Starting phenix.real_space_refine on Thu Jul 2 06:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.map" model { file = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2026/7u7n_26382.cif" } resolution = 3.47 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= 0.002 sd= 0.027 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 31 5.16 5 C 4646 2.51 5 N 1221 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7284 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1548 Classifications: {'peptide': 195} Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 173} Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2385 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 281} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1582 Classifications: {'peptide': 200} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 177} Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.61, per 1000 atoms: 0.22 Number of scatterers: 7284 At special positions: 0 Unit cell: (96.485, 123.333, 114.943, 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 31 16.00 O 1386 8.00 N 1221 7.00 C 4646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 89 " 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 301 " - " ASN A 51 " " NAG A 302 " - " ASN A 76 " " NAG B 401 " - " ASN B 131 " " NAG B 402 " - " ASN B 157 " " NAG E 1 " - " ASN B 43 " " NAG F 1 " - " ASN B 83 " " NAG G 1 " - " ASN B 61 " " NAG H 1 " - " ASN C 105 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 319.8 milliseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 17 sheets defined 21.3% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 215 through 220 removed outlier: 4.104A pdb=" N VAL B 220 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.854A pdb=" N LYS B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'D' and resid 43 through 73 removed outlier: 3.724A pdb=" N VAL D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.897A pdb=" N LEU D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.672A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 114 Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.588A pdb=" N THR D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 159 removed outlier: 3.502A pdb=" N GLY D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 196 through 226 removed outlier: 3.546A pdb=" N LYS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 3.505A pdb=" N LEU A 66 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 69 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 82 removed outlier: 3.505A pdb=" N LEU A 66 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 69 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 139 removed outlier: 7.037A pdb=" N GLY A 134 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA A 152 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP A 136 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 150 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.521A pdb=" N VAL B 47 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 44 " --> pdb=" O PHE B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.531A pdb=" N VAL B 38 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 123 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS B 103 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY B 117 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 101 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR B 119 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 99 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.739A pdb=" N GLU B 163 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 200 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.739A pdb=" N GLU B 163 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 232 removed outlier: 4.030A pdb=" N LEU B 228 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR B 243 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 230 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS B 241 " --> pdb=" O VAL B 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.627A pdb=" N ARG B 300 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 32 through 39 removed outlier: 4.715A pdb=" N SER C 38 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA C 43 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.706A pdb=" N SER C 61 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 133 through 141 removed outlier: 5.761A pdb=" N GLY C 134 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU C 150 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 178 through 183 removed outlier: 5.638A pdb=" N ARG C 179 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR C 169 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY C 181 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE C 167 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP C 166 " --> pdb=" O ALA C 204 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 747 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: 0.92 Time building geometry restraints manager: 0.75 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: 2308 1.34 - 1.46: 1793 1.46 - 1.58: 3342 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 7486 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" CB PRO A 93 " pdb=" CG PRO A 93 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.81e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 ... (remaining 7481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 10072 2.56 - 5.13: 126 5.13 - 7.69: 13 7.69 - 10.26: 2 10.26 - 12.82: 1 Bond angle restraints: 10214 Sorted by residual: angle pdb=" CA LYS B 219 " pdb=" CB LYS B 219 " pdb=" CG LYS B 219 " ideal model delta sigma weight residual 114.10 126.92 -12.82 2.00e+00 2.50e-01 4.11e+01 angle pdb=" N ASN B 83 " pdb=" CA ASN B 83 " pdb=" CB ASN B 83 " ideal model delta sigma weight residual 111.65 105.69 5.96 1.40e+00 5.10e-01 1.81e+01 angle pdb=" C ASN B 83 " pdb=" CA ASN B 83 " pdb=" CB ASN B 83 " ideal model delta sigma weight residual 111.35 117.43 -6.08 1.72e+00 3.38e-01 1.25e+01 angle pdb=" CB LYS B 219 " pdb=" CG LYS B 219 " pdb=" CD LYS B 219 " ideal model delta sigma weight residual 111.30 119.26 -7.96 2.30e+00 1.89e-01 1.20e+01 angle pdb=" N LYS B 219 " pdb=" CA LYS B 219 " pdb=" CB LYS B 219 " ideal model delta sigma weight residual 111.01 105.97 5.04 1.56e+00 4.11e-01 1.04e+01 ... (remaining 10209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3698 17.13 - 34.27: 510 34.27 - 51.40: 119 51.40 - 68.53: 35 68.53 - 85.67: 14 Dihedral angle restraints: 4376 sinusoidal: 1792 harmonic: 2584 Sorted by residual: dihedral pdb=" CA TYR B 218 " pdb=" C TYR B 218 " pdb=" N LYS B 219 " pdb=" CA LYS B 219 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ILE B 82 " pdb=" C ILE B 82 " pdb=" N ASN B 83 " pdb=" CA ASN B 83 " ideal model delta harmonic sigma weight residual 180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASP C 93 " pdb=" CB ASP C 93 " pdb=" CG ASP C 93 " pdb=" OD1 ASP C 93 " ideal model delta sinusoidal sigma weight residual -30.00 -88.00 58.00 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 973 0.055 - 0.111: 164 0.111 - 0.166: 33 0.166 - 0.222: 0 0.222 - 0.277: 4 Chirality restraints: 1174 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1171 not shown) Planarity restraints: 1291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 92 " -0.055 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 93 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.025 2.00e-02 2.50e+03 2.26e-02 6.39e+00 pdb=" CG ASN B 83 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 26 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 27 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.029 5.00e-02 4.00e+02 ... (remaining 1288 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 249 2.71 - 3.26: 6841 3.26 - 3.81: 11632 3.81 - 4.35: 13347 4.35 - 4.90: 22640 Nonbonded interactions: 54709 Sorted by model distance: nonbonded pdb=" O LEU B 124 " pdb=" OG1 THR B 152 " model vdw 2.164 3.040 nonbonded pdb=" O THR C 83 " pdb=" OG SER C 86 " model vdw 2.228 3.040 nonbonded pdb=" O TYR B 261 " pdb=" OG SER B 270 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASN B 61 " pdb=" N ALA B 62 " model vdw 2.265 3.120 nonbonded pdb=" OG SER B 229 " pdb=" OG1 THR B 243 " model vdw 2.286 3.040 ... (remaining 54704 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 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 0.084 7510 Z= 0.177 Angle : 0.768 19.966 10278 Z= 0.347 Chirality : 0.047 0.277 1174 Planarity : 0.005 0.081 1283 Dihedral : 17.191 85.666 2674 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.89 % Allowed : 27.90 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.04 (0.29), residues: 874 helix: 2.48 (0.42), residues: 155 sheet: 1.04 (0.32), residues: 273 loop : -0.14 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 55 TYR 0.016 0.001 TYR C 40 PHE 0.019 0.001 PHE D 153 TRP 0.017 0.001 TRP A 115 HIS 0.002 0.001 HIS D 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 7486) covalent geometry : angle 0.68730 / 0.33 (10214) SS BOND : bond 0.00318 / 0.20 ( 8) SS BOND : angle 0.79861 / 0.52 ( 16) hydrogen bonds : bond 0.21395 / 14.25 ( 275) hydrogen bonds : angle 7.98252 / 5.84 ( 747) link_ALPHA1-6 : bond 0.00378 / 0.24 ( 1) link_ALPHA1-6 : angle 1.33063 / 0.73 ( 3) link_BETA1-4 : bond 0.01160 / 0.71 ( 7) link_BETA1-4 : angle 4.69606 / 2.70 ( 21) link_NAG-ASN : bond 0.00731 / 0.57 ( 8) link_NAG-ASN : angle 5.64302 / 2.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 30 TYR cc_start: 0.8282 (p90) cc_final: 0.8081 (p90) REVERT: B 116 TYR cc_start: 0.8433 (t80) cc_final: 0.8091 (t80) outliers start: 7 outliers final: 5 residues processed: 200 average time/residue: 0.1054 time to fit residues: 26.7167 Evaluate side-chains 202 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain C residue 99 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 GLN B 271 GLN C 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120088 restraints weight = 12158.063| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.27 r_work: 0.3304 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7510 Z= 0.135 Angle : 0.681 17.772 10278 Z= 0.317 Chirality : 0.043 0.160 1174 Planarity : 0.005 0.054 1283 Dihedral : 6.155 77.198 970 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.20 % Allowed : 23.44 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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 (0.29), residues: 874 helix: 2.46 (0.42), residues: 158 sheet: 1.05 (0.30), residues: 283 loop : -0.24 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 55 TYR 0.015 0.002 TYR C 40 PHE 0.011 0.001 PHE B 158 TRP 0.008 0.001 TRP B 269 HIS 0.004 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7486) covalent geometry : angle 0.61496 / 0.30 (10214) SS BOND : bond 0.00297 / 0.20 ( 8) SS BOND : angle 0.93161 / 0.51 ( 16) hydrogen bonds : bond 0.04571 / 3.03 ( 275) hydrogen bonds : angle 5.51585 / 4.05 ( 747) link_ALPHA1-6 : bond 0.00417 / 0.26 ( 1) link_ALPHA1-6 : angle 1.55780 / 0.86 ( 3) link_BETA1-4 : bond 0.01047 / 0.65 ( 7) link_BETA1-4 : angle 4.13246 / 2.41 ( 21) link_NAG-ASN : bond 0.00588 / 0.45 ( 8) link_NAG-ASN : angle 4.65724 / 1.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 THR cc_start: 0.8288 (m) cc_final: 0.8087 (p) REVERT: B 54 CYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7442 (t) REVERT: B 105 ILE cc_start: 0.8478 (pt) cc_final: 0.8266 (pt) REVERT: B 114 ASN cc_start: 0.8295 (t0) cc_final: 0.8070 (t0) REVERT: B 116 TYR cc_start: 0.8437 (t80) cc_final: 0.7955 (t80) REVERT: C 209 THR cc_start: 0.8278 (p) cc_final: 0.8028 (p) REVERT: D 43 LEU cc_start: 0.8526 (mt) cc_final: 0.8087 (mp) REVERT: D 154 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7940 (mt0) outliers start: 33 outliers final: 20 residues processed: 210 average time/residue: 0.1049 time to fit residues: 28.3574 Evaluate side-chains 219 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120030 restraints weight = 12103.475| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.27 r_work: 0.3307 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7510 Z= 0.132 Angle : 0.647 15.753 10278 Z= 0.300 Chirality : 0.043 0.156 1174 Planarity : 0.005 0.054 1283 Dihedral : 5.039 72.540 958 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.82 % Allowed : 24.20 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.02 (0.29), residues: 874 helix: 2.51 (0.42), residues: 158 sheet: 1.06 (0.30), residues: 283 loop : -0.26 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 55 TYR 0.016 0.002 TYR C 40 PHE 0.015 0.001 PHE C 121 TRP 0.007 0.001 TRP B 269 HIS 0.003 0.001 HIS D 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7486) covalent geometry : angle 0.58972 / 0.29 (10214) SS BOND : bond 0.00273 / 0.20 ( 8) SS BOND : angle 0.80118 / 0.52 ( 16) hydrogen bonds : bond 0.04203 / 2.75 ( 275) hydrogen bonds : angle 4.93160 / 3.60 ( 747) link_ALPHA1-6 : bond 0.00464 / 0.29 ( 1) link_ALPHA1-6 : angle 1.29359 / 0.73 ( 3) link_BETA1-4 : bond 0.01177 / 0.72 ( 7) link_BETA1-4 : angle 4.05268 / 2.33 ( 21) link_NAG-ASN : bond 0.00657 / 0.51 ( 8) link_NAG-ASN : angle 4.04498 / 1.58 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8004 (p90) cc_final: 0.7650 (p90) REVERT: B 45 THR cc_start: 0.8320 (m) cc_final: 0.8042 (p) REVERT: B 54 CYS cc_start: 0.7726 (t) cc_final: 0.7423 (t) REVERT: B 114 ASN cc_start: 0.8345 (t0) cc_final: 0.8090 (t0) REVERT: B 116 TYR cc_start: 0.8412 (t80) cc_final: 0.8033 (t80) REVERT: C 209 THR cc_start: 0.8290 (p) cc_final: 0.7867 (p) REVERT: D 43 LEU cc_start: 0.8498 (mt) cc_final: 0.8023 (mp) REVERT: D 67 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8204 (mtp180) REVERT: D 105 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7600 (mtt90) REVERT: D 154 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7914 (mt0) outliers start: 30 outliers final: 23 residues processed: 214 average time/residue: 0.0978 time to fit residues: 27.1251 Evaluate side-chains 224 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119155 restraints weight = 12300.918| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.29 r_work: 0.3285 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7510 Z= 0.163 Angle : 0.661 14.817 10278 Z= 0.309 Chirality : 0.043 0.152 1174 Planarity : 0.005 0.055 1283 Dihedral : 4.969 63.687 958 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.20 % Allowed : 25.99 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.00 (0.28), residues: 874 helix: 2.45 (0.42), residues: 158 sheet: 1.08 (0.29), residues: 283 loop : -0.28 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 216 TYR 0.027 0.002 TYR A 205 PHE 0.015 0.001 PHE C 121 TRP 0.007 0.001 TRP C 155 HIS 0.003 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 7486) covalent geometry : angle 0.60828 / 0.30 (10214) SS BOND : bond 0.00303 / 0.20 ( 8) SS BOND : angle 0.93027 / 0.60 ( 16) hydrogen bonds : bond 0.04185 / 2.71 ( 275) hydrogen bonds : angle 4.82356 / 3.51 ( 747) link_ALPHA1-6 : bond 0.00447 / 0.28 ( 1) link_ALPHA1-6 : angle 1.31921 / 0.74 ( 3) link_BETA1-4 : bond 0.01091 / 0.68 ( 7) link_BETA1-4 : angle 3.99605 / 2.31 ( 21) link_NAG-ASN : bond 0.00642 / 0.50 ( 8) link_NAG-ASN : angle 3.85999 / 1.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8021 (p90) cc_final: 0.7694 (p90) REVERT: B 45 THR cc_start: 0.8269 (m) cc_final: 0.8043 (p) REVERT: B 54 CYS cc_start: 0.7777 (t) cc_final: 0.7476 (t) REVERT: B 116 TYR cc_start: 0.8444 (t80) cc_final: 0.8036 (t80) REVERT: C 209 THR cc_start: 0.8309 (p) cc_final: 0.8076 (p) REVERT: D 43 LEU cc_start: 0.8501 (mt) cc_final: 0.8019 (mp) REVERT: D 154 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7941 (mt0) outliers start: 33 outliers final: 27 residues processed: 216 average time/residue: 0.0948 time to fit residues: 26.3298 Evaluate side-chains 232 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 0.0000 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 63 optimal weight: 0.0570 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 overall best weight: 0.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121058 restraints weight = 12159.246| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.27 r_work: 0.3322 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7510 Z= 0.107 Angle : 0.632 14.226 10278 Z= 0.292 Chirality : 0.042 0.163 1174 Planarity : 0.004 0.053 1283 Dihedral : 4.570 53.140 958 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.57 % Allowed : 26.75 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.02 (0.29), residues: 874 helix: 2.62 (0.42), residues: 158 sheet: 0.98 (0.30), residues: 285 loop : -0.25 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 62 TYR 0.020 0.002 TYR A 205 PHE 0.014 0.001 PHE D 153 TRP 0.007 0.001 TRP A 115 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7486) covalent geometry : angle 0.58111 / 0.28 (10214) SS BOND : bond 0.00256 / 0.19 ( 8) SS BOND : angle 0.76349 / 0.49 ( 16) hydrogen bonds : bond 0.03580 / 2.31 ( 275) hydrogen bonds : angle 4.59257 / 3.33 ( 747) link_ALPHA1-6 : bond 0.00495 / 0.31 ( 1) link_ALPHA1-6 : angle 1.23450 / 0.68 ( 3) link_BETA1-4 : bond 0.01075 / 0.66 ( 7) link_BETA1-4 : angle 3.85143 / 2.22 ( 21) link_NAG-ASN : bond 0.00592 / 0.46 ( 8) link_NAG-ASN : angle 3.69083 / 1.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7991 (p90) cc_final: 0.7725 (p90) REVERT: A 183 LEU cc_start: 0.8351 (mm) cc_final: 0.8003 (mp) REVERT: A 214 GLU cc_start: 0.7242 (pp20) cc_final: 0.6798 (pp20) REVERT: B 45 THR cc_start: 0.8273 (m) cc_final: 0.8044 (p) REVERT: B 54 CYS cc_start: 0.7730 (t) cc_final: 0.7471 (t) REVERT: B 64 TYR cc_start: 0.8541 (m-80) cc_final: 0.7819 (m-80) REVERT: B 116 TYR cc_start: 0.8390 (t80) cc_final: 0.7980 (t80) REVERT: C 62 PHE cc_start: 0.8182 (m-80) cc_final: 0.7961 (m-10) REVERT: C 118 PHE cc_start: 0.8014 (m-80) cc_final: 0.7651 (m-80) REVERT: C 209 THR cc_start: 0.8316 (p) cc_final: 0.7821 (p) REVERT: D 43 LEU cc_start: 0.8409 (mt) cc_final: 0.7886 (mp) REVERT: D 67 ARG cc_start: 0.8429 (mtp180) cc_final: 0.8037 (mtp180) REVERT: D 105 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7537 (mtt90) REVERT: D 154 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: D 224 LEU cc_start: 0.8653 (mt) cc_final: 0.8367 (tp) outliers start: 28 outliers final: 23 residues processed: 217 average time/residue: 0.0902 time to fit residues: 25.3023 Evaluate side-chains 226 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 68 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120737 restraints weight = 12268.993| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.29 r_work: 0.3313 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7510 Z= 0.107 Angle : 0.624 13.718 10278 Z= 0.288 Chirality : 0.042 0.155 1174 Planarity : 0.004 0.053 1283 Dihedral : 4.254 38.683 958 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.20 % Allowed : 25.61 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.05 (0.29), residues: 874 helix: 2.65 (0.42), residues: 158 sheet: 1.01 (0.30), residues: 285 loop : -0.25 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 94 TYR 0.017 0.001 TYR A 205 PHE 0.014 0.001 PHE D 153 TRP 0.008 0.001 TRP A 115 HIS 0.004 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7486) covalent geometry : angle 0.57575 / 0.28 (10214) SS BOND : bond 0.00379 / 0.26 ( 8) SS BOND : angle 0.87837 / 0.59 ( 16) hydrogen bonds : bond 0.03481 / 2.23 ( 275) hydrogen bonds : angle 4.49686 / 3.26 ( 747) link_ALPHA1-6 : bond 0.00502 / 0.31 ( 1) link_ALPHA1-6 : angle 1.26251 / 0.70 ( 3) link_BETA1-4 : bond 0.01023 / 0.63 ( 7) link_BETA1-4 : angle 3.73962 / 2.15 ( 21) link_NAG-ASN : bond 0.00520 / 0.40 ( 8) link_NAG-ASN : angle 3.58465 / 1.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7993 (p90) cc_final: 0.7774 (p90) REVERT: A 183 LEU cc_start: 0.8392 (mm) cc_final: 0.8031 (mp) REVERT: A 214 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6797 (pp20) REVERT: B 45 THR cc_start: 0.8266 (m) cc_final: 0.8031 (p) REVERT: B 54 CYS cc_start: 0.7762 (t) cc_final: 0.7469 (t) REVERT: B 116 TYR cc_start: 0.8403 (t80) cc_final: 0.8019 (t80) REVERT: C 62 PHE cc_start: 0.8232 (m-80) cc_final: 0.8002 (m-10) REVERT: C 118 PHE cc_start: 0.8019 (m-80) cc_final: 0.7650 (m-80) REVERT: C 209 THR cc_start: 0.8294 (p) cc_final: 0.7857 (p) REVERT: D 43 LEU cc_start: 0.8395 (mt) cc_final: 0.7957 (mp) REVERT: D 154 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7904 (mt0) outliers start: 33 outliers final: 24 residues processed: 215 average time/residue: 0.1024 time to fit residues: 28.2739 Evaluate side-chains 227 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 224 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117891 restraints weight = 12213.477| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.31 r_work: 0.3276 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7510 Z= 0.214 Angle : 0.678 13.290 10278 Z= 0.320 Chirality : 0.045 0.158 1174 Planarity : 0.005 0.053 1283 Dihedral : 4.117 19.898 955 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.20 % Allowed : 25.35 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 0.97 (0.29), residues: 874 helix: 2.44 (0.42), residues: 158 sheet: 1.08 (0.30), residues: 284 loop : -0.33 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 216 TYR 0.018 0.002 TYR C 40 PHE 0.019 0.002 PHE A 166 TRP 0.011 0.001 TRP A 176 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 7486) covalent geometry : angle 0.63358 / 0.31 (10214) SS BOND : bond 0.00231 / 0.15 ( 8) SS BOND : angle 1.05827 / 0.74 ( 16) hydrogen bonds : bond 0.04345 / 2.81 ( 275) hydrogen bonds : angle 4.69729 / 3.39 ( 747) link_ALPHA1-6 : bond 0.00436 / 0.27 ( 1) link_ALPHA1-6 : angle 1.35809 / 0.78 ( 3) link_BETA1-4 : bond 0.00963 / 0.61 ( 7) link_BETA1-4 : angle 3.78232 / 2.19 ( 21) link_NAG-ASN : bond 0.00602 / 0.46 ( 8) link_NAG-ASN : angle 3.54697 / 1.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8456 (m) cc_final: 0.8247 (p) REVERT: A 168 TYR cc_start: 0.8010 (p90) cc_final: 0.7758 (p90) REVERT: A 179 LEU cc_start: 0.8406 (mt) cc_final: 0.8124 (mp) REVERT: A 214 GLU cc_start: 0.7236 (pp20) cc_final: 0.6745 (pp20) REVERT: B 45 THR cc_start: 0.8316 (m) cc_final: 0.8041 (p) REVERT: B 54 CYS cc_start: 0.7854 (t) cc_final: 0.7558 (t) REVERT: B 116 TYR cc_start: 0.8446 (t80) cc_final: 0.8051 (t80) REVERT: B 146 TRP cc_start: 0.7031 (p90) cc_final: 0.6485 (p90) REVERT: C 62 PHE cc_start: 0.8291 (m-80) cc_final: 0.8058 (m-10) REVERT: C 118 PHE cc_start: 0.8068 (m-80) cc_final: 0.7747 (m-80) REVERT: C 209 THR cc_start: 0.8317 (p) cc_final: 0.8063 (p) REVERT: D 43 LEU cc_start: 0.8505 (mt) cc_final: 0.7994 (mp) REVERT: D 91 SER cc_start: 0.8967 (m) cc_final: 0.8743 (m) REVERT: D 154 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7954 (mt0) outliers start: 33 outliers final: 31 residues processed: 217 average time/residue: 0.0937 time to fit residues: 26.2884 Evaluate side-chains 238 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119652 restraints weight = 12278.164| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.28 r_work: 0.3299 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7510 Z= 0.132 Angle : 0.648 13.328 10278 Z= 0.305 Chirality : 0.043 0.170 1174 Planarity : 0.004 0.053 1283 Dihedral : 4.046 16.800 955 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.08 % Allowed : 26.62 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 0.99 (0.29), residues: 874 helix: 2.60 (0.42), residues: 158 sheet: 0.98 (0.30), residues: 289 loop : -0.30 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 105 TYR 0.016 0.002 TYR C 40 PHE 0.015 0.001 PHE D 153 TRP 0.007 0.001 TRP D 129 HIS 0.007 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7486) covalent geometry : angle 0.60318 / 0.30 (10214) SS BOND : bond 0.00226 / 0.17 ( 8) SS BOND : angle 0.90650 / 0.61 ( 16) hydrogen bonds : bond 0.03877 / 2.50 ( 275) hydrogen bonds : angle 4.58809 / 3.30 ( 747) link_ALPHA1-6 : bond 0.00484 / 0.30 ( 1) link_ALPHA1-6 : angle 1.27457 / 0.71 ( 3) link_BETA1-4 : bond 0.01033 / 0.64 ( 7) link_BETA1-4 : angle 3.70651 / 2.14 ( 21) link_NAG-ASN : bond 0.00525 / 0.41 ( 8) link_NAG-ASN : angle 3.48556 / 1.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8361 (mt) cc_final: 0.8103 (mp) REVERT: A 183 LEU cc_start: 0.8432 (mm) cc_final: 0.8081 (mp) REVERT: A 214 GLU cc_start: 0.7217 (pp20) cc_final: 0.6674 (pp20) REVERT: B 45 THR cc_start: 0.8319 (m) cc_final: 0.8023 (p) REVERT: B 54 CYS cc_start: 0.7842 (t) cc_final: 0.7548 (t) REVERT: B 64 TYR cc_start: 0.8588 (m-80) cc_final: 0.8025 (m-80) REVERT: B 116 TYR cc_start: 0.8428 (t80) cc_final: 0.8055 (t80) REVERT: C 118 PHE cc_start: 0.8051 (m-80) cc_final: 0.7750 (m-80) REVERT: C 209 THR cc_start: 0.8289 (p) cc_final: 0.7883 (p) REVERT: D 43 LEU cc_start: 0.8438 (mt) cc_final: 0.7971 (mp) REVERT: D 67 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8227 (mtp180) REVERT: D 91 SER cc_start: 0.8915 (m) cc_final: 0.8693 (m) REVERT: D 154 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: D 224 LEU cc_start: 0.8661 (mt) cc_final: 0.8366 (tp) outliers start: 32 outliers final: 29 residues processed: 222 average time/residue: 0.0949 time to fit residues: 27.1845 Evaluate side-chains 239 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.153404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117836 restraints weight = 12126.294| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.27 r_work: 0.3280 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7510 Z= 0.189 Angle : 0.674 12.831 10278 Z= 0.320 Chirality : 0.044 0.155 1174 Planarity : 0.005 0.054 1283 Dihedral : 4.199 16.492 955 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.95 % Allowed : 26.88 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.04 (0.29), residues: 874 helix: 2.75 (0.41), residues: 152 sheet: 1.06 (0.30), residues: 286 loop : -0.30 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 105 TYR 0.017 0.002 TYR C 40 PHE 0.025 0.002 PHE C 62 TRP 0.008 0.001 TRP D 97 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 7486) covalent geometry : angle 0.63108 / 0.31 (10214) SS BOND : bond 0.00336 / 0.21 ( 8) SS BOND : angle 1.05102 / 0.72 ( 16) hydrogen bonds : bond 0.04281 / 2.77 ( 275) hydrogen bonds : angle 4.70967 / 3.39 ( 747) link_ALPHA1-6 : bond 0.00446 / 0.28 ( 1) link_ALPHA1-6 : angle 1.35572 / 0.78 ( 3) link_BETA1-4 : bond 0.01034 / 0.64 ( 7) link_BETA1-4 : angle 3.74259 / 2.18 ( 21) link_NAG-ASN : bond 0.00579 / 0.44 ( 8) link_NAG-ASN : angle 3.45254 / 1.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7912 (m-80) cc_final: 0.7702 (m-80) REVERT: A 179 LEU cc_start: 0.8470 (mt) cc_final: 0.8226 (mp) REVERT: A 214 GLU cc_start: 0.7239 (pp20) cc_final: 0.6691 (pp20) REVERT: B 45 THR cc_start: 0.8302 (m) cc_final: 0.8013 (p) REVERT: B 54 CYS cc_start: 0.7836 (t) cc_final: 0.7540 (t) REVERT: B 64 TYR cc_start: 0.8576 (m-80) cc_final: 0.8155 (m-80) REVERT: B 116 TYR cc_start: 0.8453 (t80) cc_final: 0.8040 (t80) REVERT: B 146 TRP cc_start: 0.6948 (p90) cc_final: 0.6437 (p90) REVERT: C 62 PHE cc_start: 0.8229 (m-80) cc_final: 0.7969 (m-10) REVERT: C 118 PHE cc_start: 0.8064 (m-80) cc_final: 0.7740 (m-80) REVERT: C 209 THR cc_start: 0.8285 (p) cc_final: 0.8012 (p) REVERT: D 43 LEU cc_start: 0.8480 (mt) cc_final: 0.7980 (mp) REVERT: D 91 SER cc_start: 0.8936 (m) cc_final: 0.8698 (m) REVERT: D 154 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: D 225 SER cc_start: 0.8684 (p) cc_final: 0.8480 (p) outliers start: 31 outliers final: 29 residues processed: 216 average time/residue: 0.0925 time to fit residues: 25.7945 Evaluate side-chains 235 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 0 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.155659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120102 restraints weight = 12074.149| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.27 r_work: 0.3310 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7510 Z= 0.116 Angle : 0.650 12.777 10278 Z= 0.307 Chirality : 0.043 0.171 1174 Planarity : 0.004 0.053 1283 Dihedral : 4.042 20.830 955 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.18 % Allowed : 28.28 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.05 (0.29), residues: 874 helix: 2.93 (0.42), residues: 152 sheet: 0.94 (0.30), residues: 288 loop : -0.27 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 105 TYR 0.015 0.002 TYR C 40 PHE 0.022 0.001 PHE C 62 TRP 0.009 0.001 TRP D 97 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7486) covalent geometry : angle 0.60782 / 0.30 (10214) SS BOND : bond 0.00333 / 0.23 ( 8) SS BOND : angle 0.89146 / 0.60 ( 16) hydrogen bonds : bond 0.03713 / 2.39 ( 275) hydrogen bonds : angle 4.54500 / 3.26 ( 747) link_ALPHA1-6 : bond 0.00512 / 0.32 ( 1) link_ALPHA1-6 : angle 1.25469 / 0.70 ( 3) link_BETA1-4 : bond 0.01048 / 0.64 ( 7) link_BETA1-4 : angle 3.61244 / 2.11 ( 21) link_NAG-ASN : bond 0.00494 / 0.38 ( 8) link_NAG-ASN : angle 3.37262 / 1.32 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8083 (mtpp) REVERT: A 119 PHE cc_start: 0.7911 (m-80) cc_final: 0.7658 (m-80) REVERT: A 120 VAL cc_start: 0.8258 (m) cc_final: 0.8020 (p) REVERT: A 179 LEU cc_start: 0.8316 (mt) cc_final: 0.8079 (mm) REVERT: A 214 GLU cc_start: 0.7208 (pp20) cc_final: 0.6633 (pp20) REVERT: B 45 THR cc_start: 0.8278 (m) cc_final: 0.7988 (p) REVERT: B 54 CYS cc_start: 0.7821 (t) cc_final: 0.7531 (t) REVERT: B 64 TYR cc_start: 0.8538 (m-80) cc_final: 0.8015 (m-80) REVERT: B 116 TYR cc_start: 0.8406 (t80) cc_final: 0.7999 (t80) REVERT: C 62 PHE cc_start: 0.8214 (m-80) cc_final: 0.7930 (m-10) REVERT: C 118 PHE cc_start: 0.8035 (m-80) cc_final: 0.7734 (m-80) REVERT: C 209 THR cc_start: 0.8266 (p) cc_final: 0.7850 (p) REVERT: D 43 LEU cc_start: 0.8358 (mt) cc_final: 0.7882 (mp) REVERT: D 91 SER cc_start: 0.8896 (m) cc_final: 0.8675 (m) REVERT: D 154 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: D 224 LEU cc_start: 0.8643 (mt) cc_final: 0.8356 (tp) REVERT: D 225 SER cc_start: 0.8729 (p) cc_final: 0.8512 (p) outliers start: 25 outliers final: 22 residues processed: 220 average time/residue: 0.0954 time to fit residues: 26.8492 Evaluate side-chains 228 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 74 optimal weight: 0.0970 chunk 20 optimal weight: 0.0070 chunk 2 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.154714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118980 restraints weight = 12217.859| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.28 r_work: 0.3297 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7510 Z= 0.134 Angle : 0.657 12.235 10278 Z= 0.310 Chirality : 0.043 0.158 1174 Planarity : 0.004 0.053 1283 Dihedral : 4.069 20.923 955 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.95 % Allowed : 27.64 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.10 (0.29), residues: 874 helix: 2.91 (0.42), residues: 152 sheet: 1.04 (0.30), residues: 285 loop : -0.26 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 105 TYR 0.015 0.002 TYR C 40 PHE 0.035 0.002 PHE A 166 TRP 0.011 0.001 TRP D 97 HIS 0.004 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7486) covalent geometry : angle 0.61693 / 0.30 (10214) SS BOND : bond 0.00337 / 0.23 ( 8) SS BOND : angle 0.97774 / 0.66 ( 16) hydrogen bonds : bond 0.03798 / 2.44 ( 275) hydrogen bonds : angle 4.54030 / 3.27 ( 747) link_ALPHA1-6 : bond 0.00486 / 0.30 ( 1) link_ALPHA1-6 : angle 1.31606 / 0.74 ( 3) link_BETA1-4 : bond 0.01012 / 0.62 ( 7) link_BETA1-4 : angle 3.58389 / 2.09 ( 21) link_NAG-ASN : bond 0.00527 / 0.41 ( 8) link_NAG-ASN : angle 3.29405 / 1.29 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.71 seconds wall clock time: 31 minutes 20.31 seconds (1880.31 seconds total)