Starting phenix.real_space_refine on Mon Apr 6 08:45:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q6h_72278/04_2026/9q6h_72278.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q6h_72278/04_2026/9q6h_72278.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 { model { file = "/net/cci-nas-00/data/ceres_data/9q6h_72278/04_2026/9q6h_72278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q6h_72278/04_2026/9q6h_72278.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q6h_72278/04_2026/9q6h_72278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q6h_72278/04_2026/9q6h_72278.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 60 5.16 5 C 5383 2.51 5 N 1471 2.21 5 O 1652 1.98 5 H 8275 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16841 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 9225 Classifications: {'peptide': 585} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 560} Chain: "B" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1948 Classifications: {'peptide': 131} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "C" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1886 Classifications: {'peptide': 125} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "D" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1861 Classifications: {'peptide': 124} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1921 Classifications: {'peptide': 128} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125} Time building chain proxies: 2.89, per 1000 atoms: 0.17 Number of scatterers: 16841 At special positions: 0 Unit cell: (94.053, 101.085, 135.366, 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 60 16.00 O 1652 8.00 N 1471 7.00 C 5383 6.00 H 8275 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.04 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 385 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.04 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.04 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " distance=2.04 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 118 " distance=2.04 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 118 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 118 " distance=2.04 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 113 " 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: 1.56 Conformation dependent library (CDL) restraints added in 799.1 milliseconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 50.9% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 29 through 55 removed outlier: 6.626A pdb=" N GLU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLU A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASN A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 80 Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.979A pdb=" N THR A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.736A pdb=" N ASP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.596A pdb=" N LYS A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 174 through 193 Processing helix chain 'A' and resid 197 through 230 removed outlier: 3.563A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 231 through 247 removed outlier: 3.728A pdb=" N PHE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 271 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 298 through 305 removed outlier: 4.640A pdb=" N CYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 346 through 362 Processing helix chain 'A' and resid 366 through 386 removed outlier: 3.939A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.506A pdb=" N CYS A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 422 removed outlier: 3.642A pdb=" N GLU A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Proline residue: A 403 - end of helix Proline residue: A 408 - end of helix removed outlier: 3.674A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 439 Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 465 through 491 removed outlier: 4.454A pdb=" N MET A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 507 through 515 Processing helix chain 'A' and resid 527 through 532 removed outlier: 4.061A pdb=" N PHE A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.918A pdb=" N THR A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 564 through 585 Processing helix chain 'A' and resid 587 through 608 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.729A pdb=" N TYR B 140 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.510A pdb=" N GLN E 82 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 34 removed outlier: 7.297A pdb=" N MET B 56 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA B 72 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP B 58 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'C' and resid 26 through 29 removed outlier: 3.602A pdb=" N THR C 100 " --> pdb=" O ASP C 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.648A pdb=" N SER C 145 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET C 56 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR C 72 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.648A pdb=" N SER C 145 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 29 removed outlier: 4.133A pdb=" N VAL D 27 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 27 through 29 removed outlier: 4.133A pdb=" N VAL D 27 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 32 through 34 removed outlier: 5.763A pdb=" N GLY D 32 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 119 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 57 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TRP D 58 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 32 through 34 removed outlier: 5.763A pdb=" N GLY D 32 " --> pdb=" O THR D 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 21 through 24 Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.799A pdb=" N VAL E 110 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA E 66 " --> pdb=" O TRP E 53 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ARG E 55 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N PHE E 64 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 28 through 29 515 hydrogen bonds defined for protein. 1395 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: 3.86 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8274 1.04 - 1.24: 1047 1.24 - 1.44: 2781 1.44 - 1.64: 4842 1.64 - 1.84: 77 Bond restraints: 17021 Sorted by residual: bond pdb=" N ALA D 22 " pdb=" H1 ALA D 22 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ALA B 22 " pdb=" H1 ALA B 22 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ALA E 17 " pdb=" H1 ALA E 17 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ALA C 22 " pdb=" H1 ALA C 22 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASP A 25 " pdb=" H1 ASP A 25 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 17016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 29397 1.22 - 2.43: 1156 2.43 - 3.65: 80 3.65 - 4.87: 14 4.87 - 6.09: 6 Bond angle restraints: 30653 Sorted by residual: angle pdb=" CA GLY A 39 " pdb=" C GLY A 39 " pdb=" O GLY A 39 " ideal model delta sigma weight residual 122.29 119.88 2.41 8.10e-01 1.52e+00 8.86e+00 angle pdb=" N GLY A 39 " pdb=" CA GLY A 39 " pdb=" C GLY A 39 " ideal model delta sigma weight residual 112.68 109.38 3.30 1.26e+00 6.30e-01 6.87e+00 angle pdb=" N ALA D 71 " pdb=" CA ALA D 71 " pdb=" C ALA D 71 " ideal model delta sigma weight residual 110.24 113.80 -3.56 1.41e+00 5.03e-01 6.38e+00 angle pdb=" C ASP A 332 " pdb=" N PHE A 333 " pdb=" CA PHE A 333 " ideal model delta sigma weight residual 122.49 118.84 3.65 1.55e+00 4.16e-01 5.55e+00 angle pdb=" CA GLY A 39 " pdb=" C GLY A 39 " pdb=" N GLU A 40 " ideal model delta sigma weight residual 114.88 117.63 -2.75 1.20e+00 6.94e-01 5.25e+00 ... (remaining 30648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7318 17.61 - 35.21: 543 35.21 - 52.82: 183 52.82 - 70.42: 44 70.42 - 88.03: 24 Dihedral angle restraints: 8112 sinusoidal: 4337 harmonic: 3775 Sorted by residual: dihedral pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual 93.00 36.47 56.53 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CA THR A 502 " pdb=" C THR A 502 " pdb=" N GLU A 503 " pdb=" CA GLU A 503 " ideal model delta harmonic sigma weight residual 180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASN D 73 " pdb=" C ASN D 73 " pdb=" N HIS D 74 " pdb=" CA HIS D 74 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 830 0.029 - 0.058: 321 0.058 - 0.087: 60 0.087 - 0.117: 58 0.117 - 0.146: 7 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CA VAL B 70 " pdb=" N VAL B 70 " pdb=" C VAL B 70 " pdb=" CB VAL B 70 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE E 65 " pdb=" N ILE E 65 " pdb=" C ILE E 65 " pdb=" CB ILE E 65 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1273 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " -0.017 2.00e-02 2.50e+03 9.07e-03 2.47e+00 pdb=" CG TYR A 185 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 185 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 185 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR A 185 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 185 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 331 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.42e+00 pdb=" C ALA A 331 " -0.027 2.00e-02 2.50e+03 pdb=" O ALA A 331 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 332 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 70 " -0.015 2.00e-02 2.50e+03 6.74e-03 1.82e+00 pdb=" CG TRP E 70 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP E 70 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP E 70 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 70 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 70 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 70 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 70 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 70 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP E 70 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP E 70 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP E 70 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 70 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 70 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 70 " -0.000 2.00e-02 2.50e+03 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 495 2.13 - 2.75: 31497 2.75 - 3.37: 47794 3.37 - 3.98: 60394 3.98 - 4.60: 96186 Nonbonded interactions: 236366 Sorted by model distance: nonbonded pdb="HH22 ARG A 496 " pdb=" O GLU A 516 " model vdw 1.517 2.450 nonbonded pdb=" HE ARG D 60 " pdb=" OE2 GLU D 68 " model vdw 1.530 2.450 nonbonded pdb=" O VAL B 34 " pdb=" H SER B 152 " model vdw 1.559 2.450 nonbonded pdb=" O SER B 74 " pdb="HH11 ARG B 94 " model vdw 1.593 2.450 nonbonded pdb="HE21 GLN D 61 " pdb=" O LYS D 65 " model vdw 1.595 2.450 ... (remaining 236361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8767 Z= 0.181 Angle : 0.580 5.054 11868 Z= 0.344 Chirality : 0.037 0.146 1276 Planarity : 0.004 0.032 1542 Dihedral : 14.287 88.027 3207 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1083 helix: 1.71 (0.24), residues: 439 sheet: 0.82 (0.37), residues: 198 loop : -0.30 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 89 TYR 0.026 0.002 TYR A 185 PHE 0.018 0.002 PHE A 333 TRP 0.021 0.002 TRP E 70 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8746) covalent geometry : angle 0.57522 (11826) SS BOND : bond 0.00412 ( 21) SS BOND : angle 1.34175 ( 42) hydrogen bonds : bond 0.18190 ( 489) hydrogen bonds : angle 7.05796 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 THR cc_start: 0.8588 (m) cc_final: 0.8381 (p) REVERT: A 493 VAL cc_start: 0.8626 (m) cc_final: 0.8388 (t) REVERT: A 517 VAL cc_start: 0.8681 (t) cc_final: 0.8130 (m) REVERT: A 568 LEU cc_start: 0.7717 (mt) cc_final: 0.7422 (mt) REVERT: E 90 ASP cc_start: 0.7448 (t0) cc_final: 0.5631 (t0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2657 time to fit residues: 78.4628 Evaluate side-chains 152 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN E 119 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.094651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.072166 restraints weight = 75724.288| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.50 r_work: 0.3294 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8767 Z= 0.191 Angle : 0.585 5.063 11868 Z= 0.322 Chirality : 0.039 0.201 1276 Planarity : 0.005 0.037 1542 Dihedral : 4.709 26.697 1197 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.34 % Favored : 95.48 % Rotamer: Outliers : 2.08 % Allowed : 13.60 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1083 helix: 1.61 (0.23), residues: 459 sheet: 0.28 (0.33), residues: 216 loop : -0.50 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 94 TYR 0.017 0.001 TYR A 185 PHE 0.011 0.002 PHE D 59 TRP 0.014 0.001 TRP D 75 HIS 0.009 0.002 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8746) covalent geometry : angle 0.58045 (11826) SS BOND : bond 0.00585 ( 21) SS BOND : angle 1.37943 ( 42) hydrogen bonds : bond 0.04704 ( 489) hydrogen bonds : angle 5.50642 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 THR cc_start: 0.7916 (m) cc_final: 0.7651 (p) REVERT: A 568 LEU cc_start: 0.8033 (mt) cc_final: 0.7679 (mt) REVERT: C 28 GLU cc_start: 0.6884 (mp0) cc_final: 0.5739 (mp0) REVERT: D 117 TYR cc_start: 0.8016 (m-80) cc_final: 0.7752 (m-80) REVERT: E 63 GLU cc_start: 0.9121 (pt0) cc_final: 0.8796 (mp0) REVERT: E 100 MET cc_start: 0.9284 (mtm) cc_final: 0.8857 (mpp) outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.2523 time to fit residues: 55.4203 Evaluate side-chains 149 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.094436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.071934 restraints weight = 76948.723| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.50 r_work: 0.3294 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8767 Z= 0.163 Angle : 0.569 9.081 11868 Z= 0.312 Chirality : 0.038 0.212 1276 Planarity : 0.004 0.044 1542 Dihedral : 4.670 31.154 1197 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.16 % Favored : 95.66 % Rotamer: Outliers : 1.75 % Allowed : 15.57 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1083 helix: 1.73 (0.23), residues: 462 sheet: -0.01 (0.33), residues: 217 loop : -0.49 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 49 TYR 0.014 0.001 TYR A 185 PHE 0.009 0.001 PHE A 230 TRP 0.014 0.001 TRP D 75 HIS 0.010 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8746) covalent geometry : angle 0.56099 (11826) SS BOND : bond 0.00612 ( 21) SS BOND : angle 1.70216 ( 42) hydrogen bonds : bond 0.04194 ( 489) hydrogen bonds : angle 5.28115 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.9306 (OUTLIER) cc_final: 0.8898 (m-30) REVERT: A 379 THR cc_start: 0.7923 (m) cc_final: 0.7683 (p) REVERT: A 568 LEU cc_start: 0.8058 (mt) cc_final: 0.7646 (mt) REVERT: C 28 GLU cc_start: 0.6516 (mp0) cc_final: 0.6308 (mp0) REVERT: D 101 MET cc_start: 0.2536 (tmm) cc_final: 0.1479 (mmm) REVERT: E 63 GLU cc_start: 0.9130 (pt0) cc_final: 0.8786 (mp0) REVERT: E 90 ASP cc_start: 0.8033 (t0) cc_final: 0.7777 (t0) REVERT: E 100 MET cc_start: 0.9310 (mtm) cc_final: 0.8882 (mpp) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 0.2408 time to fit residues: 48.5443 Evaluate side-chains 144 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.094149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.071621 restraints weight = 76148.362| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.50 r_work: 0.3291 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8767 Z= 0.147 Angle : 0.534 7.798 11868 Z= 0.288 Chirality : 0.037 0.195 1276 Planarity : 0.004 0.041 1542 Dihedral : 4.472 28.587 1197 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 1.75 % Allowed : 16.34 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1083 helix: 1.93 (0.24), residues: 467 sheet: -0.14 (0.32), residues: 207 loop : -0.45 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 44 TYR 0.013 0.001 TYR A 185 PHE 0.007 0.001 PHE A 592 TRP 0.013 0.001 TRP D 75 HIS 0.007 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8746) covalent geometry : angle 0.52718 (11826) SS BOND : bond 0.00327 ( 21) SS BOND : angle 1.53810 ( 42) hydrogen bonds : bond 0.03722 ( 489) hydrogen bonds : angle 5.02220 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 379 THR cc_start: 0.7987 (m) cc_final: 0.7740 (p) REVERT: B 145 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8752 (tm-30) REVERT: D 101 MET cc_start: 0.2727 (tmm) cc_final: 0.1663 (mmm) REVERT: D 140 GLN cc_start: 0.8960 (tp40) cc_final: 0.8672 (tp40) REVERT: E 63 GLU cc_start: 0.9164 (pt0) cc_final: 0.8804 (mp0) REVERT: E 90 ASP cc_start: 0.8202 (t0) cc_final: 0.7979 (t0) REVERT: E 100 MET cc_start: 0.9301 (mtm) cc_final: 0.8852 (mpp) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.2510 time to fit residues: 48.6662 Evaluate side-chains 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 50 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.093535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.071183 restraints weight = 76159.580| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 4.45 r_work: 0.3284 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8767 Z= 0.152 Angle : 0.529 7.891 11868 Z= 0.285 Chirality : 0.037 0.160 1276 Planarity : 0.004 0.041 1542 Dihedral : 4.392 27.268 1197 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 1.75 % Allowed : 16.45 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1083 helix: 2.07 (0.24), residues: 465 sheet: -0.22 (0.31), residues: 213 loop : -0.43 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 44 TYR 0.012 0.001 TYR A 185 PHE 0.007 0.001 PHE A 73 TRP 0.012 0.001 TRP D 75 HIS 0.007 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8746) covalent geometry : angle 0.52480 (11826) SS BOND : bond 0.00360 ( 21) SS BOND : angle 1.25878 ( 42) hydrogen bonds : bond 0.03591 ( 489) hydrogen bonds : angle 4.90514 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.9293 (OUTLIER) cc_final: 0.8908 (m-30) REVERT: A 316 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8067 (mp0) REVERT: A 379 THR cc_start: 0.8003 (m) cc_final: 0.7745 (p) REVERT: B 145 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8787 (tm-30) REVERT: D 101 MET cc_start: 0.2697 (tmm) cc_final: 0.1659 (mmm) REVERT: E 63 GLU cc_start: 0.9154 (pt0) cc_final: 0.8792 (mp0) REVERT: E 90 ASP cc_start: 0.8212 (t0) cc_final: 0.7979 (t0) REVERT: E 100 MET cc_start: 0.9328 (mtm) cc_final: 0.8921 (mpp) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.2380 time to fit residues: 45.5766 Evaluate side-chains 146 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.094013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.071674 restraints weight = 75941.458| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.46 r_work: 0.3292 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8767 Z= 0.131 Angle : 0.518 6.849 11868 Z= 0.277 Chirality : 0.037 0.148 1276 Planarity : 0.004 0.038 1542 Dihedral : 4.265 25.836 1197 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 1.75 % Allowed : 16.89 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1083 helix: 2.15 (0.24), residues: 470 sheet: -0.24 (0.31), residues: 214 loop : -0.42 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 94 TYR 0.012 0.001 TYR A 185 PHE 0.006 0.001 PHE C 90 TRP 0.013 0.001 TRP D 75 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8746) covalent geometry : angle 0.51429 (11826) SS BOND : bond 0.00312 ( 21) SS BOND : angle 1.15302 ( 42) hydrogen bonds : bond 0.03419 ( 489) hydrogen bonds : angle 4.77346 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8220 (t80) cc_final: 0.8019 (t80) REVERT: A 261 ASP cc_start: 0.9292 (OUTLIER) cc_final: 0.8917 (m-30) REVERT: A 316 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8065 (mp0) REVERT: A 379 THR cc_start: 0.8002 (m) cc_final: 0.7737 (p) REVERT: A 420 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8526 (tm-30) REVERT: B 145 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8842 (tm-30) REVERT: C 28 GLU cc_start: 0.6527 (mp0) cc_final: 0.6313 (mp0) REVERT: D 101 MET cc_start: 0.2758 (tmm) cc_final: 0.1732 (mmm) REVERT: E 63 GLU cc_start: 0.9166 (pt0) cc_final: 0.8772 (mp0) REVERT: E 90 ASP cc_start: 0.8233 (t0) cc_final: 0.7994 (t0) REVERT: E 100 MET cc_start: 0.9312 (mtm) cc_final: 0.8902 (mpp) outliers start: 16 outliers final: 12 residues processed: 147 average time/residue: 0.2241 time to fit residues: 44.0760 Evaluate side-chains 146 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 CYS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.070877 restraints weight = 76290.509| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 4.46 r_work: 0.3278 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8767 Z= 0.150 Angle : 0.531 7.065 11868 Z= 0.284 Chirality : 0.037 0.150 1276 Planarity : 0.004 0.038 1542 Dihedral : 4.231 26.289 1197 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.86 % Allowed : 16.89 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.26), residues: 1083 helix: 2.16 (0.24), residues: 473 sheet: -0.25 (0.32), residues: 208 loop : -0.36 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 94 TYR 0.011 0.001 TYR A 185 PHE 0.007 0.001 PHE A 73 TRP 0.012 0.001 TRP D 75 HIS 0.005 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8746) covalent geometry : angle 0.52450 (11826) SS BOND : bond 0.00381 ( 21) SS BOND : angle 1.50982 ( 42) hydrogen bonds : bond 0.03413 ( 489) hydrogen bonds : angle 4.72732 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8211 (t80) cc_final: 0.8006 (t80) REVERT: A 261 ASP cc_start: 0.9296 (OUTLIER) cc_final: 0.8917 (m-30) REVERT: A 316 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8069 (mp0) REVERT: A 379 THR cc_start: 0.7970 (m) cc_final: 0.7717 (p) REVERT: B 145 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8871 (tm-30) REVERT: C 66 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: D 101 MET cc_start: 0.2779 (tmm) cc_final: 0.1682 (mmm) REVERT: D 109 ARG cc_start: 0.9274 (mtt180) cc_final: 0.8949 (mtm-85) REVERT: E 63 GLU cc_start: 0.9190 (pt0) cc_final: 0.8779 (mp0) REVERT: E 90 ASP cc_start: 0.8229 (t0) cc_final: 0.7991 (t0) REVERT: E 100 MET cc_start: 0.9350 (mtm) cc_final: 0.8906 (mpp) REVERT: E 128 TYR cc_start: 0.8833 (t80) cc_final: 0.8592 (t80) outliers start: 17 outliers final: 14 residues processed: 142 average time/residue: 0.2394 time to fit residues: 45.3314 Evaluate side-chains 143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.071075 restraints weight = 76006.729| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.43 r_work: 0.3277 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8767 Z= 0.143 Angle : 0.525 4.966 11868 Z= 0.281 Chirality : 0.036 0.149 1276 Planarity : 0.004 0.040 1542 Dihedral : 4.192 25.418 1197 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.19 % Allowed : 17.11 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1083 helix: 2.17 (0.24), residues: 474 sheet: -0.26 (0.32), residues: 208 loop : -0.37 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 49 TYR 0.011 0.001 TYR A 185 PHE 0.007 0.001 PHE E 64 TRP 0.011 0.001 TRP D 75 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8746) covalent geometry : angle 0.51998 (11826) SS BOND : bond 0.00344 ( 21) SS BOND : angle 1.29275 ( 42) hydrogen bonds : bond 0.03288 ( 489) hydrogen bonds : angle 4.68803 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8210 (t80) cc_final: 0.8009 (t80) REVERT: A 261 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.8909 (m-30) REVERT: A 316 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8070 (mp0) REVERT: A 379 THR cc_start: 0.8001 (m) cc_final: 0.7748 (p) REVERT: B 145 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8869 (tm-30) REVERT: D 101 MET cc_start: 0.2773 (tmm) cc_final: 0.1719 (mmm) REVERT: E 55 ARG cc_start: 0.8611 (ptp90) cc_final: 0.8271 (ttp80) REVERT: E 77 TYR cc_start: 0.8406 (m-80) cc_final: 0.7567 (m-80) REVERT: E 90 ASP cc_start: 0.8194 (t0) cc_final: 0.7992 (t0) REVERT: E 100 MET cc_start: 0.9339 (mtm) cc_final: 0.8918 (mpp) REVERT: E 128 TYR cc_start: 0.8864 (t80) cc_final: 0.8604 (t80) outliers start: 20 outliers final: 17 residues