Starting phenix.real_space_refine on Sun Nov 17 20:56:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/11_2024/7q8b_13863.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/11_2024/7q8b_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/11_2024/7q8b_13863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/11_2024/7q8b_13863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/11_2024/7q8b_13863.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q8b_13863/11_2024/7q8b_13863.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: C, B, E, D Time building chain proxies: 6.49, per 1000 atoms: 0.44 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 2.19 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: 5.30 Time building geometry restraints manager: 4.13 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: 0.00 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: 1.380 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.400 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.930 ------------------------------------------------------------------------------- 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 14955 Z= 0.224 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 : 3.76 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 (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: 1.33 (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 TRP 0.010 0.001 TRP E 79 HIS 0.003 0.001 HIS C 173 PHE 0.007 0.001 PHE D 254 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG C 62 *********************** 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 : 1.719 Fit side-chains REVERT: A 305 MET cc_start: 0.8172 (tpp) cc_final: 0.7955 (mmt) REVERT: B 355 MET cc_start: 0.7734 (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: 0.3198 time to fit residues: 109.8271 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 : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 168 optimal weight: 3.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14955 Z= 0.430 Angle : 0.672 7.354 20280 Z= 0.331 Chirality : 0.053 0.169 2235 Planarity : 0.005 0.037 2605 Dihedral : 11.077 130.771 2045 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.80 % Allowed : 6.05 % Favored : 93.15 % 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: 0.97 (0.20), residues: 1840 helix: 0.51 (0.20), residues: 725 sheet: 0.13 (0.26), residues: 365 loop : 1.40 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 79 HIS 0.006 0.002 HIS A 161 PHE 0.011 0.002 PHE E 254 TYR 0.018 0.002 TYR E 294 ARG 0.005 0.001 ARG D 253 *********************** 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 173 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: C 42 GLN cc_start: 0.7888 (tt0) cc_final: 0.7662 (tt0) outliers start: 13 outliers final: 10 residues processed: 171 average time/residue: 0.2912 time to fit residues: 71.8411 Evaluate side-chains 160 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 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 E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 100 GLN D 215 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14955 Z= 0.185 Angle : 0.547 5.977 20280 Z= 0.262 Chirality : 0.047 0.135 2235 Planarity : 0.004 0.042 2605 Dihedral : 10.758 134.044 2045 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.86 % Allowed : 7.04 % Favored : 92.10 % 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: 1.28 (0.20), residues: 1840 helix: 0.88 (0.20), residues: 725 sheet: 0.15 (0.26), residues: 355 loop : 1.49 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE C 254 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG D 253 *********************** 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 179 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.759 Fit side-chains revert: symmetry clash REVERT: C 42 GLN cc_start: 0.7834 (tt0) cc_final: 0.7592 (tt0) outliers start: 14 outliers final: 9 residues processed: 173 average time/residue: 0.3236 time to fit residues: 80.3807 Evaluate side-chains 163 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 289 VAL 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 288 ASP 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 166 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN B 42 GLN B 100 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14955 Z= 0.242 Angle : 0.566 6.247 20280 Z= 0.271 Chirality : 0.049 0.134 2235 Planarity : 0.004 0.043 2605 Dihedral : 10.787 147.839 2045 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.36 % Allowed : 8.15 % Favored : 90.49 % 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: 1.25 (0.20), residues: 1840 helix: 0.92 (0.20), residues: 730 sheet: 0.10 (0.26), residues: 355 loop : 1.42 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE C 254 TYR 0.010 0.001 TYR A 143 ARG 0.002 0.000 ARG D 253 *********************** 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 178 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.808 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 172 average time/residue: 0.3058 time to fit residues: 77.4695 Evaluate side-chains 167 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 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 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 148 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 353 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 100 GLN E 215 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14955 Z= 0.344 Angle : 0.605 6.984 20280 Z= 0.292 Chirality : 0.051 0.143 2235 Planarity : 0.004 0.041 2605 Dihedral : 10.993 156.183 2045 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.42 % Allowed : 9.20 % Favored : 89.38 % 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: 1.08 (0.20), residues: 1840 helix: 0.88 (0.20), residues: 730 sheet: -0.02 (0.26), residues: 355 loop : 1.24 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE A 254 TYR 0.011 0.001 TYR C 294 ARG 0.003 0.000 ARG D 253 *********************** 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 175 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.722 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 