Starting phenix.real_space_refine on Tue Feb 3 20:02:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v6n_64803/02_2026/9v6n_64803.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v6n_64803/02_2026/9v6n_64803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v6n_64803/02_2026/9v6n_64803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v6n_64803/02_2026/9v6n_64803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v6n_64803/02_2026/9v6n_64803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v6n_64803/02_2026/9v6n_64803.map" } resolution = 3.4 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= 0.001 sd= 0.005 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 62 5.16 5 C 4074 2.51 5 N 1131 2.21 5 O 1296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6563 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3119 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 22, 'TRANS': 389} Chain: "B" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3374 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.59, per 1000 atoms: 0.24 Number of scatterers: 6563 At special positions: 0 Unit cell: (104.301, 119.671, 127.356, 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 62 16.00 O 1296 8.00 N 1131 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 281 " distance=2.03 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 456 " distance=2.05 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 434 " distance=2.03 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 413 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 852 " distance=2.03 Simple disulfide: pdb=" SG CYS B 771 " - pdb=" SG CYS B 965 " distance=2.03 Simple disulfide: pdb=" SG CYS B 777 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 783 " - pdb=" SG CYS B 832 " distance=2.04 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 823 " distance=2.03 Simple disulfide: pdb=" SG CYS B 934 " - pdb=" SG CYS B 947 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1101 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B1049 " - pdb=" SG CYS B1083 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " NAG C 3 " NAG-ASN " NAG A1301 " - " ASN A 438 " " NAG B1301 " - " ASN B 794 " " NAG C 1 " - " ASN B1035 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 298.4 milliseconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 16 sheets defined 10.3% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 188 through 193 removed outlier: 4.153A pdb=" N VAL A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.987A pdb=" N VAL A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 698 removed outlier: 3.848A pdb=" N SER B 698 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 791 Processing helix chain 'B' and resid 936 through 943 Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 1021 through 1025 removed outlier: 3.870A pdb=" N ALA B1025 " --> pdb=" O PHE B1022 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 270 removed outlier: 7.163A pdb=" N SER A 256 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 304 removed outlier: 4.040A pdb=" N ASP A 301 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 457 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 304 removed outlier: 4.040A pdb=" N ASP A 301 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 457 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 452 removed outlier: 3.604A pdb=" N THR A 363 " --> pdb=" O ARG B 775 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 396 removed outlier: 6.517A pdb=" N THR A 414 " --> pdb=" O CYS A 434 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N HIS A 436 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 482 through 486 removed outlier: 3.876A pdb=" N VAL A 492 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 556 removed outlier: 4.607A pdb=" N SER A 502 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER A 502 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N SER A 517 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N VAL A 504 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N SER A 515 