Starting phenix.real_space_refine on Sun Jun 8 04:22:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fel_29032/06_2025/8fel_29032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fel_29032/06_2025/8fel_29032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fel_29032/06_2025/8fel_29032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fel_29032/06_2025/8fel_29032.map" model { file = "/net/cci-nas-00/data/ceres_data/8fel_29032/06_2025/8fel_29032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fel_29032/06_2025/8fel_29032.cif" } resolution = 4.64 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= 0.002 sd= 0.078 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5820 2.51 5 N 1509 2.21 5 O 1821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9201 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3067 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 2 Restraints were copied for chains: C, B Time building chain proxies: 6.17, per 1000 atoms: 0.67 Number of scatterers: 9201 At special positions: 0 Unit cell: (93.96, 91.8, 172.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1821 8.00 N 1509 7.00 C 5820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 41.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 142 through 177 removed outlier: 3.854A pdb=" N GLN A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 210 removed outlier: 3.554A pdb=" N PHE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.046A pdb=" N MET A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.633A pdb=" N LEU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 removed outlier: 3.787A pdb=" N ILE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.603A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 142 through 177 removed outlier: 3.855A pdb=" N GLN B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 210 removed outlier: 3.554A pdb=" N PHE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 233 through 241 removed outlier: 4.045A pdb=" N MET B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.635A pdb=" N LEU B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.789A pdb=" N ILE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 477 removed outlier: 3.601A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 471 " --> pdb=" O ASP B 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 142 through 177 removed outlier: 3.855A pdb=" N GLN C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 210 removed outlier: 3.553A pdb=" N PHE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.613A pdb=" N GLN C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.046A pdb=" N MET C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.634A pdb=" N LEU C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 353 removed outlier: 3.789A pdb=" N ILE C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 477 removed outlier: 3.602A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS C 471 " --> pdb=" O ASP C 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 472 " --> pdb=" O TYR C 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN A 40 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS A 335 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 42 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 290 removed outlier: 3.852A pdb=" N GLN A 289 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 311 " --> pdb=" O GLN A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.693A pdb=" N ALA A 372 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN B 40 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS B 335 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS B 42 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 290 removed outlier: 3.852A pdb=" N GLN B 289 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 311 " --> pdb=" O GLN B 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 296 through 298 Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.692A pdb=" N ALA B 372 " --> pdb=" O TYR B 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 281 through 282 removed outlier: 5.940A pdb=" N ASN C 40 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N CYS C 335 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS C 42 " --> pdb=" O CYS C 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 261 through 264 removed outlier: 7.107A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 288 through 290 removed outlier: 3.853A pdb=" N GLN C 289 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 311 " --> pdb=" O GLN C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AB6, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.693A pdb=" N ALA C 372 " --> pdb=" O TYR C 379 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3033 1.34 - 1.46: 1803 1.46 - 1.58: 4410 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9318 Sorted by residual: bond pdb=" C ILE A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.76e-01 bond pdb=" C