Starting phenix.real_space_refine on Tue Mar 3 17:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u7n_26382/03_2026/7u7n_26382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u7n_26382/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u7n_26382/03_2026/7u7n_26382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u7n_26382/03_2026/7u7n_26382.map" model { file = "/net/cci-nas-00/data/ceres_data/7u7n_26382/03_2026/7u7n_26382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u7n_26382/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.90, per 1000 atoms: 0.26 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: 0.95 Conformation dependent library (CDL) restraints added in 297.6 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: 0.33 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: 0.95 Time building geometry restraints manager: 1.12 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 - 23.94: 4233 23.94 - 47.87: 374 47.87 - 71.80: 52 71.80 - 95.74: 32 95.74 - 119.67: 13 Dihedral angle restraints: 4704 sinusoidal: 2120 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=" C2 MAN F 4 " pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual -57.62 62.05 -119.67 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 4701 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: 1.550 Set stop_for_unknowns flag: 0.010 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.890 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 19.360 119.673 3002 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 covalent geometry : bond 0.00383 ( 7486) covalent geometry : angle 0.68730 (10214) SS BOND : bond 0.00318 ( 8) SS BOND : angle 0.79861 ( 16) hydrogen bonds : bond 0.21395 ( 275) hydrogen bonds : angle 7.98252 ( 747) link_ALPHA1-6 : bond 0.00378 ( 1) link_ALPHA1-6 : angle 1.33063 ( 3) link_BETA1-4 : bond 0.01160 ( 7) link_BETA1-4 : angle 4.69606 ( 21) link_NAG-ASN : bond 0.00731 ( 8) link_NAG-ASN : angle 5.64302 ( 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 : 0.257 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: 0.1117 time to fit residues: 28.0106 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 : 0.215 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3982 r_free = 0.3982 target = 0.155307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120144 restraints weight = 12146.091| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.27 r_work: 0.3304 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0853 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= 0.138 Angle : 0.711 18.225 10278 Z= 0.327 Chirality : 0.044 0.161 1174 Planarity : 0.005 0.054 1283 Dihedral : 12.004 92.778 1298 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.08 % Allowed : 23.44 % Favored : 72.48 % 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: 2.46 (0.42), residues: 158 sheet: 1.00 (0.30), residues: 290 loop : -0.26 (0.30), residues: 426 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 covalent geometry : bond 0.00307 ( 7486) covalent geometry : angle 0.63925 (10214) SS BOND : bond 0.00275 ( 8) SS BOND : angle 0.86158 ( 16) hydrogen bonds : bond 0.04422 ( 275) hydrogen bonds : angle 5.52203 ( 747) link_ALPHA1-6 : bond 0.00989 ( 1) link_ALPHA1-6 : angle 3.03367 ( 3) link_BETA1-4 : bond 0.01152 ( 7) link_BETA1-4 : angle 4.44980 ( 21) link_NAG-ASN : bond 0.00543 ( 8) link_NAG-ASN : angle 4.84950 ( 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 231 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 THR cc_start: 0.8283 (m) cc_final: 0.8081 (p) REVERT: B 54 CYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7441 (t) REVERT: B 105 ILE cc_start: 0.8474 (pt) cc_final: 0.8260 (pt) REVERT: B 114 ASN cc_start: 0.8291 (t0) cc_final: 0.8081 (t0) REVERT: B 116 TYR cc_start: 0.8439 (t80) cc_final: 0.7954 (t80) REVERT: C 209 THR cc_start: 0.8281 (p) cc_final: 0.8032 (p) REVERT: D 43 LEU cc_start: 0.8517 (mt) cc_final: 0.8082 (mp) REVERT: D 154 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7943 (mt0) outliers start: 32 outliers final: 19 residues processed: 210 average time/residue: 0.1043 time to fit residues: 27.9903 Evaluate side-chains 218 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 27 