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N CYS A 506 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N THR A 513 " --> pdb=" O CYS A 506 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS A 511 " --> pdb=" O ASN B1134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 719 through 720 removed outlier: 3.546A pdb=" N MET B1014 " --> pdb=" O SER B 887 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 887 " --> pdb=" O MET B1014 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 879 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 729 through 730 removed outlier: 6.846A pdb=" N THR B 860 " --> pdb=" O VAL B 750 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER B 752 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS B 858 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 754 " --> pdb=" O VAL B 856 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL B 856 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N CYS B 756 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP B 854 " --> pdb=" O CYS B 756 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU B 758 " --> pdb=" O CYS B 852 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 852 " --> pdb=" O GLU B 758 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN B 760 " --> pdb=" O PHE B 850 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 850 " --> pdb=" O GLN B 760 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 762 " --> pdb=" O ARG B 848 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG B 848 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 729 through 730 removed outlier: 6.846A pdb=" N THR B 860 " --> pdb=" O VAL B 750 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER B 752 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS B 858 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 754 " --> pdb=" O VAL B 856 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL B 856 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N CYS B 756 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ASP B 854 " --> pdb=" O CYS B 756 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU B 758 " --> pdb=" O CYS B 852 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 852 " --> pdb=" O GLU B 758 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN B 760 " --> pdb=" O PHE B 850 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 850 " --> pdb=" O GLN B 760 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 762 " --> pdb=" O ARG B 848 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG B 848 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 904 " --> pdb=" O VAL B 916 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AB4, first strand: chain 'B' and resid 932 through 933 Processing sheet with id=AB5, first strand: chain 'B' and resid 955 through 957 Processing sheet with id=AB6, first strand: chain 'B' and resid 1029 through 1038 removed outlier: 3.598A pdb=" N LEU B1034 " --> pdb=" O CYS B1049 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N CYS B1049 " --> pdb=" O LEU B1034 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU B1036 " --> pdb=" O ARG B1047 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG B1047 " --> pdb=" O LEU B1036 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1070 through 1071 177 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2178 1.34 - 1.47: 1540 1.47 - 1.60: 2897 1.60 - 1.73: 1 1.73 - 1.86: 75 Bond restraints: 6691 Sorted by residual: bond pdb=" N ASN B1134 " pdb=" CA ASN B1134 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.38e+01 bond pdb=" N VAL B 709 " pdb=" CA VAL B 709 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 9.08e+00 bond pdb=" N VAL B1133 " pdb=" CA VAL B1133 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.69e+00 bond pdb=" N VAL B 785 " pdb=" CA VAL B 785 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.14e-02 7.69e+03 7.87e+00 bond pdb=" CB PRO B1107 " pdb=" CG PRO B1107 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.28e+00 ... (remaining 6686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 8877 2.39 - 4.78: 132 4.78 - 7.17: 16 7.17 - 9.56: 