) REVERT: D 359 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7674 (ttmt) REVERT: E 50 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8263 (mtmt) REVERT: E 228 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7168 (mm110) outliers start: 34 outliers final: 23 residues processed: 188 average time/residue: 1.4413 time to fit residues: 295.4778 Evaluate side-chains 186 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 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 178 ILE Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 47 MET 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 142 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.117139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098221 restraints weight = 16718.582| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.20 r_work: 0.3073 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1758 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= 0.259 Angle : 0.663 9.470 20210 Z= 0.323 Chirality : 0.050 0.205 2230 Planarity : 0.005 0.047 2590 Dihedral : 10.578 168.226 2069 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.03 % Allowed : 20.06 % Favored : 77.90 % 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: 1.62 (0.20), residues: 1840 helix: 0.93 (0.19), residues: 735 sheet: 0.65 (0.27), residues: 335 loop : 1.75 (0.24), residues: 770 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 0.011 0.002 PHE C 262 TYR 0.009 0.002 TYR A 69 ARG 0.007 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04431 ( 715) hydrogen bonds : angle 4.71989 ( 1860) covalent geometry : bond 0.00628 (14905) covalent geometry : angle 0.66319 (20210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10307.69 seconds wall clock time: 178 minutes 11.21 seconds (10691.21 seconds total)