Starting phenix.real_space_refine on Thu Dec 7 22:41:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3t_18874/12_2023/8r3t_18874.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3t_18874/12_2023/8r3t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3t_18874/12_2023/8r3t_18874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3t_18874/12_2023/8r3t_18874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3t_18874/12_2023/8r3t_18874.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3t_18874/12_2023/8r3t_18874.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.80, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 4.18 Conformation dependent library (CDL) restraints added in 628.1 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: 0.41 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: 1.69 Time building geometry restraints manager: 4.39 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: 100.63 - 106.86: 388 106.86 - 113.08: 6600 113.08 - 119.30: 1522 119.30 - 125.52: 1365 125.52 - 131.74: 131 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: 2065 13.09 - 26.17: 228 26.17 - 39.25: 85 39.25 - 52.34: 27 52.34 - 65.42: 33 Dihedral angle restraints: 2438 sinusoidal: 1380 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 2435 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 1.850 nonbonded pdb=" HG SER F 293 " pdb=" OD1 ASP F 295 " model vdw 1.633 1.850 nonbonded pdb=" HG SER E 293 " pdb=" OD1 ASP E 295 " model vdw 1.722 1.850 nonbonded pdb=" OD2 ASP A 295 " pdb=" HZ2 LYS F 290 " model vdw 1.750 1.850 nonbonded pdb=" HZ1 LYS A 281 " pdb=" OD1 ASP A 283 " model vdw 1.763 1.850 ... (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 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: 3.120 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: 0.080 Extract box with map and model: 11.130 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.190 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 17 poor density : 15 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 27 average time/residue: 0.2277 time to fit residues: 8.2699 Evaluate side-chains 14 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 9 time to evaluate : 0.470 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0650 time to fit residues: 1.1608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.8980 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: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2664 Z= 0.264 Angle : 0.849 8.256 3558 Z= 0.456 Chirality : 0.056 0.136 414 Planarity : 0.004 0.024 444 Dihedral : 10.170 45.265 354 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.39 % Favored : 95.32 % Rotamer: Outliers : 2.24 % Allowed : 12.18 % 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: -2.62 (0.34), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 329 TYR 0.008 0.002 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 18 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 11 time to evaluate : 0.467 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 16 average time/residue: 0.1765 time to fit residues: 4.3662 Evaluate side-chains 12 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 9 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0656 time to fit residues: 0.9341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3526 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= 0.194 Angle : 0.704 6.327 3558 Z= 0.379 Chirality : 0.054 0.131 414 Planarity : 0.004 0.031 444 Dihedral : 9.573 46.214 354 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.96 % Allowed : 12.82 % Favored : 86.22 % 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: -2.61 (0.35), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (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 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 12 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 9 time to evaluate : 0.465 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 11 average time/residue: 0.1200 time to fit residues: 2.5967 Evaluate side-chains 10 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0717 time to fit residues: 0.7084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4108 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= 0.210 Angle : 0.660 5.144 3558 Z= 0.355 Chirality : 0.054 0.131 414 Planarity : 0.004 0.034 444 Dihedral : 9.240 44.398 354 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.28 % Allowed : 13.78 % Favored : 84.94 % 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: -2.39 (0.37), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.28), 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 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 15 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 11 time to evaluate : 0.450 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 12 average time/residue: 0.2016 time to fit residues: 3.7846 Evaluate side-chains 11 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0692 time to fit residues: 0.7649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4484 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= 0.215 Angle : 0.643 5.007 3558 Z= 0.347 Chirality : 0.054 0.131 414 Planarity : 0.004 0.030 444 Dihedral : 9.167 44.056 354 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.64 % Allowed : 15.71 % Favored : 83.65 % 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: -2.45 (0.37), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.008 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 10 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 8 time to evaluate : 0.477 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 9 average time/residue: 0.2766 time to fit residues: 3.7074 Evaluate side-chains 8 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4706 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= 0.188 Angle : 0.607 4.893 3558 Z= 0.327 Chirality : 0.053 0.129 414 Planarity : 0.004 0.032 444 Dihedral : 8.953 43.493 354 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.32 % Allowed : 17.63 % Favored : 82.05 % 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: -2.48 (0.36), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 TYR 0.008 0.001 TYR A 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 9 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.412 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 8 average time/residue: 0.2457 time to fit residues: 3.0754 Evaluate side-chains 8 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4902 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= 0.183 Angle : 0.597 4.971 3558 Z= 0.321 Chirality : 0.053 0.129 414 Planarity : 0.004 0.034 444 Dihedral : 8.755 43.216 354 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.64 % Allowed : 18.27 % 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: -2.53 (0.36), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 TYR 0.009 0.001 TYR A 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 10 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 8 time to evaluate : 0.479 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 10 average time/residue: 0.2155 time to fit residues: 3.4272 Evaluate side-chains 8 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2664 Z= 0.235 Angle : 0.631 5.030 3558 Z= 0.341 Chirality : 0.054 0.131 414 Planarity : 0.004 0.032 444 Dihedral : 8.972 41.584 354 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.32 % Allowed : 19.23 % Favored : 80.45 % 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: -2.58 (0.36), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.012 0.002 TYR B 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 9 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.442 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.2320 time to fit residues: 3.3350 Evaluate side-chains 9 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0698 time to fit residues: 0.7297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5203 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= 0.196 Angle : 0.595 4.824 3558 Z= 0.321 Chirality : 0.053 0.128 414 Planarity : 0.004 0.034 444 Dihedral : 8.803 41.853 354 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.32 % Allowed : 18.91 % 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: -2.55 (0.36), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 329 TYR 0.009 0.002 TYR B 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 9 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.417 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 8 average time/residue: 0.2335 time to fit residues: 2.9672 Evaluate side-chains 8 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2664 Z= 0.234 Angle : 0.613 4.916 3558 Z= 0.332 Chirality : 0.053 0.130 414 Planarity : 0.004 0.033 444 Dihedral : 8.873 41.407 354 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.32 % Allowed : 18.59 % 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: -2.64 (0.35), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 TYR 0.010 0.002 TYR B 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 9 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.396 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 9 average time/residue: 0.2395 time to fit residues: 3.3209 Evaluate side-chains 8 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.157015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.139698 restraints weight = 8777.625| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 2.36 r_work: 0.4336 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4220 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5365 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= 0.200 Angle : 0.597 4.803 3558 Z= 0.322 Chirality : 0.053 0.128 414 Planarity : 0.004 0.034 444 Dihedral : 8.788 41.400 354 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.56 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 19.55 % Favored : 80.45 % 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: -2.63 (0.36), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 TYR 0.009 0.002 TYR D 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.75 seconds wall clock time: 49 minutes 2.84 seconds (2942.84 seconds total)