7 9.56 - 11.95: 3 Bond angle restraints: 9035 Sorted by residual: angle pdb=" CA PRO B1107 " pdb=" N PRO B1107 " pdb=" CD PRO B1107 " ideal model delta sigma weight residual 112.00 102.51 9.49 1.40e+00 5.10e-01 4.59e+01 angle pdb=" CA CYS A 456 " pdb=" CB CYS A 456 " pdb=" SG CYS A 456 " ideal model delta sigma weight residual 114.40 124.01 -9.61 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CA ASP A 225 " pdb=" C ASP A 225 " pdb=" N PRO A 226 " ideal model delta sigma weight residual 120.58 117.52 3.06 7.40e-01 1.83e+00 1.71e+01 angle pdb=" N PRO B1119 " pdb=" CA PRO B1119 " pdb=" C PRO B1119 " ideal model delta sigma weight residual 114.75 107.89 6.86 1.70e+00 3.46e-01 1.63e+01 angle pdb=" CB MET B 733 " pdb=" CG MET B 733 " pdb=" SD MET B 733 " ideal model delta sigma weight residual 112.70 124.65 -11.95 3.00e+00 1.11e-01 1.59e+01 ... (remaining 9030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.87: 3662 20.87 - 41.74: 392 41.74 - 62.61: 93 62.61 - 83.48: 12 83.48 - 104.35: 8 Dihedral angle restraints: 4167 sinusoidal: 1724 harmonic: 2443 Sorted by residual: dihedral pdb=" CA LYS A 180 " pdb=" C LYS A 180 " pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta harmonic sigma weight residual -180.00 -133.69 -46.31 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CB CYS B1029 " pdb=" SG CYS B1029 " pdb=" SG CYS B1101 " pdb=" CB CYS B1101 " ideal model delta sinusoidal sigma weight residual -86.00 -19.87 -66.13 1 1.00e+01 1.00e-02 5.72e+01 dihedral pdb=" CB CYS A 402 " pdb=" SG CYS A 402 " pdb=" SG CYS A 413 " pdb=" CB CYS A 413 " ideal model delta sinusoidal sigma weight residual 93.00 31.77 61.23 1 1.00e+01 1.00e-02 4.98e+01 ... (remaining 4164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 822 0.055 - 0.109: 155 0.109 - 0.164: 31 0.164 - 0.219: 5 0.219 - 0.273: 4 Chirality restraints: 1017 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG C 3 " pdb=" O4 NAG C 2 " pdb=" C2 NAG C 3 " pdb=" O5 NAG C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.93e+00 chirality pdb=" CA LEU B 981 " pdb=" N LEU B 981 " pdb=" C LEU B 981 " pdb=" CB LEU B 981 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1014 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.352 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG C 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.130 2.00e-02 2.50e+03 1.07e-01 1.42e+02 pdb=" C7 NAG C 1 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.170 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B1106 " 0.077 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO B1107 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO B1107 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B1107 " 0.060 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1115 2.77 - 3.30: 6168 3.30 - 3.83: 10499 3.83 - 4.37: 12293 4.37 - 4.90: 21101 Nonbonded interactions: 51176 Sorted by model distance: nonbonded pdb=" OE2 GLU A 376 " pdb=" OG1 THR A 384 " model vdw 2.235 3.040 nonbonded pdb=" O SER B 898 " pdb=" OG SER B 898 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 797 " pdb=" OE1 GLU B 799 " model vdw 2.258 3.040 nonbonded pdb=" O SER A 495 " pdb=" OG1 THR A 520 " model vdw 2.269 3.040 nonbonded pdb=" O CYS B1029 " pdb=" NH1 ARG B1106 " model vdw 2.283 3.120 ... (remaining 51171 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 0.135 6716 Z= 0.234 Angle : 0.732 11.952 9090 Z= 0.390 Chirality : 0.048 0.273 1017 Planarity : 0.012 0.303 1172 Dihedral : 17.903 104.353 2537 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.41 % Favored : 94.12 % Rotamer: Outliers : 5.73 % Allowed : 23.19 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -2.01 (0.28), residues: 850 helix: -2.40 (0.50), residues: 78 sheet: -0.71 (0.31), residues: 302 loop : -1.55 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.008 0.001 TYR A 459 PHE 0.009 0.001 PHE B 744 TRP 0.009 0.001 TRP B 885 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6691) covalent geometry : angle 0.71999 ( 9035) SS BOND : bond 0.00445 ( 20) SS BOND : angle 1.70615 ( 40) hydrogen bonds : bond 0.25179 ( 168) hydrogen bonds : angle 9.85150 ( 