Starting phenix.real_space_refine on Thu Mar 6 07:46:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3t_18874/03_2025/8r3t_18874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3t_18874/03_2025/8r3t_18874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r3t_18874/03_2025/8r3t_18874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3t_18874/03_2025/8r3t_18874.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3t_18874/03_2025/8r3t_18874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3t_18874/03_2025/8r3t_18874.cif" } resolution = 3.1 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= 0.001 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: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 1644 2.51 5 N 492 2.21 5 O 486 1.98 5 H 2804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5438 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 906 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 907 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 906 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56} Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 906 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56} Chain: "E" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 906 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56} Chain: "F" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 907 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 56} Time building chain proxies: 3.41, per 1000 atoms: 0.63 Number of scatterers: 5438 At special positions: 0 Unit cell: (66.066, 92.202, 54.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 486 8.00 N 492 7.00 C 1644 6.00 H 2804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 322 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 322 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 322 " distance=2.05 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 322 " distance=2.05 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 322 " distance=2.04 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 322 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 361.6 milliseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 55.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 290 removed outlier: 6.424A pdb=" N GLN A 276 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASN F 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 278 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LYS F 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 280 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ASP F 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 282 " --> pdb=" O ASP F 283 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N SER F 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 284 " --> pdb=" O SER F 285 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL F 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASN A 286 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER F 289 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN A 288 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N CYS F 291 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 290 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS B 274 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ILE C 277 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER C 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 284 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL C 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 286 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER C 289 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN B 288 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS C 291 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS B 290 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS C 274 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE D 277 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 276 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASN D 279 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 278 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LYS D 281 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS C 280 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASP D 283 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU C 282 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER D 285 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 284 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 287 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN C 286 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER D 289 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN C 288 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N CYS D 291 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS C 290 " --> pdb=" O CYS D 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 296 removed outlier: 6.719A pdb=" N ASP A 295 " --> pdb=" O ASN F 296 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS B 294 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 295 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 305 through 309 removed outlier: 6.689A pdb=" N SER A 305 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE F 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN A 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER B 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ILE C 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.457A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N CYS F 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS A 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N SER C 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N CYS C 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS D 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 330 removed outlier: 6.021A pdb=" N LEU B 325 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE F 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN B 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N HIS F 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 1.60 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2804 1.12 - 1.30: 432 1.30 - 1.47: 791 1.47 - 1.64: 1429 1.64 - 1.81: 12 Bond restraints: 5468 Sorted by residual: bond pdb=" N TYR D 310 " pdb=" H TYR D 310 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ILE C 278 " pdb=" H ILE C 278 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N LYS C 290 " pdb=" H LYS C 290 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N TYR C 310 " pdb=" H TYR C 310 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD2 HIS F 330 " pdb=" HD2 HIS F 330 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 5463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 8170 2.41 - 4.83: 1311 4.83 - 7.24: 487 7.24 - 9.65: 30 9.65 - 12.07: 8 Bond angle restraints: 10006 Sorted by residual: angle pdb=" C LYS D 311 " pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " ideal model delta sigma weight residual 110.17 122.24 -12.07 1.97e+00 2.58e-01 3.75e+01 angle pdb=" CA ASP C 295 " pdb=" CB ASP C 295 " pdb=" CG ASP C 295 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" CA ASP F 295 " pdb=" CB ASP F 295 " pdb=" CG ASP F 295 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" CA ASP D 295 " pdb=" CB ASP D 295 " pdb=" CG ASP D 295 " ideal model delta sigma weight residual 112.60 118.51 -5.91 1.00e+00 1.00e+00 3.49e+01 angle pdb=" C LYS B 311 " pdb=" CA LYS B 311 " pdb=" CB LYS B 311 " ideal model delta sigma weight residual 110.17 121.74 -11.57 1.97e+00 2.58e-01 3.45e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.09: 2087 13.09 - 26.17: 240 26.17 - 39.25: 100 39.25 - 52.34: 48 52.34 - 65.42: 47 Dihedral angle restraints: 2522 sinusoidal: 1464 harmonic: 1058 Sorted by residual: dihedral pdb=" CA LEU C 325 " pdb=" C LEU C 325 " pdb=" N GLY C 326 " pdb=" CA GLY C 326 " ideal model delta harmonic sigma weight residual 180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LEU B 325 " pdb=" C LEU B 325 " pdb=" N GLY B 326 " pdb=" CA GLY B 326 " ideal model delta harmonic sigma weight residual -180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" C LYS B 311 " pdb=" N LYS B 311 " pdb=" CA LYS B 311 " pdb=" CB LYS B 311 " ideal model delta harmonic sigma weight residual -122.60 -137.47 14.87 0 2.50e+00 1.60e-01 3.54e+01 ... (remaining 