169 average time/residue: 0.2780 time to fit residues: 69.4527 Evaluate side-chains 166 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 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 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 132 LEU 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 60 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 353 GLN B 42 GLN B 100 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14955 Z= 0.277 Angle : 0.582 6.507 20280 Z= 0.279 Chirality : 0.049 0.136 2235 Planarity : 0.004 0.041 2605 Dihedral : 11.018 162.588 2045 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.36 % Allowed : 9.75 % Favored : 88.89 % 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: 1.10 (0.20), residues: 1840 helix: 0.92 (0.20), residues: 730 sheet: -0.03 (0.26), residues: 355 loop : 1.23 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE E 254 TYR 0.010 0.001 TYR A 143 ARG 0.002 0.000 ARG D 253 *********************** 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 173 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.683 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 166 average time/residue: 0.2859 time to fit residues: 69.7774 Evaluate side-chains 168 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 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 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 172 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 353 GLN 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 100 GLN E 215 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14955 Z= 0.271 Angle : 0.581 6.603 20280 Z= 0.277 Chirality : 0.049 0.137 2235 Planarity : 0.004 0.042 2605 Dihedral : 11.088 171.786 2045 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.42 % Allowed : 10.12 % Favored : 88.46 % 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: 1.12 (0.20), residues: 1840 helix: 0.96 (0.20), residues: 730 sheet: -0.04 (0.26), residues: 355 loop : 1.22 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS A 161 PHE 0.010 0.001 PHE A 254 TYR 0.009 0.001 TYR A 143 ARG 0.002 0.000 ARG D 253 *********************** 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 178 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: B 270 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7131 (mt-10) outliers start: 23 outliers final: 19 residues processed: 171 average time/residue: 0.2767 time to fit residues: 69.5705 Evaluate side-chains 171 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 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 132 LEU 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 71 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 215 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14955 Z= 0.160 Angle : 0.538 6.475 20280 Z= 0.253 Chirality : 0.047 0.130 2235 Planarity : 0.004 0.045 2605 Dihedral : 10.952 172.568 2045 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.74 % Allowed : 11.17 % Favored : 88.09 % 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: 1.17 (0.20), residues: 1840 helix: 0.97 (0.20), residues: 760 sheet: 0.10 (0.26), residues: 355 loop : 1.23 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.002 0.001 HIS D 161 PHE 0.008 0.001 PHE D 254 TYR 0.008 0.001 TYR C 143 ARG 0.001 0.000 ARG D 253 *********************** 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 168 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.728 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 163 average time/residue: 0.2936 time to fit residues: 69.7178 Evaluate side-chains 159 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 225 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 215 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14955 Z= 0.166 Angle : 0.540 6.782 20280 Z= 0.253 Chirality : 0.047 0.129 2235 Planarity : 0.004 0.044 2605 Dihedral : 10.809 178.850 2045 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.68 % Allowed : 11.36 % Favored : 87.96 % 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: 1.34 (0.20), residues: 1840 helix: 1.06 (0.20), residues: 760 sheet: 0.29 (0.25), residues: 360 loop : 1.32 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.002 0.001 HIS B 161 PHE 0.009 0.001 PHE B 254 TYR 0.008 0.001 TYR C 143 ARG 0.001 0.000 ARG D 253 *********************** 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 164 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.838 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 159 average time/residue: 0.2948 time to fit residues: 69.4392 Evaluate side-chains 161 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 289 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 225 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 116 optimal weight: 0.0010 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 215 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14955 Z= 0.297 Angle : 0.589 7.254 20280 Z= 0.281 Chirality : 0.050 0.141 2235 Planarity : 0.004 0.044 2605 Dihedral : 10.962 179.970 2045 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.74 % Allowed : 11.42 % Favored : 87.84 % 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: 1.06 (0.20), residues: 1840 helix: 0.91 (0.20), residues: 760 sheet: 0.06 (0.26), residues: 355 loop : 1.11 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS A 173 PHE 0.011 0.001 PHE C 254 TYR 0.009 0.001 TYR E 143 ARG 0.003 0.000 ARG A 335 ********************** 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 164 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: B 270 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7119 (mt-10) outliers start: 12 outliers final: 11 residues processed: 159 average time/residue: 0.3023 time to fit residues: 71.9175 Evaluate side-chains 164 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 225 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.089312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.077474 restraints weight = 23042.632| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.12 r_work: 0.2725 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2811 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: