Starting phenix.real_space_refine on Wed Feb 12 05:59:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u7n_26382/02_2025/7u7n_26382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u7n_26382/02_2025/7u7n_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_26382/02_2025/7u7n_26382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u7n_26382/02_2025/7u7n_26382.map" model { file = "/net/cci-nas-00/data/ceres_data/7u7n_26382/02_2025/7u7n_26382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u7n_26382/02_2025/7u7n_26382.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.71, per 1000 atoms: 0.65 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: 2.00 Conformation dependent library (CDL) restraints added in 974.1 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: 1.01 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: 2.14 Time building geometry restraints manager: 2.27 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: 0.850 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- 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 7486 Z= 0.264 Angle : 0.687 12.824 10214 Z= 0.327 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.001 TRP A 115 HIS 0.002 0.001 HIS D 150 PHE 0.019 0.001 PHE D 153 TYR 0.016 0.001 TYR C 40 ARG 0.006 0.000 ARG D 55 *********************** 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 : 0.741 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: 0.2575 time to fit residues: 63.9560 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 : 0.849 ------------------------------------------------------------------------------- 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 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.0270 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.155926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120906 restraints weight = 12001.609| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.26 r_work: 0.3310 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7486 Z= 0.192 Angle : 0.635 7.846 10214 Z= 0.306 Chirality : 0.044 0.165 1174 Planarity : 0.005 0.053 1283 Dihedral : 11.640 90.555 1298 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.08 % Allowed : 23.31 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 874 helix: 2.49 (0.42), residues: 158 sheet: 0.93 (0.30), residues: 292 loop : -0.24 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 269 HIS 0.004 0.001 HIS B 167 PHE 0.011 0.001 PHE B 158 TYR 0.014 0.002 TYR C 40 ARG 0.004 0.000 ARG D 55 *********************** 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 230 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7958 (p90) cc_final: 0.7655 (p90) REVERT: B 45 THR cc_start: 0.8286 (m) cc_final: 0.8081 (p) REVERT: B 49 VAL cc_start: 0.8447 (t) cc_final: 0.8127 (p) REVERT: B 54 CYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7437 (t) REVERT: B 105 ILE cc_start: 0.8490 (pt) cc_final: 0.8280 (pt) REVERT: B 114 ASN cc_start: 0.8293 (t0) cc_final: 0.8065 (t0) REVERT: B 116 TYR cc_start: 0.8420 (t80) cc_final: 0.7920 (t80) REVERT: C 209 THR cc_start: 0.8287 (p) cc_final: 0.8033 (p) REVERT: D 43 LEU cc_start: 0.8514 (mt) cc_final: 0.8040 (mp) REVERT: D 154 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: D 224 LEU cc_start: 0.8665 (mt) cc_final: 0.8334 (tp) outliers start: 32 outliers final: 19 residues processed: 208 average time/residue: 0.2489 time to fit residues: 66.3362 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 : 0.768 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 0.0170 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.150799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115400 restraints weight = 12179.841| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.23 r_work: 0.3236 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 7486 Z= 0.534 Angle : 0.758 9.208 10214 Z= 0.372 Chirality : 0.051 0.192 1174 Planarity : 0.006 0.055 1283 Dihedral : 9.282 76.146 1286 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.35 % Allowed : 24.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 874 helix: 1.90 (0.42), residues: 158 sheet: 0.86 (0.29), residues: 290 loop : -0.54 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 155 HIS 0.005 0.001 HIS D 208 PHE 0.032 0.003 PHE C 121 TYR 0.023 0.003 TYR C 40 ARG 0.005 0.001 ARG D 216 *********************** 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 254 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 SER cc_start: 0.8372 (m) cc_final: 0.8045 (t) REVERT: A 155 THR cc_start: 0.8500 (m) cc_final: 0.8222 (p) REVERT: A 179 LEU cc_start: 0.8490 (mt) cc_final: 0.8245 (mp) REVERT: A 210 MET cc_start: 0.7896 (mmm) cc_final: 0.7671 (mmm) REVERT: B 45 THR cc_start: 0.8357 (m) cc_final: 0.8079 (p) REVERT: B 54 CYS cc_start: 0.7862 (t) cc_final: 0.7549 (t) REVERT: B 146 TRP cc_start: 0.7245 (p90) cc_final: 0.6773 (p90) REVERT: C 118 PHE cc_start: 0.8109 (m-80) cc_final: 0.7788 (m-80) REVERT: D 43 LEU cc_start: 0.8629 (mt) cc_final: 0.8201 (mp) REVERT: D 154 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7935 (mt0) outliers start: 42 outliers final: 33 residues processed: 228 average time/residue: 0.2357 time to fit residues: 68.2297 Evaluate side-chains 244 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 125 GLN 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 B residue 40 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 134 CYS 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 89 CYS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.153392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118174 restraints weight = 12173.564| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.26 r_work: 0.3278 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7486 Z= 0.231 Angle : 0.656 9.642 10214 Z= 0.319 Chirality : 0.045 0.187 1174 Planarity : 0.005 0.055 1283 Dihedral : 7.631 61.378 1286 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.84 % Allowed : 26.37 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 874 helix: 2.53 (0.42), residues: 152 sheet: 0.87 (0.29), residues: 292 loop : -0.46 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 155 HIS 0.006 0.001 HIS B 59 PHE 0.025 0.002 PHE A 226 TYR 0.017 0.002 TYR C 40 ARG 0.004 0.000 ARG B 150 *********************** 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 249 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8472 (m) cc_final: 0.8213 (p) REVERT: A 168 TYR cc_start: 0.7988 (p90) cc_final: 0.7680 (p90) REVERT: A 179 LEU cc_start: 0.8385 (mt) cc_final: 0.8073 (mp) REVERT: B 45 THR cc_start: 0.8343 (m) cc_final: 0.8012 (p) REVERT: B 54 CYS cc_start: 0.7856 (t) cc_final: 0.7570 (t) REVERT: B 84 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8141 (ptt180) REVERT: B 116 TYR cc_start: 0.8441 (t80) cc_final: 0.8066 (t80) REVERT: B 146 TRP cc_start: 0.7101 (p90) cc_final: 0.6567 (p90) REVERT: D 43 LEU cc_start: 0.8491 (mt) cc_final: 0.8060 (mp) REVERT: D 105 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7661 (mtt-85) REVERT: D 154 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7901 (mt0) outliers start: 38 outliers final: 26 residues processed: 221 average time/residue: 0.2418 time to fit residues: 68.0879 Evaluate side-chains 235 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 84 ARG 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 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 80 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 81 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 0.0470 chunk 42 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.152623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117262 restraints weight = 12106.348| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.26 r_work: 0.3258 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7486 Z= 0.308 Angle : 0.650 9.872 10214 Z= 0.319 Chirality : 0.045 0.189 1174 Planarity : 0.005 0.054 1283 Dihedral : 6.389 49.748 1286 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.22 % Allowed : 26.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 874 helix: 2.46 (0.41), residues: 152 sheet: 0.98 (0.30), residues: 285 loop : -0.53 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 155 HIS 0.004 0.001 HIS B 167 PHE 0.022 0.002 PHE A 226 TYR 0.027 0.002 TYR A 205 ARG 0.007 0.000 ARG B 150 *********************** 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 253 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7508 (tt0) cc_final: 0.7284 (tt0) REVERT: A 155 THR cc_start: 0.8471 (m) cc_final: 0.8207 (p) REVERT: A 168 TYR cc_start: 0.7989 (p90) cc_final: 0.7729 (p90) REVERT: A 179 LEU cc_start: 0.8477 (mt) cc_final: 0.8203 (mp) REVERT: A 214 GLU cc_start: 0.7215 (pp20) cc_final: 0.6661 (pp20) REVERT: B 45 THR cc_start: 0.8284 (m) cc_final: 0.8020 (p) REVERT: B 54 CYS cc_start: 