2519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 265 0.088 - 0.177: 114 0.177 - 0.265: 28 0.265 - 0.353: 2 0.353 - 0.442: 5 Chirality restraints: 414 Sorted by residual: chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA LYS D 311 " pdb=" N LYS D 311 " pdb=" C LYS D 311 " pdb=" CB LYS D 311 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 411 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.133 2.00e-02 2.50e+03 6.19e-02 1.15e+02 pdb=" CG TYR B 310 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.031 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.102 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " 0.093 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.122 2.00e-02 2.50e+03 5.96e-02 1.07e+02 pdb=" CG TYR F 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.116 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.051 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.108 2.00e-02 2.50e+03 5.12e-02 7.88e+01 pdb=" CG TYR C 310 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.097 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.055 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.026 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 577 2.23 - 2.82: 10474 2.82 - 3.41: 14060 3.41 - 4.01: 19022 4.01 - 4.60: 28200 Nonbonded interactions: 72333 Sorted by model distance: nonbonded pdb=" HG SER C 293 " pdb=" OD1 ASP C 295 " model vdw 1.633 2.450 nonbonded pdb=" HG SER F 293 " pdb=" OD1 ASP F 295 " model vdw 1.633 2.450 nonbonded pdb=" HG SER E 293 " pdb=" OD1 ASP E 295 " model vdw 1.722 2.450 nonbonded pdb=" OD2 ASP A 295 " pdb=" HZ2 LYS F 290 " model vdw 1.750 2.450 nonbonded pdb=" HZ1 LYS A 281 " pdb=" OD1 ASP A 283 " model vdw 1.763 2.450 ... (remaining 72328 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 273 through 329 or (resid 330 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 331)) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 273 through 329 or (resid 330 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or nam \ e HE1)) or resid 331)) } 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=0.00 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: 2.350 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.011 0.039 2664 Z= 0.751 Angle : 2.117 12.066 3558 Z= 1.396 Chirality : 0.106 0.442 414 Planarity : 0.011 0.060 444 Dihedral : 14.975 59.058 1026 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 1.75 % Allowed : 2.05 % Favored : 96.20 % Rotamer: Outliers : 5.45 % Allowed : 9.94 % Favored : 84.62 % Cbeta Deviations : 1.92 % Peptide Plane: Cis-proline : 50.00 % 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: -1.86 (0.36), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS A 329 TYR 0.097 0.038 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 15 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7694 (t0) REVERT: B 314 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7334 (t0) REVERT: C 314 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7049 (t0) REVERT: D 314 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7732 (t70) REVERT: F 314 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7212 (t0) outliers start: 17 outliers final: 5 residues processed: 27 average time/residue: 0.2312 time to fit residues: 8.3414 Evaluate side-chains 19 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 9 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain F residue 314 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.161564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.141694 restraints weight = 8740.682| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 2.60 r_work: 0.4477 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4352 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2664 Z= 0.246 Angle : 0.829 7.253 3558 Z= 0.449 Chirality : 0.056 0.132 414 Planarity : 0.003 0.023 444 Dihedral : 13.115 57.481 369 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 1.17 % Allowed : 3.51 % Favored : 95.32 % Rotamer: Outliers : 5.45 % Allowed : 9.62 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 50.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 329 TYR 0.008 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 13 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7473 (t0) REVERT: B 314 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.6883 (t0) REVERT: C 314 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.6737 (t0) REVERT: D 314 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7371 (t0) REVERT: F 314 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.6727 (t0) REVERT: F 322 CYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6714 (m) outliers start: 17 outliers final: 5 residues processed: 26 average time/residue: 0.1582 time to fit residues: 6.2447 Evaluate side-chains 20 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 9 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 322 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN C 296 ASN E 296 ASN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.163872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.145800 restraints weight = 8976.743| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 2.54 r_work: 0.4424 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4306 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2664 Z= 0.222 Angle : 0.739 5.822 3558 Z= 0.399 Chirality : 0.055 0.133 414 Planarity : 0.004 0.026 444 Dihedral : 12.510 59.854 368 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.13 % Allowed : 7.69 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 50.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.35), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 TYR 0.004 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 11 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7500 (t0) REVERT: B 314 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.6986 (t0) REVERT: C 314 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.6847 (t0) REVERT: D 314 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7219 (t0) REVERT: F 314 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.6782 (t0) REVERT: F 322 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6900 (m) outliers start: 16 outliers final: 4 residues processed: 22 average time/residue: 0.1649 time to fit residues: 5.4322 Evaluate side-chains 22 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 12 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 322 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN C 296 ASN F 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.166999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.148663 restraints weight = 8707.482| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 2.40 r_work: 0.4446 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4324 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2664 Z= 0.191 Angle : 0.677 5.690 3558 Z= 0.365 Chirality : 0.054 0.128 414 Planarity : 0.003 0.027 444 Dihedral : 11.880 58.682 365 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.85 % Allowed : 10.58 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 50.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.35), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 TYR 0.008 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 10 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7623 (t0) REVERT: B 314 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.6982 (t0) REVERT: C 314 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.6756 (t0) REVERT: D 314 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7144 (t0) REVERT: F 314 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.6831 (t0) REVERT: F 322 CYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6963 (m) outliers start: 12 outliers final: 1 residues processed: 17 average time/residue: 0.1792 time to fit residues: 4.6397 Evaluate side-chains 17 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 322 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 ASN C 296 ASN E 296 ASN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.155828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.138439 restraints weight = 9565.590| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 2.58 r_work: 0.4370 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4255 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2664 Z= 0.240 Angle : 0.688 5.704 3558 Z= 0.371 Chirality : 0.054 0.133 414 Planarity : 0.003 0.026 444 Dihedral : 11.720 58.764 365 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.17 % Allowed : 12.82 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 50.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.35), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 TYR 0.006 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 9 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7514 (t0) REVERT: B 314 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.6999 (t0) REVERT: C 314 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.6755 (t0) REVERT: F 314 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.6727 (t0) REVERT: F 322 CYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6962 (m) outliers start: 13 outliers final: 3 residues processed: 17 average time/residue: 0.1752 time to fit residues: 4.6033 Evaluate side-chains 17 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 9 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 322 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.161501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.143449 restraints weight = 8975.317| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 2.48 r_work: 0.4401 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4290 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2664 Z= 0.194 Angle : 0.651 5.572 3558 Z= 0.351 Chirality : 0.054 0.130 414 Planarity : 0.003 0.026 444 Dihedral : 11.580 58.283 365 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.88 % Allowed : 14.10 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 41.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.34), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 TYR 0.008 0.002 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 10 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7526 (t0) REVERT: B 314 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.6937 (t0) REVERT: C 314 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.6726 (t0) REVERT: F 314 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.6724 (t0) outliers start: 9 outliers final: 2 residues processed: 14 average time/residue: 0.1866 time to fit residues: 3.9686 Evaluate side-chains 16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 314 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN D 296 ASN E 296 ASN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.155906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.138252 restraints weight = 9497.010| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.61 r_work: 0.4368 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4248 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2664 Z= 0.216 Angle : 0.657 5.437 3558 Z= 0.354 Chirality : 0.054 0.132 414 Planarity : 0.003 0.026 444 Dihedral : 11.395 56.653 365 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 50.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.34), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 TYR 0.009 0.001 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7508 (t0) REVERT: B 314 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7016 (t0) REVERT: C 314 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.6761 (t0) REVERT: F 314 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.6861 (t0) outliers start: 8 outliers final: 3 residues processed: 13 average time/residue: 0.2096 time to fit residues: 4.2095 Evaluate side-chains 16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 314 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.161410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.143114 restraints weight = 9544.181| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 2.62 r_work: 0.4385 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4261 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2664 Z= 0.193 Angle : 0.640 5.340 3558 Z= 0.345 Chirality : 0.054 0.130 414 Planarity : 0.003 0.026 444 Dihedral : 11.254 56.379 365 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.88 % Allowed : 16.03 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 41.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.34), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.009 0.001 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 11 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7545 (t0) REVERT: B 314 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7012 (t0) REVERT: C 314 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.6737 (t0) REVERT: F 314 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.6871 (t0) outliers start: 9 outliers final: 2 residues processed: 15 average time/residue: 0.2066 time to fit residues: 4.6375 Evaluate side-chains 16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 314 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN D 296 ASN E 296 ASN F 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.155713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.138318 restraints weight = 9526.353| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 2.55 r_work: 0.4373 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4254 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2664 Z= 0.207 Angle : 0.644 5.275 3558 Z= 0.347 Chirality : 0.054 0.131 414 Planarity : 0.003 0.025 444 Dihedral : 11.032 56.110 363 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.53 % Allowed : 15.71 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 41.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 TYR 0.009 0.001 TYR F 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 10 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7558 (t0) REVERT: B 314 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7059 (t0) REVERT: C 314 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.6828 (t0) REVERT: F 314 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.6899 (t0) outliers start: 11 outliers final: 1 residues processed: 16 average time/residue: 0.1870 time to fit residues: 4.5814 Evaluate side-chains 16 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN D 296 ASN E 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.156408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.139267 restraints weight = 9674.632| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 2.59 r_work: 0.4390 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4275 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2664 Z= 0.192 Angle : 0.627 5.273 3558 Z= 0.336 Chirality : 0.053 0.132 414 Planarity : 0.003 0.026 444 Dihedral : 10.820 54.910 363 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.88 % Allowed : 16.03 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 41.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.010 0.002 TYR F 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7487 (t0) REVERT: B 314 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.6901 (t0) REVERT: C 296 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7837 (m110) REVERT: C 314 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6705 (t0) REVERT: F 314 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.6792 (t0) outliers start: 9 outliers final: 2 residues processed: 13 average time/residue: 0.1933 time to fit residues: 3.8612 Evaluate side-chains 17 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 291 CYS Chi-restraints excluded: chain F residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN E 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.156384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.139284 restraints weight = 9695.618| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.59 r_work: 0.4391 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4276 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.220 2664 Z= 0.499 Angle : 1.406 59.199 3558 Z= 0.870 Chirality : 0.055 0.272 414 Planarity : 0.003 0.026 444 Dihedral : 10.827 54.907 363 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.24 % Allowed : 16.03 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 41.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 TYR 0.010 0.002 TYR F 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.67 seconds wall clock time: 71 minutes 51.42 seconds (4311.42 seconds total)