Starting phenix.real_space_refine on Mon Apr 6 00:29:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q8b_13863/04_2026/7q8b_13863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q8b_13863/04_2026/7q8b_13863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q8b_13863/04_2026/7q8b_13863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q8b_13863/04_2026/7q8b_13863.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q8b_13863/04_2026/7q8b_13863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q8b_13863/04_2026/7q8b_13863.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 15 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9195 2.51 5 N 2470 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2895 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.53, per 1000 atoms: 0.17 Number of scatterers: 14640 At special positions: 0 Unit cell: (79.54, 98.94, 194, 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 115 16.00 P 15 15.00 Mg 5 11.99 O 2840 8.00 N 2470 7.00 C 9195 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 624.2 milliseconds 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: 3430 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 30 sheets defined 50.8% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 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: 3.508A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.755A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.540A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.640A pdb=" N VAL 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 202 through 217 removed outlier: 3.626A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 262 through 267 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 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.538A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) 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 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.630A pdb=" N GLN A 353 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 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 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: 3.507A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.755A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.539A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.640A pdb=" N VAL 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 202 through 217 removed outlier: 3.626A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 262 through 267 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 305 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.538A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) 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 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.632A pdb=" N GLN B 353 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 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 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: 3.507A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.755A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.539A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.640A pdb=" N VAL 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 202 through 217 removed outlier: 3.626A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 262 through 267 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 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.538A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) 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 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.631A pdb=" N GLN C 353 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 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 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: 3.507A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.754A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.540A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.641A pdb=" N VAL 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 202 through 217 removed outlier: 3.627A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 262 through 267 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 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.538A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) 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 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.630A pdb=" N GLN D 353 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR 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 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: 3.507A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.755A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.539A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.640A pdb=" N VAL 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 202 through 217 removed outlier: 3.625A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 234 Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 257 through 261 Processing helix chain 'E' and resid 262 through 267 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 305 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.539A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) 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 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.631A pdb=" N GLN E 353 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.035A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 105 " --> pdb=" O GLY A 135 " (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: 6.151A pdb=" N ILE A 297 