processed: 143 average time/residue: 0.2404 time to fit residues: 45.9662 Evaluate side-chains 144 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 137 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.070952 restraints weight = 76495.910| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 4.45 r_work: 0.3276 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8767 Z= 0.149 Angle : 0.542 6.465 11868 Z= 0.289 Chirality : 0.036 0.149 1276 Planarity : 0.004 0.045 1542 Dihedral : 4.220 25.428 1197 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.08 % Allowed : 17.43 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1083 helix: 2.21 (0.24), residues: 473 sheet: -0.25 (0.33), residues: 207 loop : -0.42 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 49 TYR 0.011 0.001 TYR A 185 PHE 0.011 0.001 PHE E 64 TRP 0.011 0.001 TRP E 135 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8746) covalent geometry : angle 0.53563 (11826) SS BOND : bond 0.00346 ( 21) SS BOND : angle 1.47581 ( 42) hydrogen bonds : bond 0.03347 ( 489) hydrogen bonds : angle 4.67926 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.9284 (OUTLIER) cc_final: 0.8905 (m-30) REVERT: A 316 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8072 (mp0) REVERT: A 379 THR cc_start: 0.7992 (m) cc_final: 0.7740 (p) REVERT: B 145 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8862 (tm-30) REVERT: D 101 MET cc_start: 0.2786 (tmm) cc_final: 0.1727 (mmm) REVERT: E 63 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8357 (pm20) REVERT: E 77 TYR cc_start: 0.8396 (m-80) cc_final: 0.7540 (m-80) REVERT: E 100 MET cc_start: 0.9329 (mtm) cc_final: 0.8910 (mpp) REVERT: E 128 TYR cc_start: 0.8858 (t80) cc_final: 0.8592 (t80) outliers start: 19 outliers final: 17 residues processed: 135 average time/residue: 0.2406 time to fit residues: 43.2199 Evaluate side-chains 140 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 137 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.093584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.071483 restraints weight = 75485.097| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 4.47 r_work: 0.3292 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8767 Z= 0.129 Angle : 0.535 5.927 11868 Z= 0.285 Chirality : 0.036 0.149 1276 Planarity : 0.004 0.052 1542 Dihedral : 4.147 25.474 1197 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.86 % Allowed : 17.65 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.26), residues: 1083 helix: 2.26 (0.24), residues: 473 sheet: -0.30 (0.32), residues: 217 loop : -0.37 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 49 TYR 0.010 0.001 TYR A 185 PHE 0.009 0.001 PHE E 64 TRP 0.009 0.001 TRP D 75 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8746) covalent geometry : angle 0.52919 (11826) SS BOND : bond 0.00298 ( 21) SS BOND : angle 1.41832 ( 42) hydrogen bonds : bond 0.03236 ( 489) hydrogen bonds : angle 4.59401 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.8908 (m-30) REVERT: A 316 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8058 (mp0) REVERT: A 379 THR cc_start: 0.8054 (m) cc_final: 0.7792 (p) REVERT: D 101 MET cc_start: 0.2760 (tmm) cc_final: 0.1761 (mmm) REVERT: E 63 GLU cc_start: 0.8668 (pm20) cc_final: 0.8435 (pm20) REVERT: E 77 TYR cc_start: 0.8379 (m-80) cc_final: 0.7508 (m-80) REVERT: E 100 MET cc_start: 0.9322 (mtm) cc_final: 0.8927 (mpp) REVERT: E 128 TYR cc_start: 0.8873 (t80) cc_final: 0.8613 (t80) REVERT: E 137 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8362 (tp-100) outliers start: 17 outliers final: 16 residues processed: 136 average time/residue: 0.2308 time to fit residues: 41.8018 Evaluate side-chains 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 115 CYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.093980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.071901 restraints weight = 75354.213| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.48 r_work: 0.3302 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8767 Z= 0.116 Angle : 0.527 6.098 11868 Z= 0.279 Chirality : 0.036 0.147 1276 Planarity : 0.004 0.054 1542 Dihedral : 4.066 24.427 1197 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.75 % Allowed : 17.76 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1083 helix: 2.34 (0.24), residues: 472 sheet: -0.28 (0.32), residues: 217 loop : -0.39 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 49 TYR 0.010 0.001 TYR A 394 PHE 0.008 0.001 PHE E 64 TRP 0.014 0.001 TRP E 127 HIS 0.006 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8746) covalent geometry : angle 0.52058 (11826) SS BOND : bond 0.00292 ( 21) SS BOND : angle 1.44272 ( 42) hydrogen bonds : bond 0.03160 ( 489) hydrogen bonds : angle 4.52131 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4928.38 seconds wall clock time: 84 minutes 3.27 seconds (5043.27 seconds total)