450) link_BETA1-4 : bond 0.00282 ( 2) link_BETA1-4 : angle 1.51395 ( 6) link_NAG-ASN : bond 0.00449 ( 3) link_NAG-ASN : angle 2.44673 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.8246 (m-80) cc_final: 0.7934 (m-80) REVERT: A 498 PHE cc_start: 0.7847 (p90) cc_final: 0.7556 (p90) REVERT: A 525 LYS cc_start: 0.8918 (tttt) cc_final: 0.8607 (tppt) REVERT: A 526 TYR cc_start: 0.8330 (m-80) cc_final: 0.8109 (m-80) REVERT: B 1040 TYR cc_start: 0.8969 (p90) cc_final: 0.8705 (p90) REVERT: B 1043 ASN cc_start: 0.8281 (m-40) cc_final: 0.7973 (m110) REVERT: B 1066 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8827 (p0) REVERT: B 1082 GLN cc_start: 0.8939 (mm110) cc_final: 0.8667 (mp10) outliers start: 42 outliers final: 16 residues processed: 146 average time/residue: 0.0858 time to fit residues: 16.5762 Evaluate side-chains 88 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067409 restraints weight = 17473.719| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.98 r_work: 0.2834 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6716 Z= 0.208 Angle : 0.725 11.312 9090 Z= 0.351 Chirality : 0.046 0.266 1017 Planarity : 0.004 0.050 1172 Dihedral : 10.590 76.162 1033 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.64 % Allowed : 21.83 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.65 (0.28), residues: 850 helix: -1.32 (0.60), residues: 73 sheet: -0.53 (0.31), residues: 298 loop : -1.43 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.011 0.001 TYR A 459 PHE 0.016 0.001 PHE B 826 TRP 0.005 0.001 TRP B 885 HIS 0.007 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6691) covalent geometry : angle 0.70910 ( 9035) SS BOND : bond 0.00390 ( 20) SS BOND : angle 1.29062 ( 40) hydrogen bonds : bond 0.04733 ( 168) hydrogen bonds : angle 6.76005 ( 450) link_BETA1-4 : bond 0.01131 ( 2) link_BETA1-4 : angle 3.43485 ( 6) link_NAG-ASN : bond 0.00654 ( 3) link_NAG-ASN : angle 3.31229 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.9236 (p90) cc_final: 0.8994 (p90) REVERT: A 498 PHE cc_start: 0.8139 (p90) cc_final: 0.7838 (p90) REVERT: A 525 LYS cc_start: 0.8945 (tttt) cc_final: 0.8560 (mtpp) REVERT: B 1008 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8314 (mm-40) REVERT: B 1040 TYR cc_start: 0.9058 (p90) cc_final: 0.8720 (p90) REVERT: B 1043 ASN cc_start: 0.8377 (m-40) cc_final: 0.7924 (m110) REVERT: B 1082 GLN cc_start: 0.9060 (mm110) cc_final: 0.8801 (mm-40) REVERT: B 1084 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8671 (tt0) REVERT: B 1098 MET cc_start: 0.9272 (mmm) cc_final: 0.8605 (mmm) REVERT: B 1109 LEU cc_start: 0.8782 (tp) cc_final: 0.8563 (mt) outliers start: 34 outliers final: 16 residues processed: 102 average time/residue: 0.0731 time to fit residues: 10.3785 Evaluate side-chains 78 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 36 optimal weight: 0.0470 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068549 restraints weight = 17287.389| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.96 r_work: 0.2863 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6716 Z= 0.125 Angle : 0.633 10.067 9090 Z= 0.307 Chirality : 0.044 0.252 1017 Planarity : 0.004 0.040 1172 Dihedral : 7.286 49.090 1019 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.82 % Allowed : 22.24 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.70 (0.28), residues: 850 helix: -1.37 (0.59), residues: 79 sheet: -0.57 (0.31), residues: 295 loop : -1.45 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.014 0.001 TYR B 913 PHE 0.014 0.001 PHE B 826 TRP 0.004 0.001 TRP B 763 HIS 0.007 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6691) covalent geometry : angle 0.61794 ( 9035) SS BOND : bond 0.00332 ( 20) SS BOND : angle 0.98404 ( 40) hydrogen bonds : bond 0.03910 ( 168) hydrogen bonds : angle 5.98315 ( 450) link_BETA1-4 : bond 0.00934 ( 2) link_BETA1-4 : angle 3.94434 ( 6) link_NAG-ASN : bond 0.00466 ( 3) link_NAG-ASN : angle 2.68010 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8868 (tptp) cc_final: 0.8553 (tptp) REVERT: A 375 PHE cc_start: 0.9250 (p90) cc_final: 0.9028 (p90) REVERT: A 525 LYS cc_start: 0.8907 (tttt) cc_final: 0.8521 (mtpp) REVERT: B 818 CYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7883 (p) REVERT: B 926 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 1008 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8303 (mm-40) REVERT: B 1014 MET cc_start: 0.8486 (tmm) cc_final: 0.8265 (tmm) REVERT: B 1040 TYR cc_start: 0.9069 (p90) cc_final: 0.8795 (p90) REVERT: B 1043 ASN cc_start: 0.8344 (m-40) cc_final: 0.7945 (m-40) REVERT: B 1082 GLN cc_start: 0.9083 (mm110) cc_final: 0.8811 (mm-40) REVERT: B 1084 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8682 (tt0) outliers start: 28 outliers final: 18 residues processed: 97 average time/residue: 0.0645 time to fit residues: 9.0175 Evaluate side-chains 90 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1029 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 0.0980 chunk 74 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.100702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067558 restraints weight = 17336.739| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.92 r_work: 0.2841 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6716 Z= 0.141 Angle : 0.630 9.840 9090 Z= 0.302 Chirality : 0.044 0.250 1017 Planarity : 0.004 0.040 1172 Dihedral : 6.144 48.794 1016 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.37 % Allowed : 23.19 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.61 (0.28), residues: 850 helix: -0.92 (0.65), residues: 73 sheet: -0.51 (0.30), residues: 294 loop : -1.46 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1106 TYR 0.010 0.001 TYR B 913 PHE 0.019 0.001 PHE A 498 TRP 0.004 0.001 TRP B 763 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6691) covalent geometry : angle 0.61274 ( 9035) SS BOND : bond 0.00289 ( 20) SS BOND : angle 1.24385 ( 40) hydrogen bonds : bond 0.03514 ( 168) hydrogen bonds : angle 5.59225 ( 450) link_BETA1-4 : bond 0.00983 ( 2) link_BETA1-4 : angle 3.90952 ( 6) link_NAG-ASN : bond 0.00419 ( 3) link_NAG-ASN : angle 2.61818 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.9255 (p90) cc_final: 0.9037 (p90) REVERT: A 525 LYS cc_start: 0.8909 (tttt) cc_final: 0.8491 (mtpp) REVERT: A 543 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6530 (m90) REVERT: B 733 MET cc_start: 0.8633 (mmm) cc_final: 0.8271 (mmm) REVERT: B 818 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 1008 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8347 (mm-40) REVERT: B 1014 MET cc_start: 0.8455 (tmm) cc_final: 0.8122 (tmm) REVERT: B 1040 TYR cc_start: 0.9045 (p90) cc_final: 0.8794 (p90) REVERT: B 1043 ASN cc_start: 0.8336 (m-40) cc_final: 0.7963 (m-40) REVERT: B 1082 GLN cc_start: 0.9069 (mm110) cc_final: 0.8794 (mm-40) REVERT: B 1084 GLN cc_start: 0.9261 (tp-100) cc_final: 0.8679 (tt0) outliers start: 32 outliers final: 21 residues processed: 99 average time/residue: 0.0701 time to fit residues: 9.7610 Evaluate side-chains 92 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1029 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 39 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.101562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068945 restraints weight = 17298.882| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.77 r_work: 0.2869 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6716 Z= 0.123 Angle : 0.616 9.757 9090 Z= 0.297 Chirality : 0.043 0.245 1017 Planarity : 0.004 0.037 1172 Dihedral : 5.677 48.992 1015 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.96 % Allowed : 23.60 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.63 (0.28), residues: 850 helix: -0.96 (0.63), residues: 73 sheet: -0.54 (0.30), residues: 292 loop : -1.45 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.010 0.001 TYR B 913 PHE 0.015 0.001 PHE A 498 TRP 0.003 0.000 TRP B 763 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6691) covalent geometry : angle 0.59675 ( 9035) SS BOND : bond 0.00449 ( 20) SS BOND : angle 1.45196 ( 40) hydrogen bonds : bond 0.03276 ( 168) hydrogen bonds : angle 5.38045 ( 450) link_BETA1-4 : bond 0.00985 ( 2) link_BETA1-4 : angle 3.82820 ( 6) link_NAG-ASN : bond 0.00443 ( 3) link_NAG-ASN : angle 2.59504 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.9230 (p90) cc_final: 0.9018 (p90) REVERT: A 525 LYS cc_start: 0.8874 (tttt) cc_final: 0.8456 (mtpp) REVERT: A 543 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6370 (m170) REVERT: B 758 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 818 CYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7914 (p) REVERT: B 926 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8418 (tm-30) REVERT: B 1008 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8316 (mm-40) REVERT: B 1040 TYR cc_start: 0.9006 (p90) cc_final: 0.8791 (p90) REVERT: B 1043 ASN cc_start: 0.8266 (m-40) cc_final: 0.7879 (m-40) REVERT: B 1082 GLN cc_start: 0.9067 (mm110) cc_final: 0.8790 (mm-40) REVERT: B 1084 GLN cc_start: 0.9224 (tp-100) cc_final: 0.8651 (tt0) outliers start: 29 outliers final: 21 residues processed: 97 average time/residue: 0.0640 time to fit residues: 8.7954 Evaluate side-chains 91 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1029 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064910 restraints weight = 17739.901| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.98 r_work: 0.2786 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6716 Z= 0.244 Angle : 0.655 9.637 9090 Z= 0.324 Chirality : 0.044 0.253 1017 Planarity : 0.004 0.039 1172 Dihedral : 5.848 50.534 1015 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.96 % Allowed : 23.87 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.57 (0.28), residues: 850 helix: -0.56 (0.67), residues: 68 sheet: -0.57 (0.30), residues: 290 loop : -1.42 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1106 TYR 0.009 0.001 TYR B 762 PHE 0.018 0.001 PHE A 203 TRP 0.005 0.001 TRP B 855 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 6691) covalent geometry : angle 0.63674 ( 9035) SS BOND : bond 0.00472 ( 20) SS BOND : angle 1.49082 ( 40) hydrogen bonds : bond 0.03587 ( 168) hydrogen bonds : angle 5.49366 ( 450) link_BETA1-4 : bond 0.00845 ( 2) link_BETA1-4 : angle 3.67685 ( 6) link_NAG-ASN : bond 0.00485 ( 3) link_NAG-ASN : angle 2.64185 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.9281 (p90) cc_final: 0.9027 (p90) REVERT: A 525 LYS cc_start: 0.8847 (tttt) cc_final: 0.8216 (mmmt) REVERT: A 543 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6596 (m170) REVERT: B 926 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8855 (tm-30) REVERT: B 971 ASP cc_start: 0.8707 (t0) cc_final: 0.8472 (t0) REVERT: B 989 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8940 (t) REVERT: B 1008 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8354 (mm-40) REVERT: B 1040 TYR cc_start: 0.9024 (p90) cc_final: 0.8777 (p90) REVERT: B 1082 GLN cc_start: 0.9057 (mm110) cc_final: 0.8796 (mm-40) outliers start: 29 outliers final: 24 residues processed: 85 average time/residue: 0.0632 time to fit residues: 7.8975 Evaluate side-chains 78 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1029 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1084 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.099507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.066534 restraints weight = 17349.851| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.89 r_work: 0.2822 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6716 Z= 0.169 Angle : 0.648 14.278 9090 Z= 0.313 Chirality : 0.044 0.247 1017 Planarity : 0.004 0.038 1172 Dihedral : 5.757 50.530 1015 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.96 % Allowed : 24.42 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.64 (0.28), residues: 850 helix: -1.02 (0.63), residues: 74 sheet: -0.67 (0.29), residues: 297 loop : -1.36 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1106 TYR 0.010 0.001 TYR B 913 PHE 0.012 0.001 PHE A 498 TRP 0.003 0.001 TRP B 763 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6691) covalent geometry : angle 0.63169 ( 9035) SS BOND : bond 0.00426 ( 20) SS BOND : angle 1.29737 ( 40) hydrogen bonds : bond 0.03334 ( 168) hydrogen bonds : angle 5.40954 ( 450) link_BETA1-4 : bond 0.01005 ( 2) link_BETA1-4 : angle 3.78999 ( 6) link_NAG-ASN : bond 0.00451 ( 3) link_NAG-ASN : angle 2.65448 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.9261 (m-80) cc_final: 0.8840 (m-80) REVERT: A 331 LYS cc_start: 0.8915 (tptp) cc_final: 0.8599 (tptp) REVERT: A 375 PHE cc_start: 0.9255 (p90) cc_final: 0.9006 (p90) REVERT: A 525 LYS cc_start: 0.8834 (tttt) cc_final: 0.8222 (mmmt) REVERT: A 543 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6502 (m170) REVERT: B 971 ASP cc_start: 0.8669 (t0) cc_final: 0.8397 (t0) REVERT: B 989 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.8929 (t) REVERT: B 1040 TYR cc_start: 0.9004 (p90) cc_final: 0.8752 (p90) REVERT: B 1098 MET cc_start: 0.9399 (mmm) cc_final: 0.8714 (tpp) outliers start: 29 outliers final: 24 residues processed: 81 average time/residue: 0.0719 time to fit residues: 8.4316 Evaluate side-chains 81 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1115 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.066733 restraints weight = 17276.117| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.76 r_work: 0.2832 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6716 Z= 0.165 Angle : 0.630 13.120 9090 Z= 0.308 Chirality : 0.043 0.251 1017 Planarity : 0.004 0.037 1172 Dihedral : 5.695 50.501 1013 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.23 % Allowed : 23.74 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.61 (0.28), residues: 850 helix: -0.96 (0.63), residues: 74 sheet: -0.63 (0.29), residues: 297 loop : -1.35 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 776 TYR 0.009 0.001 TYR B 913 PHE 0.013 0.001 PHE A 498 TRP 0.002 0.001 TRP B 885 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6691) covalent geometry : angle 0.61411 ( 9035) SS BOND : bond 0.00426 ( 20) SS BOND : angle 1.22319 ( 40) hydrogen bonds : bond 0.03213 ( 168) hydrogen bonds : angle 5.33730 ( 450) link_BETA1-4 : bond 0.01032 ( 2) link_BETA1-4 : angle 3.78634 ( 6) link_NAG-ASN : bond 0.00429 ( 3) link_NAG-ASN : angle 2.54380 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.9269 (m-80) cc_final: 0.8860 (m-80) REVERT: A 331 LYS cc_start: 0.8951 (tptp) cc_final: 0.8623 (tptp) REVERT: A 525 LYS cc_start: 0.8818 (tttt) cc_final: 0.8286 (mmmt) REVERT: A 543 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6413 (m170) REVERT: B 818 CYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7941 (p) REVERT: B 926 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 971 ASP cc_start: 0.8646 (t0) cc_final: 0.8299 (t0) REVERT: B 989 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8923 (t) REVERT: B 1008 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8221 (mm-40) REVERT: B 1040 TYR cc_start: 0.8997 (p90) cc_final: 0.8745 (p90) REVERT: B 1082 GLN cc_start: 0.8993 (mm110) cc_final: 0.8745 (mm-40) outliers start: 31 outliers final: 25 residues processed: 88 average time/residue: 0.0617 time to fit residues: 7.8562 Evaluate side-chains 83 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1115 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066679 restraints weight = 17495.844| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.77 r_work: 0.2830 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6716 Z= 0.168 Angle : 0.653 14.412 9090 Z= 0.319 Chirality : 0.043 0.250 1017 Planarity : 0.004 0.038 1172 Dihedral : 5.730 50.512 1013 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.09 % Allowed : 23.74 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -1.60 (0.28), residues: 850 helix: -0.93 (0.64), residues: 74 sheet: -0.54 (0.31), residues: 280 loop : -1.41 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1106 TYR 0.009 0.001 TYR B 913 PHE 0.013 0.001 PHE A 498 TRP 0.002 0.001 TRP B 763 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6691) covalent geometry : angle 0.63711 ( 9035) SS BOND : bond 0.00386 ( 20) SS BOND : angle 1.21629 ( 40) hydrogen bonds : bond 0.03249 ( 168) hydrogen bonds : angle 5.32262 ( 450) link_BETA1-4 : bond 0.01055 ( 2) link_BETA1-4 : angle 3.79065 ( 6) link_NAG-ASN : bond 0.00420 ( 3) link_NAG-ASN : angle 2.52402 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.9271 (m-80) cc_final: 0.8868 (m-80) REVERT: A 331 LYS cc_start: 0.8951 (tptp) cc_final: 0.8622 (tptp) REVERT: A 525 LYS cc_start: 0.8807 (tttt) cc_final: 0.8290 (mmmt) REVERT: A 543 HIS cc_start: 0.7045 (OUTLIER) cc_final: 0.6395 (m170) REVERT: B 971 ASP cc_start: 0.8639 (t0) cc_final: 0.8290 (t0) REVERT: B 989 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.8930 (t) REVERT: B 1040 TYR cc_start: 0.8993 (p90) cc_final: 0.8739 (p90) outliers start: 30 outliers final: 25 residues processed: 82 average time/residue: 0.0581 time to fit residues: 6.7906 Evaluate side-chains 88 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 0.0970 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.100455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068156 restraints weight = 17002.611| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.72 r_work: 0.2863 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6716 Z= 0.121 Angle : 0.639 15.196 9090 Z= 0.311 Chirality : 0.043 0.244 1017 Planarity : 0.004 0.036 1172 Dihedral : 5.585 50.206 1013 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.41 % Allowed : 24.56 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -1.57 (0.28), residues: 850 helix: -0.92 (0.63), residues: 74 sheet: -0.48 (0.31), residues: 278 loop : -1.40 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 776 TYR 0.010 0.001 TYR B 913 PHE 0.016 0.001 PHE A 498 TRP 0.002 0.000 TRP B 885 HIS 0.006 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6691) covalent geometry : angle 0.62420 ( 9035) SS BOND : bond 0.00349 ( 20) SS BOND : angle 1.06405 ( 40) hydrogen bonds : bond 0.03019 ( 168) hydrogen bonds : angle 5.12485 ( 450) link_BETA1-4 : bond 0.01094 ( 2) link_BETA1-4 : angle 3.79638 ( 6) link_NAG-ASN : bond 0.00434 ( 3) link_NAG-ASN : angle 2.46583 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8946 (tptp) cc_final: 0.8581 (tptp) REVERT: A 525 LYS cc_start: 0.8801 (tttt) cc_final: 0.8286 (mmmt) REVERT: A 543 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.6284 (m170) REVERT: B 971 ASP cc_start: 0.8593 (t0) cc_final: 0.8225 (t0) REVERT: B 989 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.8922 (t) REVERT: B 1008 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8215 (mm-40) REVERT: B 1040 TYR cc_start: 0.8984 (p90) cc_final: 0.8730 (p90) REVERT: B 1082 GLN cc_start: 0.8999 (mm110) cc_final: 0.8756 (mm-40) REVERT: B 1098 MET cc_start: 0.9398 (mmm) cc_final: 0.8800 (tpp) outliers start: 25 outliers final: 20 residues processed: 88 average time/residue: 0.0595 time to fit residues: 7.5546 Evaluate side-chains 79 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 413 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 486 CYS Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 873 ILE Chi-restraints excluded: chain B residue 915 ILE Chi-restraints excluded: chain B residue 931 GLU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.098140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065459 restraints weight = 17489.783| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.77 r_work: 0.2803 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6716 Z= 0.238 Angle : 0.694 13.704 9090 Z= 0.344 Chirality : 0.044 0.254 1017 Planarity : 0.004 0.040 1172 Dihedral : 5.744 50.490 1013 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.27 % Allowed : 24.83 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.55 (0.28), residues: 850 helix: -0.46 (0.68), residues: 68 sheet: -0.55 (0.29), residues: 290 loop : -1.41 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 714 TYR 0.009 0.001 TYR B 762 PHE 0.020 0.001 PHE A 203 TRP 0.008 0.001 TRP B 821 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 6691) covalent geometry : angle 0.67589 ( 9035) SS BOND : bond 0.00500 ( 20) SS BOND : angle 1.68295 ( 40) hydrogen bonds : bond 0.03492 ( 168) hydrogen bonds : angle 5.29011 ( 450) link_BETA1-4 : bond 0.00956 ( 2) link_BETA1-4 : angle 3.66996 ( 6) link_NAG-ASN : bond 0.00433 ( 3) link_NAG-ASN : angle 2.46932 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.47 seconds wall clock time: 31 minutes 6.43 seconds (1866.43 seconds total)