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.156295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121048 restraints weight = 12115.928| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.27 r_work: 0.3312 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7510 Z= 0.123 Angle : 0.668 15.719 10278 Z= 0.303 Chirality : 0.044 0.171 1174 Planarity : 0.005 0.054 1283 Dihedral : 8.390 73.997 1286 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.08 % Allowed : 23.95 % 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: 1.03 (0.29), residues: 874 helix: 2.55 (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 0.006 0.000 ARG B 150 TYR 0.015 0.002 TYR C 40 PHE 0.013 0.001 PHE C 121 TRP 0.006 0.001 TRP B 164 HIS 0.003 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7486) covalent geometry : angle 0.60645 (10214) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.78113 ( 16) hydrogen bonds : bond 0.04037 ( 275) hydrogen bonds : angle 4.82184 ( 747) link_ALPHA1-6 : bond 0.01643 ( 1) link_ALPHA1-6 : angle 3.26810 ( 3) link_BETA1-4 : bond 0.01210 ( 7) link_BETA1-4 : angle 4.34570 ( 21) link_NAG-ASN : bond 0.00675 ( 8) link_NAG-ASN : angle 4.03367 ( 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 236 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7987 (p90) cc_final: 0.7694 (p90) REVERT: B 45 THR cc_start: 0.8332 (m) cc_final: 0.8054 (p) REVERT: B 54 CYS cc_start: 0.7721 (t) cc_final: 0.7442 (t) REVERT: B 64 TYR cc_start: 0.8541 (m-80) cc_final: 0.7876 (m-80) REVERT: B 116 TYR cc_start: 0.8396 (t80) cc_final: 0.8007 (t80) REVERT: C 62 PHE cc_start: 0.8302 (m-80) cc_final: 0.7861 (m-10) REVERT: C 118 PHE cc_start: 0.8016 (m-80) cc_final: 0.7649 (m-80) REVERT: C 193 VAL cc_start: 0.7550 (m) cc_final: 0.7342 (m) REVERT: C 209 THR cc_start: 0.8295 (p) cc_final: 0.7865 (p) REVERT: D 43 LEU cc_start: 0.8482 (mt) cc_final: 0.7986 (mp) REVERT: D 67 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8206 (mtp180) REVERT: D 105 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7555 (mtt90) REVERT: D 154 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7893 (mt0) outliers start: 32 outliers final: 23 residues processed: 214 average time/residue: 0.0991 time to fit residues: 27.1916 Evaluate side-chains 225 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 204 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.0040 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118375 restraints weight = 12300.602| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.30 r_work: 0.3273 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7510 Z= 0.201 Angle : 0.695 14.711 10278 Z= 0.324 Chirality : 0.045 0.173 1174 Planarity : 0.005 0.055 1283 Dihedral : 6.788 59.947 1286 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.08 % Allowed : 25.86 % Favored : 70.06 % 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: 0.94 (0.28), residues: 874 helix: 2.36 (0.42), residues: 158 sheet: 1.09 (0.29), residues: 283 loop : -0.33 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.018 0.002 TYR C 40 PHE 0.020 0.002 PHE C 121 TRP 0.009 0.001 TRP C 155 HIS 0.003 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 7486) covalent geometry : angle 0.63992 (10214) SS BOND : bond 0.00621 ( 8) SS BOND : angle 1.01319 ( 16) hydrogen bonds : bond 0.04503 ( 275) hydrogen bonds : angle 4.86490 ( 747) link_ALPHA1-6 : bond 0.02150 ( 1) link_ALPHA1-6 : angle 2.26073 ( 3) link_BETA1-4 : bond 0.01166 ( 7) link_BETA1-4 : angle 4.28733 ( 21) link_NAG-ASN : bond 0.00683 ( 8) link_NAG-ASN : angle 3.87560 ( 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 237 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.8037 (p90) cc_final: 0.7756 (p90) REVERT: B 45 THR cc_start: 0.8289 (m) cc_final: 0.8044 (p) REVERT: B 54 CYS cc_start: 0.7836 (t) cc_final: 0.7547 (t) REVERT: B 116 TYR cc_start: 0.8466 (t80) cc_final: 0.8121 (t80) REVERT: B 146 TRP cc_start: 0.6957 (p90) cc_final: 0.6480 (p90) REVERT: C 118 PHE cc_start: 0.8055 (m-80) cc_final: 0.7725 (m-80) REVERT: C 209 THR cc_start: 0.8332 (p) cc_final: 0.8101 (p) REVERT: D 43 LEU cc_start: 0.8531 (mt) cc_final: 0.8053 (mp) REVERT: D 91 SER cc_start: 0.8956 (m) cc_final: 0.8733 (m) REVERT: D 105 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7658 (mtt90) REVERT: D 154 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7962 (mt0) outliers start: 32 outliers final: 27 residues processed: 216 average time/residue: 0.1013 time to fit residues: 27.6333 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 : 0.254 ------------------------------------------------------------------------------- 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 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 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 218 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.0030 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.154592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118949 restraints weight = 12159.158| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.28 r_work: 0.3291 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7510 Z= 0.130 Angle : 0.653 14.544 10278 Z= 0.302 Chirality : 0.043 0.179 1174 Planarity : 0.005 0.053 1283 Dihedral : 6.039 51.353 1286 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.33 % Allowed : 25.61 % Favored : 70.06 % 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 (0.29), residues: 874 helix: 2.52 (0.42), residues: 158 sheet: 1.04 (0.30), residues: 283 loop : -0.28 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.027 0.002 TYR A 205 PHE 0.012 0.001 PHE D 153 TRP 0.008 0.001 TRP A 176 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7486) covalent geometry : angle 0.59897 (10214) SS BOND : bond 0.00473 ( 8) SS BOND : angle 0.85179 ( 16) hydrogen bonds : bond 0.04001 ( 275) hydrogen bonds : angle 4.71076 ( 747) link_ALPHA1-6 : bond 0.01515 ( 1) link_ALPHA1-6 : angle 1.31172 ( 3) link_BETA1-4 : bond 0.01161 ( 7) link_BETA1-4 : angle 4.11308 ( 21) link_NAG-ASN : bond 0.00621 ( 8) link_NAG-ASN : angle 3.77791 ( 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 240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7990 (p90) cc_final: 0.7765 (p90) REVERT: A 183 LEU cc_start: 0.8363 (mm) cc_final: 0.8023 (mp) REVERT: B 45 THR cc_start: 0.8276 (m) cc_final: 0.8030 (p) REVERT: B 54 CYS cc_start: 0.7765 (t) cc_final: 0.7465 (t) REVERT: B 116 TYR cc_start: 0.8420 (t80) cc_final: 0.8104 (t80) REVERT: C 62 PHE cc_start: 0.8258 (m-80) cc_final: 0.7980 (m-10) REVERT: C 118 PHE cc_start: 0.8035 (m-80) cc_final: 0.7727 (m-80) REVERT: C 209 THR cc_start: 0.8316 (p) cc_final: 0.7856 (p) REVERT: D 43 LEU cc_start: 0.8482 (mt) cc_final: 0.7998 (mp) REVERT: D 91 SER cc_start: 0.8936 (m) cc_final: 0.8727 (m) REVERT: D 105 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7655 (mtt90) REVERT: D 154 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7913 (mt0) outliers start: 34 outliers final: 25 residues processed: 217 average time/residue: 0.0983 time to fit residues: 27.1431 Evaluate side-chains 230 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 81 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.154580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119184 restraints weight = 12260.424| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.31 r_work: 0.3291 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7510 Z= 0.156 Angle : 0.651 14.152 10278 Z= 0.303 Chirality : 0.043 0.174 1174 Planarity : 0.004 0.053 1283 Dihedral : 5.561 45.808 1283 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 1.00 (0.29), residues: 874 helix: 2.44 (0.42), residues: 158 sheet: 1.08 (0.30), 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 0.023 0.002 TYR A 205 PHE 0.014 0.001 PHE C 121 TRP 0.007 0.001 TRP C 155 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7486) covalent geometry : angle 0.59855 (10214) SS BOND : bond 0.00451 ( 8) SS BOND : angle 0.86334 ( 16) hydrogen bonds : bond 0.04090 ( 275) hydrogen bonds : angle 4.69725 ( 747) link_ALPHA1-6 : bond 0.01201 ( 1) link_ALPHA1-6 : angle 1.28169 ( 3) link_BETA1-4 : bond 0.01115 ( 7) link_BETA1-4 : angle 4.04884 ( 21) link_NAG-ASN : bond 0.00599 ( 8) link_NAG-ASN : angle 3.73021 ( 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 243 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8436 (m) cc_final: 0.8234 (p) REVERT: A 168 TYR cc_start: 0.7997 (p90) cc_final: 0.7753 (p90) REVERT: A 179 LEU cc_start: 0.8410 (mt) cc_final: 0.8134 (mp) REVERT: A 214 GLU cc_start: 0.7204 (pp20) cc_final: 0.6712 (pp20) REVERT: B 45 THR cc_start: 0.8294 (m) cc_final: 0.8032 (p) REVERT: B 54 CYS cc_start: 0.7787 (t) cc_final: 0.7499 (t) REVERT: B 116 TYR cc_start: 0.8438 (t80) cc_final: 0.8071 (t80) REVERT: C 118 PHE cc_start: 0.8045 (m-80) cc_final: 0.7706 (m-80) REVERT: C 209 THR cc_start: 0.8281 (p) cc_final: 0.8011 (p) REVERT: D 43 LEU cc_start: 0.8465 (mt) cc_final: 0.7973 (mp) REVERT: D 91 SER cc_start: 0.8914 (m) cc_final: 0.8698 (m) REVERT: D 154 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7941 (mt0) outliers start: 32 outliers final: 28 residues processed: 223 average time/residue: 0.1028 time to fit residues: 29.2696 Evaluate side-chains 238 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 66 optimal weight: 0.0980 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.155546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120260 restraints weight = 12236.762| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.31 r_work: 0.3304 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7510 Z= 0.124 Angle : 0.641 13.819 10278 Z= 0.299 Chirality : 0.043 0.179 1174 Planarity : 0.004 0.053 1283 Dihedral : 5.338 47.165 1283 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.46 % Allowed : 27.26 % Favored : 68.28 % 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: 1.03 (0.29), residues: 874 helix: 2.58 (0.42), residues: 158 sheet: 0.99 (0.30), residues: 287 loop : -0.23 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 205 TYR 0.019 0.002 TYR A 205 PHE 0.020 0.001 PHE A 166 TRP 0.007 0.001 TRP C 48 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7486) covalent geometry : angle 0.59065 (10214) SS BOND : bond 0.00294 ( 8) SS BOND : angle 0.98516 ( 16) hydrogen bonds : bond 0.03784 ( 275) hydrogen bonds : angle 4.57436 ( 747) link_ALPHA1-6 : bond 0.01063 ( 1) link_ALPHA1-6 : angle 1.17594 ( 3) link_BETA1-4 : bond 0.01092 ( 7) link_BETA1-4 : angle 3.94317 ( 21) link_NAG-ASN : bond 0.00570 ( 8) link_NAG-ASN : angle 3.64531 ( 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 245 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8058 (mtpp) REVERT: A 179 LEU cc_start: 0.8331 (mt) cc_final: 0.8125 (mp) REVERT: A 183 LEU cc_start: 0.8412 (mm) cc_final: 0.8053 (mp) REVERT: A 214 GLU cc_start: 0.7242 (pp20) cc_final: 0.6719 (pp20) REVERT: B 45 THR cc_start: 0.8291 (m) cc_final: 0.8025 (p) REVERT: B 54 CYS cc_start: 0.7786 (t) cc_final: 0.7496 (t) REVERT: B 64 TYR cc_start: 0.8625 (m-80) cc_final: 0.8013 (m-80) REVERT: B 116 TYR cc_start: 0.8402 (t80) cc_final: 0.8072 (t80) REVERT: C 118 PHE cc_start: 0.8016 (m-80) cc_final: 0.7713 (m-80) REVERT: C 209 THR cc_start: 0.8290 (p) cc_final: 0.7872 (p) REVERT: D 43 LEU cc_start: 0.8428 (mt) cc_final: 0.7934 (mp) REVERT: D 67 ARG cc_start: 0.8472 (mtp180) cc_final: 0.8235 (mtp180) REVERT: D 91 SER cc_start: 0.8910 (m) cc_final: 0.8688 (m) REVERT: D 154 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7930 (mt0) outliers start: 35 outliers final: 31 residues processed: 223 average time/residue: 0.0959 time to fit residues: 27.1482 Evaluate side-chains 240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 40 LEU 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 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 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.155243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119823 restraints weight = 12314.318| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.33 r_work: 0.3300 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7510 Z= 0.140 Angle : 0.654 13.533 10278 Z= 0.305 Chirality : 0.043 0.179 1174 Planarity : 0.004 0.053 1283 Dihedral : 5.244 41.934 1283 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.33 % Allowed : 27.13 % 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: 1.00 (0.29), residues: 874 helix: 2.53 (0.42), residues: 158 sheet: 1.02 (0.30), residues: 285 loop : -0.27 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 94 TYR 0.019 0.002 TYR A 205 PHE 0.014 0.001 PHE D 153 TRP 0.007 0.001 TRP D 97 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7486) covalent geometry : angle 0.60556 (10214) SS BOND : bond 0.00323 ( 8) SS BOND : angle 1.03784 ( 