ILE C 179 " pdb=" N PRO C 180 " ideal model delta sigma weight residual 1.334 1.354 -0.021 2.34e-02 1.83e+03 7.68e-01 bond pdb=" C ILE B 179 " pdb=" N PRO B 180 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.67e-01 bond pdb=" N GLY B 36 " pdb=" CA GLY B 36 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.90e-01 bond pdb=" N GLY C 36 " pdb=" CA GLY C 36 " ideal model delta sigma weight residual 1.445 1.451 -0.007 8.30e-03 1.45e+04 6.54e-01 ... (remaining 9313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 12435 0.97 - 1.94: 159 1.94 - 2.91: 45 2.91 - 3.88: 6 3.88 - 4.85: 9 Bond angle restraints: 12654 Sorted by residual: angle pdb=" CA TYR B 468 " pdb=" CB TYR B 468 " pdb=" CG TYR B 468 " ideal model delta sigma weight residual 113.90 118.53 -4.63 1.80e+00 3.09e-01 6.63e+00 angle pdb=" CA TYR C 468 " pdb=" CB TYR C 468 " pdb=" CG TYR C 468 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 angle pdb=" CA TYR A 468 " pdb=" CB TYR A 468 " pdb=" CG TYR A 468 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.48e+00 angle pdb=" C PRO C 84 " pdb=" N VAL C 85 " pdb=" CA VAL C 85 " ideal model delta sigma weight residual 121.97 126.32 -4.35 1.80e+00 3.09e-01 5.84e+00 angle pdb=" C PRO A 84 " pdb=" N VAL A 85 " pdb=" CA VAL A 85 " ideal model delta sigma weight residual 121.97 126.30 -4.33 1.80e+00 3.09e-01 5.79e+00 ... (remaining 12649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5124 17.77 - 35.54: 429 35.54 - 53.31: 165 53.31 - 71.08: 15 71.08 - 88.85: 6 Dihedral angle restraints: 5739 sinusoidal: 2271 harmonic: 3468 Sorted by residual: dihedral pdb=" CB CYS B 326 " pdb=" SG CYS B 326 " pdb=" SG CYS B 335 " pdb=" CB CYS B 335 " ideal model delta sinusoidal sigma weight residual 93.00 123.72 -30.72 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB CYS C 326 " pdb=" SG CYS C 326 " pdb=" SG CYS C 335 " pdb=" CB CYS C 335 " ideal model delta sinusoidal sigma weight residual 93.00 123.70 -30.70 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual 93.00 123.67 -30.67 1 1.00e+01 1.00e-02 1.34e+01 ... (remaining 5736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 968 0.024 - 0.048: 307 0.048 - 0.072: 123 0.072 - 0.096: 66 0.096 - 0.120: 78 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ILE C 57 " pdb=" N ILE C 57 " pdb=" C ILE C 57 " pdb=" CB ILE C 57 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 57 " pdb=" N ILE B 57 " pdb=" C ILE B 57 " pdb=" CB ILE B 57 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ILE C 321 " pdb=" N ILE C 321 " pdb=" C ILE C 321 " pdb=" CB ILE C 321 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1539 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 468 " -0.007 2.00e-02 2.50e+03 6.63e-03 8.78e-01 pdb=" CG TYR C 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 468 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 468 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 468 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 468 " -0.007 2.00e-02 2.50e+03 6.61e-03 8.73e-01 pdb=" CG TYR A 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 468 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 468 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 468 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 468 " -0.007 2.00e-02 2.50e+03 6.50e-03 8.46e-01 pdb=" CG TYR B 468 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 468 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 468 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 468 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 468 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 468 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 468 " -0.000 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 433 2.73 - 3.27: 9487 3.27 - 3.82: 14639 3.82 - 4.36: 16541 4.36 - 4.90: 26898 Nonbonded interactions: 67998 Sorted by model distance: nonbonded pdb=" NH1 ARG B 388 " pdb=" O THR B 392 " model vdw 2.191 3.120 nonbonded pdb=" NH1 ARG C 388 " pdb=" O THR C 392 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG A 388 " pdb=" O THR A 392 " model vdw 2.192 3.120 nonbonded pdb=" O SER B 186 " pdb=" OG1 THR B 189 " model vdw 2.206 3.040 nonbonded pdb=" O SER A 186 " pdb=" OG1 THR A 189 " model vdw 2.206 3.040 ... (remaining 67993 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.170 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.880 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3825 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 : 0.001 0.021 9333 Z= 0.072 Angle : 0.349 4.845 12684 Z= 0.194 Chirality : 0.039 0.120 1542 Planarity : 0.002 0.020 1617 Dihedral : 14.882 88.852 3462 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.98 % Allowed : 17.28 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1173 helix: 1.32 (0.24), residues: 414 sheet: -0.98 (0.54), residues: 87 loop : -1.02 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 303 HIS 0.000 0.000 HIS B 253 PHE 0.002 0.000 PHE A 230 TYR 0.016 0.001 TYR C 468 ARG 0.001 0.000 ARG C 220 Details of bonding type rmsd hydrogen bonds : bond 0.20319 ( 381) hydrogen bonds : angle 8.04656 ( 1071) SS BOND : bond 0.00048 ( 15) SS BOND : angle 0.10459 ( 30) covalent geometry : bond 0.00127 ( 9318) covalent geometry : angle 0.34932 (12654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.373 Fit side-chains REVERT: A 168 ASP cc_start: 0.8283 (t0) cc_final: 0.8005 (m-30) REVERT: A 273 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.4942 (pt) outliers start: 7 outliers final: 1 residues processed: 30 average time/residue: 0.1338 time to fit residues: 5.3102 Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.088460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.083307 restraints weight = 24762.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.083946 restraints weight = 22575.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.084527 restraints weight = 18985.233| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4145 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9333 Z= 0.118 Angle : 0.575 7.231 12684 Z= 0.295 Chirality : 0.043 0.177 1542 Planarity : 0.003 0.020 1617 Dihedral : 3.485 14.769 1269 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1173 helix: 2.07 (0.25), residues: 429 sheet: -0.98 (0.52), residues: 87 loop : -0.98 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.003 0.002 HIS B 253 PHE 0.013 0.001 PHE B 230 TYR 0.007 0.001 TYR A 270 ARG 0.004 0.001 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 381) hydrogen bonds : angle 5.54602 ( 1071) SS BOND : bond 0.00473 ( 15) SS BOND : angle 1.50903 ( 30) covalent geometry : bond 0.00233 ( 9318) covalent geometry : angle 0.57121 (12654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.569 Fit side-chains REVERT: A 142 MET cc_start: 0.1232 (mmp) cc_final: 0.0751 (tpt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1150 time to fit residues: 2.8545 Evaluate side-chains 8 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.0670 chunk 41 optimal weight: 0.0370 chunk 83 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 36 optimal weight: 9.9990 chunk 100 optimal weight: 0.0050 chunk 101 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 76 optimal weight: 0.0370 overall best weight: 0.0688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.088921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.083442 restraints weight = 24820.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.084156 restraints weight = 18721.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.084755 restraints weight = 14385.360| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4378 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9333 Z= 0.095 Angle : 0.496 7.617 12684 Z= 0.252 Chirality : 0.041 0.153 1542 Planarity : 0.002 0.013 1617 Dihedral : 3.267 13.763 1269 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1173 helix: 1.84 (0.24), residues: 447 sheet: -0.97 (0.52), residues: 87 loop : -1.01 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.003 0.002 HIS B 253 PHE 0.011 0.001 PHE B 230 TYR 0.012 0.001 TYR A 468 ARG 0.002 0.000 ARG B 388 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 381) hydrogen bonds : angle 5.08680 ( 1071) SS BOND : bond 0.00768 ( 15) SS BOND : angle 0.87724 ( 30) covalent geometry : bond 0.00171 ( 9318) covalent geometry : angle 0.49521 (12654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.389 Fit side-chains REVERT: A 142 MET cc_start: 0.1680 (mmp) cc_final: 0.1143 (tpt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1475 time to fit residues: 3.9313 Evaluate side-chains 9 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 0.0770 chunk 110 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 72 optimal weight: 0.0980 chunk 77 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 overall best weight: 0.1694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.088837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.083263 restraints weight = 24662.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.084025 restraints weight = 18064.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.084589 restraints weight = 14324.275| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4403 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9333 Z= 0.086 Angle : 0.470 7.429 12684 Z= 0.239 Chirality : 0.041 0.138 1542 Planarity : 0.002 0.013 1617 Dihedral : 3.298 13.822 1269 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1173 helix: 2.09 (0.24), residues: 444 sheet: -0.95 (0.55), residues: 87 loop : -1.02 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.002 0.001 HIS B 253 PHE 0.009 0.001 PHE C 230 TYR 0.013 0.001 TYR B 468 ARG 0.001 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 381) hydrogen bonds : angle 4.74133 ( 1071) SS BOND : bond 0.00226 ( 15) SS BOND : angle 0.84961 ( 30) covalent geometry : bond 0.00165 ( 9318) covalent geometry : angle 0.46903 (12654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.372 Fit side-chains REVERT: A 142 MET cc_start: 0.1475 (mmp) cc_final: 0.0989 (tpt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1028 time to fit residues: 2.3763 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 81 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.089412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.084641 restraints weight = 24756.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.085177 restraints weight = 20543.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.085410 restraints weight = 15203.690| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4351 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9333 Z= 0.086 Angle : 0.476 6.764 12684 Z= 0.246 Chirality : 0.041 0.131 1542 Planarity : 0.002 0.016 1617 Dihedral : 3.321 17.304 1269 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1173 helix: 2.19 (0.24), residues: 444 sheet: -1.17 (0.50), residues: 99 loop : -0.93 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.004 0.003 HIS B 253 PHE 0.009 0.001 PHE C 230 TYR 0.014 0.001 TYR B 468 ARG 0.001 0.000 ARG A 64 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 381) hydrogen bonds : angle 4.55695 ( 1071) SS BOND : bond 0.00141 ( 15) SS BOND : angle 1.03301 ( 30) covalent geometry : bond 0.00168 ( 9318) covalent geometry : angle 0.47434 (12654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.382 Fit side-chains REVERT: A 142 MET cc_start: 0.1039 (mmp) cc_final: 0.0547 (tpt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1017 time to fit residues: 2.3243 Evaluate side-chains 9 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 32 optimal weight: 0.0170 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 0.0170 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 115 optimal weight: 0.0170 chunk 9 optimal weight: 5.9990 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.089273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.084768 restraints weight = 25227.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.085097 restraints weight = 19117.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.085422 restraints weight = 15628.814| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4294 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9333 Z= 0.082 Angle : 0.473 6.804 12684 Z= 0.240 Chirality : 0.041 0.130 1542 Planarity : 0.002 0.017 1617 Dihedral : 3.167 12.500 1269 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1173 helix: 2.23 (0.24), residues: 444 sheet: -0.95 (0.56), residues: 84 loop : -0.91 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 303 HIS 0.001 0.001 HIS A 253 PHE 0.009 0.001 PHE A 230 TYR 0.015 0.001 TYR B 468 ARG 0.001 0.000 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.02517 ( 381) hydrogen bonds : angle 4.45019 ( 1071) SS BOND : bond 0.00160 ( 15) SS BOND : angle 0.48114 ( 30) covalent geometry : bond 0.00157 ( 9318) covalent geometry : angle 0.47252 (12654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.383 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1082 time to fit residues: 2.1891 Evaluate side-chains 8 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.0570 chunk 1 optimal weight: 0.0030 chunk 74 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 0.0470 chunk 73 optimal weight: 0.0770 overall best weight: 0.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.089317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.084258 restraints weight = 24802.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.084874 restraints weight = 18811.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.085258 restraints weight = 14262.296| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4286 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9333 Z= 0.081 Angle : 0.474 6.461 12684 Z= 0.241 Chirality : 0.041 0.131 1542 Planarity : 0.002 0.021 1617 Dihedral : 3.089 12.137 1269 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1173 helix: 2.11 (0.24), residues: 444 sheet: -0.77 (0.56), residues: 84 loop : -0.86 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 303 HIS 0.001 0.001 HIS B 253 PHE 0.009 0.001 PHE C 230 TYR 0.007 0.000 TYR C 270 ARG 0.001 0.000 ARG C 309 Details of bonding type rmsd hydrogen bonds : bond 0.02464 ( 381) hydrogen bonds : angle 4.36480 ( 1071) SS BOND : bond 0.00162 ( 15) SS BOND : angle 0.87243 ( 30) covalent geometry : bond 0.00154 ( 9318) covalent geometry : angle 0.47260 (12654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1001 time to fit residues: 2.0345 Evaluate side-chains 8 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 chunk 60 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.086231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.083220 restraints weight = 25158.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.083170 restraints weight = 24470.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.083169 restraints weight = 17293.002| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4462 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9333 Z= 0.096 Angle : 0.509 6.777 12684 Z= 0.263 Chirality : 0.042 0.141 1542 Planarity : 0.002 0.025 1617 Dihedral : 3.476 15.781 1269 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1173 helix: 2.28 (0.24), residues: 444 sheet: -0.71 (0.56), residues: 84 loop : -0.96 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 303 HIS 0.000 0.000 HIS A 253 PHE 0.010 0.001 PHE C 230 TYR 0.007 0.001 TYR B 270 ARG 0.009 0.001 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.02458 ( 381) hydrogen bonds : angle 4.18979 ( 1071) SS BOND : bond 0.00818 ( 15) SS BOND : angle 0.74274 ( 30) covalent geometry : bond 0.00189 ( 9318) covalent geometry : angle 0.50824 (12654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.412 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1103 time to fit residues: 2.2224 Evaluate side-chains 9 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.081195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.077088 restraints weight = 24993.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.076894 restraints weight = 21997.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.076397 restraints weight = 22419.452| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5183 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9333 Z= 0.201 Angle : 0.741 16.787 12684 Z= 0.393 Chirality : 0.048 0.206 1542 Planarity : 0.004 0.025 1617 Dihedral : 4.872 30.398 1269 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1173 helix: 1.83 (0.24), residues: 453 sheet: -0.84 (0.53), residues: 84 loop : -1.01 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 303 HIS 0.006 0.004 HIS A 253 PHE 0.040 0.003 PHE B 475 TYR 0.014 0.002 TYR C 243 ARG 0.005 0.001 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 381) hydrogen bonds : angle 4.42140 ( 1071) SS BOND : bond 0.00439 ( 15) SS BOND : angle 2.25957 ( 30) covalent geometry : bond 0.00425 ( 9318) covalent geometry : angle 0.73397 (12654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1464 time to fit residues: 3.2896 Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 0.3980 chunk 3 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.078461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.074582 restraints weight = 23147.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.074436 restraints weight = 21776.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.074421 restraints weight = 20460.931| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4785 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9333 Z= 0.102 Angle : 0.541 6.894 12684 Z= 0.284 Chirality : 0.042 0.130 1542 Planarity : 0.004 0.062 1617 Dihedral : 3.957 14.796 1269 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1173 helix: 1.94 (0.24), residues: 450 sheet: -0.53 (0.57), residues: 84 loop : -0.91 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 303 HIS 0.001 0.001 HIS A 253 PHE 0.012 0.002 PHE A 475 TYR 0.010 0.001 TYR B 468 ARG 0.005 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.02602 ( 381) hydrogen bonds : angle 4.15250 ( 1071) SS BOND : bond 0.00377 ( 15) SS BOND : angle 0.73107 ( 30) covalent geometry : bond 0.00211 ( 9318) covalent geometry : angle 0.54034 (12654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1379 time to fit residues: 2.8372 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.0050 chunk 81 optimal weight: 0.0020 chunk 79 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 111 optimal weight: 0.0770 chunk 57 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 89 optimal weight: 0.0050 chunk 62 optimal weight: 3.9990 overall best weight: 0.0372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.085404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.079963 restraints weight = 24728.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.080162 restraints weight = 23042.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.080162 restraints weight = 20572.574| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4842 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9333 Z= 0.089 Angle : 0.506 5.588 12684 Z= 0.258 Chirality : 0.042 0.154 1542 Planarity : 0.003 0.051 1617 Dihedral : 3.626 16.315 1269 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1173 helix: 1.78 (0.24), residues: 447 sheet: -0.49 (0.58), residues: 84 loop : -1.01 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS A 253 PHE 0.020 0.002 PHE B 475 TYR 0.011 0.001 TYR B 468 ARG 0.002 0.000 ARG A 388 Details of bonding type rmsd hydrogen bonds : bond 0.02483 ( 381) hydrogen bonds : angle 3.98803 ( 1071) SS BOND : bond 0.00283 ( 15) SS BOND : angle 0.43222 ( 30) covalent geometry : bond 0.00185 ( 9318) covalent geometry : angle 0.50620 (12654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.97 seconds wall clock time: 43 minutes 59.51 seconds (2639.51 seconds total)