0.7860 (t) cc_final: 0.7568 (t) REVERT: B 146 TRP cc_start: 0.7162 (p90) cc_final: 0.6612 (p90) REVERT: B 249 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5504 (mt) REVERT: D 43 LEU cc_start: 0.8553 (mt) cc_final: 0.8117 (mp) REVERT: D 91 SER cc_start: 0.8963 (m) cc_final: 0.8761 (m) REVERT: D 154 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7908 (mt0) outliers start: 41 outliers final: 33 residues processed: 228 average time/residue: 0.2154 time to fit residues: 62.9136 Evaluate side-chains 247 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 B residue 40 LEU 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 134 CYS 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 249 ILE Chi-restraints excluded: chain B residue 321 THR 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 88 SER 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 C residue 209 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118395 restraints weight = 12109.145| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.29 r_work: 0.3258 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7486 Z= 0.246 Angle : 0.626 10.036 10214 Z= 0.305 Chirality : 0.044 0.182 1174 Planarity : 0.005 0.054 1283 Dihedral : 5.786 45.375 1283 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.10 % Allowed : 27.64 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.28), residues: 874 helix: 2.59 (0.41), residues: 152 sheet: 0.97 (0.30), residues: 285 loop : -0.50 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 155 HIS 0.003 0.001 HIS B 167 PHE 0.017 0.002 PHE D 153 TYR 0.023 0.002 TYR A 205 ARG 0.004 0.000 ARG D 105 *********************** 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 255 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8450 (m) cc_final: 0.8196 (p) REVERT: A 179 LEU cc_start: 0.8499 (mt) cc_final: 0.8055 (mp) REVERT: A 180 GLU cc_start: 0.8207 (tp30) cc_final: 0.7937 (tp30) REVERT: A 214 GLU cc_start: 0.7251 (pp20) cc_final: 0.6687 (pp20) REVERT: B 45 THR cc_start: 0.8300 (m) cc_final: 0.8033 (p) REVERT: B 54 CYS cc_start: 0.7823 (t) cc_final: 0.7532 (t) REVERT: B 146 TRP cc_start: 0.7132 (p90) cc_final: 0.6580 (p90) REVERT: D 43 LEU cc_start: 0.8480 (mt) cc_final: 0.8021 (mp) REVERT: D 91 SER cc_start: 0.8968 (m) cc_final: 0.8760 (m) REVERT: D 154 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7930 (mt0) outliers start: 40 outliers final: 33 residues processed: 231 average time/residue: 0.2336 time to fit residues: 68.9259 Evaluate side-chains 247 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 40 LEU 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 249 ILE Chi-restraints excluded: chain B residue 321 THR 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 88 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS B 167 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119084 restraints weight = 11984.040| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.25 r_work: 0.3289 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7486 Z= 0.220 Angle : 0.616 9.905 10214 Z= 0.300 Chirality : 0.044 0.178 1174 Planarity : 0.005 0.054 1283 Dihedral : 5.488 43.774 1283 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.22 % Allowed : 28.03 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 874 helix: 2.71 (0.42), residues: 152 sheet: 1.00 (0.30), residues: 285 loop : -0.44 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 155 HIS 0.007 0.001 HIS B 167 PHE 0.020 0.001 PHE D 153 TYR 0.021 0.002 TYR A 205 ARG 0.005 0.000 ARG D 62 *********************** 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 253 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8096 (mtpp) REVERT: A 155 THR cc_start: 0.8432 (m) cc_final: 0.8185 (p) REVERT: A 179 LEU cc_start: 0.8500 (mt) cc_final: 0.8110 (mp) REVERT: A 180 GLU cc_start: 0.8217 (tp30) cc_final: 0.7940 (tp30) REVERT: A 183 LEU cc_start: 0.8434 (mm) cc_final: 0.8097 (mp) REVERT: A 214 GLU cc_start: 0.7231 (pp20) cc_final: 0.6679 (pp20) REVERT: B 45 THR cc_start: 0.8289 (m) cc_final: 0.8020 (p) REVERT: B 54 CYS cc_start: 0.7781 (t) cc_final: 0.7499 (t) REVERT: B 116 TYR cc_start: 0.8429 (t80) cc_final: 0.8021 (t80) REVERT: B 146 TRP cc_start: 0.7081 (p90) cc_final: 0.6528 (p90) REVERT: B 249 ILE cc_start: 0.5677 (OUTLIER) cc_final: 0.4920 (tp) REVERT: C 149 TRP cc_start: 0.8274 (p90) cc_final: 0.7775 (p90) REVERT: D 43 LEU cc_start: 0.8488 (mt) cc_final: 0.8019 (mp) REVERT: D 91 SER cc_start: 0.8965 (m) cc_final: 0.8734 (m) REVERT: D 149 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8354 (mtt180) REVERT: D 154 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7906 (mt0) outliers start: 41 outliers final: 32 residues processed: 232 average time/residue: 0.2391 time to fit residues: 70.6106 Evaluate side-chains 243 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 40 LEU 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 134 CYS 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 249 ILE Chi-restraints excluded: chain B residue 321 THR 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 89 CYS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.154272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119299 restraints weight = 12045.071| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.24 r_work: 0.3293 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7486 Z= 0.209 Angle : 0.615 9.961 10214 Z= 0.300 Chirality : 0.044 0.177 1174 Planarity : 0.005 0.054 1283 Dihedral : 5.266 42.597 1283 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.59 % Allowed : 28.54 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 874 helix: 2.82 (0.42), residues: 152 sheet: 1.05 (0.30), residues: 282 loop : -0.43 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 67 HIS 0.003 0.001 HIS D 150 PHE 0.022 0.001 PHE A 166 TYR 0.019 0.002 TYR A 205 ARG 0.005 0.000 ARG D 145 *********************** 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 244 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8104 (mtpp) REVERT: A 155 THR cc_start: 0.8448 (m) cc_final: 0.8244 (p) REVERT: A 183 LEU cc_start: 0.8448 (mm) cc_final: 0.8092 (mp) REVERT: A 214 GLU cc_start: 0.7241 (pp20) cc_final: 0.6672 (pp20) REVERT: B 45 THR cc_start: 0.8289 (m) cc_final: 0.8009 (p) REVERT: B 54 CYS cc_start: 0.7763 (t) cc_final: 0.7473 (t) REVERT: B 64 TYR cc_start: 0.8548 (m-80) cc_final: 0.7969 (m-80) REVERT: B 116 TYR cc_start: 0.8444 (t80) cc_final: 0.8081 (t80) REVERT: B 146 TRP cc_start: 0.7063 (p90) cc_final: 0.6544 (p90) REVERT: B 249 ILE cc_start: 0.5634 (OUTLIER) cc_final: 0.5403 (mt) REVERT: C 118 PHE cc_start: 0.8033 (m-80) cc_final: 0.7707 (m-80) REVERT: C 149 TRP cc_start: 0.8274 (p90) cc_final: 0.7777 (p90) REVERT: C 209 THR cc_start: 0.8364 (p) cc_final: 0.8126 (p) REVERT: D 43 LEU cc_start: 0.8464 (mt) cc_final: 0.7983 (mp) REVERT: D 91 SER cc_start: 0.8936 (m) cc_final: 0.8717 (m) REVERT: D 149 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8350 (mtt180) REVERT: D 154 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7937 (mt0) outliers start: 36 outliers final: 29 residues processed: 224 average time/residue: 0.2261 time to fit residues: 64.4867 Evaluate side-chains 237 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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 249 ILE 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 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.153347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118249 restraints weight = 12241.370| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.28 r_work: 0.3274 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7486 Z= 0.275 Angle : 0.648 10.178 10214 Z= 0.317 Chirality : 0.045 0.174 1174 Planarity : 0.005 0.054 1283 Dihedral : 5.355 41.370 1283 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.97 % Allowed : 28.54 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 874 helix: 2.68 (0.42), residues: 152 sheet: 1.00 (0.30), residues: 284 loop : -0.48 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 97 HIS 0.003 0.001 HIS A 167 PHE 0.024 0.002 PHE A 166 TYR 0.019 0.002 TYR A 205 ARG 0.004 0.000 ARG D 105 *********************** 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 251 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7908 (m-80) cc_final: 0.7703 (m-80) REVERT: A 155 THR cc_start: 0.8454 (m) cc_final: 0.8200 (p) REVERT: A 214 GLU cc_start: 0.7224 (pp20) cc_final: 0.6657 (pp20) REVERT: B 45 THR cc_start: 0.8306 (m) cc_final: 0.8025 (p) REVERT: B 54 CYS cc_start: 0.7795 (t) cc_final: 0.7511 (t) REVERT: B 64 TYR cc_start: 0.8596 (m-80) cc_final: 0.8132 (m-80) REVERT: B 116 TYR cc_start: 0.8438 (t80) cc_final: 0.8091 (t80) REVERT: B 146 TRP cc_start: 0.7119 (p90) cc_final: 0.6588 (p90) REVERT: B 249 ILE cc_start: 0.5635 (OUTLIER) cc_final: 0.4879 (tp) REVERT: C 149 