16) hydrogen bonds : bond 0.03885 ( 275) hydrogen bonds : angle 4.59083 ( 747) link_ALPHA1-6 : bond 0.00955 ( 1) link_ALPHA1-6 : angle 1.17830 ( 3) link_BETA1-4 : bond 0.01079 ( 7) link_BETA1-4 : angle 3.92051 ( 21) link_NAG-ASN : bond 0.00553 ( 8) link_NAG-ASN : angle 3.60685 ( 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 245 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 LEU cc_start: 0.8416 (mm) cc_final: 0.8057 (mp) REVERT: A 214 GLU cc_start: 0.7242 (pp20) cc_final: 0.6714 (pp20) REVERT: B 45 THR cc_start: 0.8301 (m) cc_final: 0.8027 (p) REVERT: B 54 CYS cc_start: 0.7786 (t) cc_final: 0.7499 (t) REVERT: B 64 TYR cc_start: 0.8619 (m-80) cc_final: 0.8024 (m-80) REVERT: B 116 TYR cc_start: 0.8441 (t80) cc_final: 0.8058 (t80) REVERT: C 118 PHE cc_start: 0.8014 (m-80) cc_final: 0.7740 (m-80) REVERT: C 209 THR cc_start: 0.8304 (p) cc_final: 0.8031 (p) REVERT: D 43 LEU cc_start: 0.8440 (mt) cc_final: 0.7937 (mp) REVERT: D 67 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8227 (mtp180) REVERT: D 91 SER cc_start: 0.8901 (m) cc_final: 0.8676 (m) REVERT: D 149 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8387 (mtt180) REVERT: D 154 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7942 (mt0) outliers start: 34 outliers final: 32 residues processed: 223 average time/residue: 0.0973 time to fit residues: 27.7840 Evaluate side-chains 243 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 98 ASN 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 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 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 89 ASP 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: 3.9990 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.154711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119190 restraints weight = 12171.910| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.30 r_work: 0.3299 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7510 Z= 0.147 Angle : 0.660 13.320 10278 Z= 0.308 Chirality : 0.044 0.181 1174 Planarity : 0.004 0.053 1283 Dihedral : 5.136 39.173 1283 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.95 % Allowed : 28.03 % Favored : 68.03 % 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: 1.11 (0.29), residues: 874 helix: 2.81 (0.41), residues: 152 sheet: 1.04 (0.30), residues: 286 loop : -0.21 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 105 TYR 0.017 0.002 TYR A 205 PHE 0.013 0.001 PHE C 121 TRP 0.007 0.001 TRP D 97 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7486) covalent geometry : angle 0.61202 (10214) SS BOND : bond 0.00416 ( 8) SS BOND : angle 1.03944 ( 16) hydrogen bonds : bond 0.03933 ( 275) hydrogen bonds : angle 4.59878 ( 747) link_ALPHA1-6 : bond 0.00888 ( 1) link_ALPHA1-6 : angle 1.17397 ( 3) link_BETA1-4 : bond 0.01066 ( 7) link_BETA1-4 : angle 3.91449 ( 21) link_NAG-ASN : bond 0.00546 ( 8) link_NAG-ASN : angle 3.56339 ( 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 : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8229 (tp30) cc_final: 0.7990 (tp30) REVERT: A 183 LEU cc_start: 0.8427 (mm) cc_final: 0.8075 (mp) REVERT: A 214 GLU cc_start: 0.7239 (pp20) cc_final: 0.6689 (pp20) REVERT: B 45 THR cc_start: 0.8327 (m) cc_final: 0.8038 (p) REVERT: B 54 CYS cc_start: 0.7768 (t) cc_final: 0.7487 (t) REVERT: B 64 TYR cc_start: 0.8626 (m-80) cc_final: 0.8081 (m-80) REVERT: B 116 TYR cc_start: 0.8422 (t80) cc_final: 0.8043 (t80) REVERT: C 209 THR cc_start: 0.8307 (p) cc_final: 0.8033 (p) REVERT: D 43 LEU cc_start: 0.8431 (mt) cc_final: 0.7897 (mp) REVERT: D 67 ARG cc_start: 0.8464 (mtp180) cc_final: 0.8223 (mtp180) REVERT: D 91 SER cc_start: 0.8909 (m) cc_final: 0.8678 (m) REVERT: D 154 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: D 224 LEU cc_start: 0.8657 (mt) cc_final: 0.8316 (tp) outliers start: 31 outliers final: 29 residues processed: 218 average time/residue: 0.0982 time to fit residues: 27.2996 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 : 0.242 ------------------------------------------------------------------------------- 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 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 33 VAL Chi-restraints excluded: chain C residue 80 LEU 