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.034A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 105 " --> pdb=" O GLY B 135 " (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: 6.151A pdb=" N ILE B 297 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 237 through 240 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.035A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLY C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C 105 " --> pdb=" O GLY C 135 " (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: 6.150A pdb=" N ILE C 297 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.034A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY D 135 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU D 105 " --> pdb=" O GLY D 135 " (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: 6.151A pdb=" N ILE D 297 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 237 through 240 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.034A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLY E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU E 105 " --> pdb=" O GLY E 135 " (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: 6.150A pdb=" N ILE E 297 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 237 through 240 715 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4765 1.34 - 1.46: 2258 1.46 - 1.57: 7712 1.57 - 1.69: 15 1.69 - 1.81: 205 Bond restraints: 14955 Sorted by residual: bond pdb=" O3 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" O3 PO4 E 803 " pdb=" P PO4 E 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" O3 PO4 C 803 " pdb=" P PO4 C 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" O3 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" O3 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.60e+00 ... (remaining 14950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 19785 1.17 - 2.34: 315 2.34 - 3.50: 110 3.50 - 4.67: 35 4.67 - 5.84: 35 Bond angle restraints: 20280 Sorted by residual: angle pdb=" O1B ADP B 802 " pdb=" PB ADP B 802 " pdb=" O3B ADP B 802 " ideal model delta sigma weight residual 119.90 114.06 5.84 3.00e+00 1.11e-01 3.79e+00 angle pdb=" O1B ADP D 802 " pdb=" PB ADP D 802 " pdb=" O3B ADP D 802 " ideal model delta sigma weight residual 119.90 114.07 5.83 3.00e+00 1.11e-01 3.77e+00 angle pdb=" O1B ADP C 802 " pdb=" PB ADP C 802 " pdb=" O3B ADP C 802 " ideal model delta sigma weight residual 119.90 114.10 5.80 3.00e+00 1.11e-01 3.74e+00 angle pdb=" O1B ADP A 802 " pdb=" PB ADP A 802 " pdb=" O3B ADP A 802 " ideal model delta sigma weight residual 119.90 114.11 5.79 3.00e+00 1.11e-01 3.73e+00 angle pdb=" O1B ADP E 802 " pdb=" PB ADP E 802 " pdb=" O3B ADP E 802 " ideal model delta sigma weight residual 119.90 114.12 5.78 3.00e+00 1.11e-01 3.72e+00 ... (remaining 20275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.11: 8940 29.11 - 58.22: 85 58.22 - 87.32: 0 87.32 - 116.43: 5 116.43 - 145.54: 10 Dihedral angle restraints: 9040 sinusoidal: 3700 harmonic: 5340 Sorted by residual: dihedral pdb=" C5' ADP E 802 " pdb=" O5' ADP E 802 " pdb=" PA ADP E 802 " pdb=" O2A ADP E 802 " ideal model delta sinusoidal sigma weight residual 300.00 154.46 145.54 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP C 802 " pdb=" O5' ADP C 802 " pdb=" PA ADP C 802 " pdb=" O2A ADP C 802 " ideal model delta sinusoidal sigma weight residual 300.00 154.49 145.52 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual 300.00 154.49 145.52 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 9037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1073 0.024 - 0.048: 585 0.048 - 0.073: 287 0.073 - 0.097: 127 0.097 - 0.121: 163 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CA ILE C 297 " pdb=" N ILE C 297 " pdb=" C ILE C 297 " pdb=" CB ILE C 297 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA ILE B 297 " pdb=" N ILE B 297 " pdb=" C ILE B 297 " pdb=" CB ILE B 297 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 2232 not shown) Planarity restraints: 2605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 90 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C PHE E 90 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE E 90 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR E 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 90 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C PHE B 90 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE B 90 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 90 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" C PHE A 90 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE A 90 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 2602 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 124 2.59 - 3.17: 12054 3.17 - 3.74: 22403 3.74 - 4.32: 33273 4.32 - 4.90: 55782 Nonbonded interactions: 123636 Sorted by model distance: nonbonded pdb="MG MG C 801 " pdb=" O2B ADP C 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG B 801 " pdb=" O2B ADP B 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG A 801 " pdb=" O2B ADP A 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG E 801 " pdb=" O2B ADP E 802 " model vdw 2.012 2.170 nonbonded pdb="MG MG D 801 " pdb=" O2B ADP D 802 " model vdw 2.012 2.170 ... (remaining 123631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 0.063 14960 Z= 0.163 Angle : 0.502 5.840 20280 Z= 0.234 Chirality : 0.046 0.121 2235 Planarity : 0.004 0.027 2605 Dihedral : 10.849 145.539 5610 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1840 helix: 0.78 (0.20), residues: 730 sheet: 0.20 (0.28), residues: 330 loop : 1.63 