TRP cc_start: 0.8274 (p90) cc_final: 0.7775 (p90) REVERT: C 209 THR cc_start: 0.8340 (p) cc_final: 0.8131 (p) REVERT: D 43 LEU cc_start: 0.8513 (mt) cc_final: 0.8036 (mp) REVERT: D 91 SER cc_start: 0.8947 (m) cc_final: 0.8728 (m) REVERT: D 154 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7956 (mt0) outliers start: 39 outliers final: 33 residues processed: 230 average time/residue: 0.2303 time to fit residues: 67.3835 Evaluate side-chains 240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 249 ILE 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 89 CYS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 100 LEU 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 11 optimal weight: 0.2980 chunk 38 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.155103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119882 restraints weight = 12341.720| |-----------------------------------------------------------------------------| r_work (start): 0.3479 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: 0.7519 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.182 Angle : 0.617 10.082 10214 Z= 0.301 Chirality : 0.043 0.179 1174 Planarity : 0.005 0.052 1283 Dihedral : 5.063 40.102 1283 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.57 % Allowed : 30.19 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.29), residues: 874 helix: 2.86 (0.42), residues: 152 sheet: 0.92 (0.30), residues: 285 loop : -0.41 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 97 HIS 0.002 0.001 HIS A 167 PHE 0.020 0.001 PHE A 166 TYR 0.016 0.002 TYR C 40 ARG 0.003 0.000 ARG D 145 ********************** 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 243 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8122 (mtpp) REVERT: A 119 PHE cc_start: 0.7882 (m-80) cc_final: 0.7631 (m-80) REVERT: A 120 VAL cc_start: 0.8271 (m) cc_final: 0.8046 (p) REVERT: A 183 LEU cc_start: 0.8453 (mm) cc_final: 0.8104 (mp) REVERT: A 214 GLU cc_start: 0.7239 (pp20) cc_final: 0.6650 (pp20) REVERT: B 45 THR cc_start: 0.8286 (m) cc_final: 0.7997 (p) REVERT: B 54 CYS cc_start: 0.7732 (t) cc_final: 0.7441 (t) REVERT: B 64 TYR cc_start: 0.8533 (m-80) cc_final: 0.7959 (m-80) REVERT: B 116 TYR cc_start: 0.8426 (t80) cc_final: 0.8067 (t80) REVERT: B 249 ILE cc_start: 0.5548 (OUTLIER) cc_final: 0.5330 (mt) REVERT: C 118 PHE cc_start: 0.7995 (m-80) cc_final: 0.7713 (m-80) REVERT: C 149 TRP cc_start: 0.8258 (p90) cc_final: 0.7750 (p90) REVERT: C 209 THR cc_start: 0.8353 (p) cc_final: 0.8110 (p) REVERT: D 43 LEU cc_start: 0.8442 (mt) cc_final: 0.7927 (mp) REVERT: D 91 SER cc_start: 0.8865 (m) cc_final: 0.8658 (m) REVERT: D 154 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: D 224 LEU cc_start: 0.8617 (mt) cc_final: 0.8337 (tp) outliers start: 28 outliers final: 25 residues processed: 228 average time/residue: 0.2287 time to fit residues: 66.7379 Evaluate side-chains 240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 192 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 105 ILE 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 249 ILE 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 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 100 LEU 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 44 optimal weight: 0.0000 chunk 45 optimal weight: 0.4980 chunk 40 optimal weight: 40.0000 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.0070 chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- 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 = 0.155426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120294 restraints weight = 12030.044| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.24 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: 0.7511 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7486 Z= 0.184 Angle : 0.609 10.023 10214 Z= 0.295 Chirality : 0.043 0.172 1174 Planarity : 0.005 0.052 1283 Dihedral : 4.919 38.891 1283 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.44 % Allowed : 30.32 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 874 helix: 2.86 (0.42), residues: 152 sheet: 0.94 (0.30), residues: 282 loop : -0.39 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 97 HIS 0.001 0.000 HIS D 150 PHE 0.014 0.001 PHE D 153 TYR 0.016 0.001 TYR A 205 ARG 0.006 0.000 ARG D 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.27 seconds wall clock time: 67 minutes 23.65 seconds (4043.65 seconds total)