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 89 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN 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: 5.9990 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.155527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120061 restraints weight = 12109.956| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.30 r_work: 0.3307 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7510 Z= 0.131 Angle : 0.653 13.169 10278 Z= 0.306 Chirality : 0.043 0.184 1174 Planarity : 0.004 0.053 1283 Dihedral : 5.008 38.036 1283 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.33 % Allowed : 28.03 % Favored : 67.64 % 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: 1.11 (0.29), residues: 874 helix: 2.88 (0.41), residues: 152 sheet: 1.03 (0.30), residues: 284 loop : -0.21 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 105 TYR 0.016 0.002 TYR A 205 PHE 0.030 0.001 PHE A 166 TRP 0.008 0.001 TRP D 97 HIS 0.004 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7486) covalent geometry : angle 0.60539 (10214) SS BOND : bond 0.00332 ( 8) SS BOND : angle 0.98746 ( 16) hydrogen bonds : bond 0.03805 ( 275) hydrogen bonds : angle 4.56014 ( 747) link_ALPHA1-6 : bond 0.00875 ( 1) link_ALPHA1-6 : angle 1.19124 ( 3) link_BETA1-4 : bond 0.01082 ( 7) link_BETA1-4 : angle 3.91190 ( 21) link_NAG-ASN : bond 0.00522 ( 8) link_NAG-ASN : angle 3.53307 ( 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 237 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8046 (mtpp) REVERT: A 180 GLU cc_start: 0.8250 (tp30) cc_final: 0.7970 (tp30) REVERT: A 183 LEU cc_start: 0.8427 (mm) cc_final: 0.8075 (mp) REVERT: A 214 GLU cc_start: 0.7241 (pp20) cc_final: 0.6682 (pp20) REVERT: B 45 THR cc_start: 0.8299 (m) cc_final: 0.8009 (p) REVERT: B 54 CYS cc_start: 0.7779 (t) cc_final: 0.7499 (t) REVERT: B 64 TYR cc_start: 0.8619 (m-80) cc_final: 0.8005 (m-80) REVERT: B 116 TYR cc_start: 0.8423 (t80) cc_final: 0.8042 (t80) REVERT: C 209 THR cc_start: 0.8289 (p) cc_final: 0.7921 (p) REVERT: D 43 LEU cc_start: 0.8405 (mt) cc_final: 0.7919 (mp) REVERT: D 67 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8232 (mtp180) REVERT: D 91 SER cc_start: 0.8904 (m) cc_final: 0.8669 (m) REVERT: D 154 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: D 224 LEU cc_start: 0.8643 (mt) cc_final: 0.8309 (tp) outliers start: 34 outliers final: 32 residues processed: 217 average time/residue: 0.0987 time to fit residues: 26.9790 Evaluate side-chains 236 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 44 VAL Chi-restraints excluded: chain C residue 80 LEU 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 89 ASP 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 77 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 56 optimal weight: 8.9990 chunk 74 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.155786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120390 restraints weight = 12212.681| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.31 r_work: 0.3312 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1906 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= 0.120 Angle : 0.649 13.000 10278 Z= 0.303 Chirality : 0.043 0.184 1174 Planarity : 0.004 0.052 1283 Dihedral : 4.902 37.145 1283 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.69 % Allowed : 28.66 % Favored : 67.64 % 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: 1.14 (0.29), residues: 874 helix: 2.91 (0.41), residues: 152 sheet: 1.05 (0.30), residues: 283 loop : -0.20 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 105 TYR 0.016 0.002 TYR A 205 PHE 0.017 0.001 PHE A 226 TRP 0.011 0.001 TRP D 97 HIS 0.005 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7486) covalent geometry : angle 0.60143 (10214) SS BOND : bond 0.00362 ( 8) SS BOND : angle 0.96608 ( 16) hydrogen bonds : bond 0.03661 ( 275) hydrogen bonds : angle 4.50714 ( 747) link_ALPHA1-6 : bond 0.00867 ( 1) link_ALPHA1-6 : angle 1.20544 ( 3) link_BETA1-4 : bond 0.01075 ( 7) link_BETA1-4 : angle 3.88012 ( 21) link_NAG-ASN : bond 0.00506 ( 8) link_NAG-ASN : angle 3.49739 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.88 seconds wall clock time: 31 minutes 58.84 seconds (1918.84 seconds total)