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 62 TYR 0.011 0.001 TYR B 143 PHE 0.007 0.001 PHE D 254 TRP 0.010 0.001 TRP E 79 HIS 0.003 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00360 (14955) covalent geometry : angle 0.50191 (20280) hydrogen bonds : bond 0.21848 ( 705) hydrogen bonds : angle 7.89310 ( 1845) Misc. bond : bond 0.00075 ( 5) *********************** 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 242 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.586 Fit side-chains REVERT: A 305 MET cc_start: 0.8172 (tpp) cc_final: 0.7955 (mmt) REVERT: B 355 MET cc_start: 0.7735 (mtp) cc_final: 0.7444 (mtp) REVERT: C 42 GLN cc_start: 0.7819 (tt0) cc_final: 0.7566 (tt0) REVERT: E 82 MET cc_start: 0.8937 (tpt) cc_final: 0.8728 (tpt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1430 time to fit residues: 49.4498 Evaluate side-chains 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 235 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 100 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.088885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.077710 restraints weight = 23217.956| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.01 r_work: 0.2743 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14960 Z= 0.267 Angle : 0.683 7.542 20280 Z= 0.336 Chirality : 0.053 0.146 2235 Planarity : 0.005 0.037 2605 Dihedral : 11.033 130.817 2045 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.93 % Allowed : 6.17 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1840 helix: 0.50 (0.20), residues: 725 sheet: 0.13 (0.26), residues: 365 loop : 1.36 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 253 TYR 0.019 0.002 TYR C 294 PHE 0.012 0.002 PHE D 223 TRP 0.015 0.002 TRP E 79 HIS 0.006 0.002 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00658 (14955) covalent geometry : angle 0.68296 (20280) hydrogen bonds : bond 0.04850 ( 705) hydrogen bonds : angle 5.99312 ( 1845) Misc. bond : bond 0.00107 ( 5) *********************** 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 175 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7729 (mtm180) REVERT: B 355 MET cc_start: 0.8301 (mtp) cc_final: 0.8029 (mtp) REVERT: E 95 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.7915 (mtm180) outliers start: 15 outliers final: 12 residues processed: 172 average time/residue: 0.1364 time to fit residues: 34.2253 Evaluate side-chains 160 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR 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 79 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 235 ASN A 296 ASN B 42 GLN C 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 42 GLN D 100 GLN D 215 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 296 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.080440 restraints weight = 23225.895| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.12 r_work: 0.2783 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14960 Z= 0.098 Angle : 0.536 5.922 20280 Z= 0.256 Chirality : 0.046 0.133 2235 Planarity : 0.004 0.041 2605 Dihedral : 10.678 131.708 2045 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.68 % Allowed : 7.10 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1840 helix: 0.95 (0.20), residues: 725 sheet: 0.22 (0.26), residues: 355 loop : 1.54 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 253 TYR 0.009 0.001 TYR A 143 PHE 0.009 0.001 PHE D 254 TRP 0.010 0.001 TRP C 79 HIS 0.002 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00221 (14955) covalent geometry : angle 0.53628 (20280) hydrogen bonds : bond 0.03349 ( 705) hydrogen bonds : angle 5.54788 ( 1845) Misc. bond : bond 0.00011 ( 5) *********************** 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 177 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7798 (mtm180) REVERT: B 95 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7883 (mtm180) REVERT: E 95 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7907 (mtm180) outliers start: 11 outliers final: 7 residues processed: 171 average time/residue: 0.1408 time to fit residues: 34.3631 Evaluate side-chains 160 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 42 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.086891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.074741 restraints weight = 23548.437| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.16 r_work: 0.2675 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 14960 Z= 0.368 Angle : 0.731 7.475 20280 Z= 0.360 Chirality : 0.057 0.168 2235 Planarity : 0.005 0.044 2605 Dihedral : 11.303 160.190 2045 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.60 % Allowed : 8.40 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1840 helix: 0.35 (0.19), residues: 755 sheet: -0.23 (0.27), residues: 330 loop : 1.08 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 253 TYR 0.017 0.002 TYR C 294 PHE 0.013 0.002 PHE A 200 TRP 0.018 0.003 TRP C 79 HIS 0.006 0.002 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00908 (14955) covalent geometry : angle 0.73146 (20280) hydrogen bonds : bond 0.05027 ( 705) hydrogen bonds : angle 5.67249 ( 1845) Misc. bond : bond 0.00218 ( 5) *********************** 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 175 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8426 (mtt-85) cc_final: 0.7923 (mtm180) REVERT: B 95 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.8059 (mtm180) outliers start: 26 outliers final: 19 residues processed: 168 average time/residue: 0.1277 time to fit residues: 31.6783 Evaluate side-chains 161 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 96 VAL 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 117 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 215 GLN A 235 ASN B 42 GLN B 100 GLN C 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 215 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.090854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.079120 restraints weight = 23142.329| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.12 r_work: 0.2757 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14960 Z= 0.109 Angle : 0.551 6.292 20280 Z= 0.262 Chirality : 0.047 0.133 2235 Planarity : 0.004 0.045 2605 Dihedral : 10.984 163.699 2045 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.93 % Allowed : 9.81 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1840 helix: 0.90 (0.20), residues: 730 sheet: -0.00 (0.26), residues: 355 loop : 1.24 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.009 0.001 TYR C 143 PHE 0.009 0.001 PHE D 254 TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00255 (14955) covalent geometry : angle 0.55079 (20280) hydrogen bonds : bond 0.03112 ( 705) hydrogen bonds : angle 5.36696 ( 1845) Misc. bond : bond 0.00023 ( 5) *********************** 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 167 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.7795 (mtm180) REVERT: A 355 MET cc_start: 0.8448 (mtp) cc_final: 0.8209 (mtp) REVERT: B 95 ARG cc_start: 0.8316 (mtt-85) cc_final: 0.7998 (mtm180) REVERT: E 240 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8130 (tm-30) outliers start: 15 outliers final: 10 residues processed: 161 average time/residue: 0.1197 time to fit residues: 28.9652 Evaluate side-chains 157 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 240 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 184 optimal weight: 0.0040 chunk 108 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 100 GLN A 215 GLN B 42 GLN B 100 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 215 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 215 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.078229 restraints weight = 23184.719| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.12 r_work: 0.2740 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14960 Z= 0.144 Angle : 0.567 6.546 20280 Z= 0.269 Chirality : 0.048 0.137 2235 Planarity : 0.004 0.042 2605 Dihedral : 11.059 170.677 2045 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 10.56 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1840 helix: 0.99 (0.20), residues: 730 sheet: 0.00 (0.26), residues: 355 loop : 1.25 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.010 0.001 TYR A 143 PHE 0.010 0.001 PHE A 254 TRP 0.011 0.001 TRP C 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00355 (14955) covalent geometry : angle 0.56721 (20280) hydrogen bonds : bond 0.03297 ( 705) hydrogen bonds : angle 5.29855 ( 1845) Misc. bond : bond 0.00076 ( 5) *********************** 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 164 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.7902 (mtm180) REVERT: A 353 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8215 (mm110) REVERT: B 95 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.8077 (mtm180) REVERT: E 240 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8181 (tm-30) outliers start: 15 outliers final: 10 residues processed: 158 average time/residue: 0.1178 time to fit residues: 27.9481 Evaluate side-chains 154 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 240 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 96 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 100 GLN A 215 GLN B 42 GLN B 100 GLN C 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.088290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.076467 restraints weight = 23175.900| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.12 r_work: 0.2707 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14960 Z= 0.238 Angle : 0.633 6.913 20280 Z= 0.305 Chirality : 0.052 0.150 2235 Planarity : 0.004 0.041 2605 Dihedral : 11.292 176.705 2045 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.05 % Allowed : 11.23 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1840 helix: 0.67 (0.20), residues: 755 sheet: -0.11 (0.26), residues: 330 loop : 1.06 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.011 0.002 TYR D 294 PHE 0.012 0.001 PHE C 254 TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00590 (14955) covalent geometry : angle 0.63254 (20280) hydrogen bonds : bond 0.03952 ( 705) hydrogen bonds : angle 5.36435 ( 1845) Misc. bond : bond 0.00135 ( 5) *********************** 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 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8442 (mtt-85) cc_final: 0.7977 (mtm180) REVERT: B 95 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.8071 (mtm180) REVERT: B 270 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: C 247 MET cc_start: 0.8900 (ptt) cc_final: 0.8535 (ptt) outliers start: 17 outliers final: 14 residues processed: 160 average time/residue: 0.1210 time to fit residues: 29.1276 Evaluate side-chains 161 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 225 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 100 GLN B 42 GLN B 100 GLN C 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.076677 restraints weight = 23356.179| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.12 r_work: 0.2710 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14960 Z= 0.215 Angle : 0.621 6.841 20280 Z= 0.299 Chirality : 0.051 0.148 2235 Planarity : 0.004 0.040 2605 Dihedral : 11.305 175.909 2045 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.23 % Allowed : 11.42 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1840 helix: 0.61 (0.20), residues: 760 sheet: -0.13 (0.27), residues: 330 loop : 0.98 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 255 TYR 0.010 0.001 TYR C 294 PHE 0.011 0.001 PHE E 254 TRP 0.013 0.002 TRP C 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00535 (14955) covalent geometry : angle 0.62147 (20280) hydrogen bonds : bond 0.03803 ( 705) hydrogen bonds : angle 5.34540 ( 1845) Misc. bond : bond 0.00116 ( 5) *********************** 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 169 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8440 (mtt-85) cc_final: 0.7989 (mtm180) REVERT: B 95 ARG cc_start: 0.8339 (mtt-85) cc_final: 0.8079 (mtm180) REVERT: B 270 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: C 247 MET cc_start: 0.8914 (ptt) cc_final: 0.8596 (ptt) outliers start: 20 outliers final: 17 residues processed: 163 average time/residue: 0.1224 time to fit residues: 30.2237 Evaluate side-chains 162 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 42 GLN B 100 GLN C 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.089594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.077800 restraints weight = 23277.456| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.12 r_work: 0.2733 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14960 Z= 0.150 Angle : 0.582 6.856 20280 Z= 0.277 Chirality : 0.049 0.139 2235 Planarity : 0.004 0.040 2605 Dihedral : 11.209 178.538 2045 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.05 % Allowed : 11.54 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1840 helix: 0.94 (0.20), residues: 730 sheet: -0.10 (0.26), residues: 355 loop : 1.10 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 253 TYR 0.009 0.001 TYR C 143 PHE 0.010 0.001 PHE A 254 TRP 0.011 0.002 TRP B 79 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00370 (14955) covalent geometry : angle 0.58202 (20280) hydrogen bonds : bond 0.03348 ( 705) hydrogen bonds : angle 5.26326 ( 1845) Misc. bond : bond 0.00079 ( 5) *********************** 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 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.7972 (mtm180) REVERT: B 95 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8107 (mtm180) REVERT: B 270 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: C 247 MET cc_start: 0.8899 (ptt) cc_final: 0.8597 (ptt) outliers start: 17 outliers final: 15 residues processed: 159 average time/residue: 0.1193 time to fit residues: 28.5312 Evaluate side-chains 163 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 225 GLU 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 134 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 135 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.0870 chunk 129 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 42 GLN B 100 GLN C 42 GLN C 296 ASN D 42 GLN D 100 GLN D 296 ASN E 215 GLN E 371 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.080252 restraints weight = 23076.266| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.11 r_work: 0.2781 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14960 Z= 0.091 Angle : 0.542 7.076 20280 Z= 0.255 Chirality : 0.046 0.130 2235 Planarity : 0.004 0.047 2605 Dihedral : 10.606 175.695 2045 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.49 % Allowed : 12.10 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1840 helix: 0.96 (0.20), residues: 760 sheet: 0.08 (0.26), residues: 355 loop : 1.17 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.008 0.001 TYR C 143 PHE 0.007 0.001 PHE D 254 TRP 0.012 0.001 TRP B 79 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00214 (14955) covalent geometry : angle 0.54225 (20280) hydrogen bonds : bond 0.02713 ( 705) hydrogen bonds : angle 5.12423 ( 1845) Misc. bond : bond 0.00040 ( 5) ********************** 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 157 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7833 (mtm180) REVERT: A 355 MET cc_start: 0.8329 (mtp) cc_final: 0.8126 (mtp) REVERT: B 95 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.8058 (mtm180) REVERT: C 247 MET cc_start: 0.8864 (ptt) cc_final: 0.8662 (ptt) outliers start: 8 outliers final: 5 residues processed: 153 average time/residue: 0.1232 time to fit residues: 28.3646 Evaluate side-chains 151 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 148 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN D 100 GLN E 215 GLN E 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.081277 restraints weight = 23011.585| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.11 r_work: 0.2796 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14960 Z= 0.090 Angle : 0.539 6.929 20280 Z= 0.251 Chirality : 0.046 0.135 2235 Planarity : 0.004 0.046 2605 Dihedral : 9.419 154.416 2045 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.37 % Allowed : 12.47 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1840 helix: 1.24 (0.20), residues: 760 sheet: 0.28 (0.26), residues: 355 loop : 1.34 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 335 TYR 0.008 0.001 TYR B 143 PHE 0.009 0.001 PHE D 254 TRP 0.010 0.001 TRP B 79 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00213 (14955) covalent geometry : angle 0.53896 (20280) hydrogen bonds : bond 0.02637 ( 705) hydrogen bonds : angle 5.01276 ( 1845) Misc. bond : bond 0.00047 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2898.61 seconds wall clock time: 50 minutes 42.06 seconds (3042.06 seconds total)