Starting phenix.real_space_refine on Fri Jul 25 09:27:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u7n_26382/07_2025/7u7n_26382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u7n_26382/07_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_26382/07_2025/7u7n_26382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2025/7u7n_26382.map" model { file = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_2025/7u7n_26382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u7n_26382/07_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-5711/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: 4.97, per 1000 atoms: 0.68 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: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.89 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: 2.09 Time building geometry restraints manager: 2.41 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.590 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 8) link_NAG-ASN : angle 5.64302 ( 24) 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) hydrogen bonds : bond 0.21395 ( 275) hydrogen bonds : angle 7.98252 ( 747) SS BOND : bond 0.00318 ( 8) SS BOND : angle 0.79861 ( 16) covalent geometry : bond 0.00383 ( 7486) covalent geometry : angle 0.68730 (10214) *********************** 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 : 0.717 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: 0.2833 time to fit residues: 71.1731 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 : 1.379 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120905 restraints weight = 12001.608| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.26 r_work: 0.3306 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 7510 Z= 0.128 Angle : 0.707 18.138 10278 Z= 0.323 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 8) link_NAG-ASN : angle 4.81814 ( 24) link_ALPHA1-6 : bond 0.01152 ( 1) link_ALPHA1-6 : angle 3.10326 ( 3) link_BETA1-4 : bond 0.01121 ( 7) link_BETA1-4 : angle 4.47680 ( 21) hydrogen bonds : bond 0.04406 ( 275) hydrogen bonds : angle 5.46190 ( 747) SS BOND : bond 0.00409 ( 8) SS BOND : angle 0.87777 ( 16) covalent geometry : bond 0.00282 ( 7486) covalent geometry : angle 0.63528 (10214) *********************** 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 : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7959 (p90) cc_final: 0.7656 (p90) REVERT: B 45 THR cc_start: 0.8285 (m) cc_final: 0.8081 (p) REVERT: B 49 VAL cc_start: 0.8445 (t) cc_final: 0.8124 (p) REVERT: B 54 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7443 (t) REVERT: B 105 ILE cc_start: 0.8489 (pt) cc_final: 0.8279 (pt) REVERT: B 114 ASN cc_start: 0.8292 (t0) cc_final: 0.8064 (t0) REVERT: B 116 TYR cc_start: 0.8419 (t80) cc_final: 0.7917 (t80) REVERT: C 209 THR cc_start: 0.8287 (p) cc_final: 0.8033 (p) REVERT: D 43 LEU cc_start: 0.8512 (mt) cc_final: 0.8038 (mp) REVERT: D 154 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: D 224 LEU cc_start: 0.8664 (mt) cc_final: 0.8332 (tp) outliers start: 32 outliers final: 19 residues processed: 208 average time/residue: 0.2909 time to fit residues: 77.0921 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 : 0.821 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.149435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114100 restraints weight = 12183.711| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.22 r_work: 0.3213 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 7510 Z= 0.461 Angle : 0.896 15.342 10278 Z= 0.429 Chirality : 0.055 0.222 1174 Planarity : 0.007 0.058 1283 Dihedral : 9.125 74.004 1286 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.99 % Allowed : 24.59 % Favored : 69.43 % 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: 0.34 (0.28), residues: 874 helix: 1.78 (0.42), residues: 152 sheet: 0.77 (0.29), residues: 291 loop : -0.73 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 155 HIS 0.005 0.002 HIS B 167 PHE 0.037 0.003 PHE C 121 TYR 0.026 0.003 TYR B 79 ARG 0.007 0.001 ARG D 216 Details of bonding type rmsd link_NAG-ASN : bond 0.01054 ( 8) link_NAG-ASN : angle 4.26577 ( 24) link_ALPHA1-6 : bond 0.01441 ( 1) link_ALPHA1-6 : angle 3.48653 ( 3) link_BETA1-4 : bond 0.01371 ( 7) link_BETA1-4 : angle 4.66916 ( 21) hydrogen bonds : bond 0.06582 ( 275) hydrogen bonds : angle 5.64259 ( 747) SS BOND : bond 0.00530 ( 8) SS BOND : angle 1.38264 ( 16) covalent geometry : bond 0.01012 ( 7486) covalent geometry : angle 0.84527 (10214) *********************** 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 257 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8524 (m) cc_final: 0.8238 (p) REVERT: A 179 LEU cc_start: 0.8568 (mt) cc_final: 0.8316 (mp) REVERT: A 210 MET cc_start: 0.7958 (mmm) cc_final: 0.7671 (mmm) REVERT: B 37 VAL cc_start: 0.8500 (t) cc_final: 0.8235 (m) REVERT: B 45 THR cc_start: 0.8377 (m) cc_final: 0.8082 (p) REVERT: B 54 CYS cc_start: 0.7883 (t) cc_final: 0.7583 (t) REVERT: B 146 TRP cc_start: 0.7442 (p90) cc_final: 0.6967 (p90) REVERT: C 118 PHE cc_start: 0.8115 (m-80) cc_final: 0.7850 (m-80) REVERT: D 43 LEU cc_start: 0.8619 (mt) cc_final: 0.8182 (mp) outliers start: 47 outliers final: 36 residues processed: 227 average time/residue: 0.2278 time to fit residues: 66.2146 Evaluate side-chains 246 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 81 VAL 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 120 VAL Chi-restraints excluded: chain A residue 122 LEU 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 139 PHE 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 321 THR Chi-restraints excluded: chain C residue 33 VAL 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 119 VAL Chi-restraints excluded: chain C residue 147 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: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.152812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117501 restraints weight = 12192.438| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.27 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: 0.7547 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7510 Z= 0.156 Angle : 0.715 15.274 10278 Z= 0.334 Chirality : 0.045 0.198 1174 Planarity : 0.005 0.054 1283 Dihedral : 7.599 59.920 1286 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.61 % Allowed : 25.73 % Favored : 68.66 % 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: 0.67 (0.28), residues: 874 helix: 2.56 (0.42), residues: 150 sheet: 0.75 (0.29), residues: 295 loop : -0.53 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 197 HIS 0.008 0.001 HIS B 59 PHE 0.016 0.001 PHE C 62 TYR 0.018 0.002 TYR C 40 ARG 0.004 0.000 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 8) link_NAG-ASN : angle 4.07453 ( 24) link_ALPHA1-6 : bond 0.01907 ( 1) link_ALPHA1-6 : angle 2.72578 ( 3) link_BETA1-4 : bond 0.01196 ( 7) link_BETA1-4 : angle 4.43953 ( 21) hydrogen bonds : bond 0.04650 ( 275) hydrogen bonds : angle 5.00104 ( 747) SS BOND : bond 0.00266 ( 8) SS BOND : angle 0.95141 ( 16) covalent geometry : bond 0.00348 ( 7486) covalent geometry : angle 0.65686 (10214) *********************** 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 260 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8475 (m) cc_final: 0.8220 (p) REVERT: A 168 TYR cc_start: 0.7978 (p90) cc_final: 0.7676 (p90) REVERT: A 179 LEU cc_start: 0.8445 (mt) cc_final: 0.8118 (mp) REVERT: A 210 MET cc_start: 0.7948 (mmm) cc_final: 0.7745 (mmm) REVERT: B 45 THR cc_start: 0.8329 (m) cc_final: 0.7991 (p) REVERT: B 54 CYS cc_start: 0.7880 (t) cc_final: 0.7588 (t) REVERT: B 116 TYR cc_start: 0.8464 (t80) cc_final: 0.8109 (t80) REVERT: B 146 TRP cc_start: 0.7148 (p90) cc_final: 0.6677 (p90) REVERT: B 249 ILE cc_start: 0.5660 (OUTLIER) cc_final: 0.5441 (mt) REVERT: C 118 PHE cc_start: 0.8056 (m-80) cc_final: 0.7751 (m-80) REVERT: C 133 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7465 (mt-10) REVERT: D 43 LEU cc_start: 0.8545 (mt) cc_final: 0.8117 (mp) REVERT: D 105 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7669 (mtt-85) outliers start: 44 outliers final: 33 residues processed: 228 average time/residue: 0.2366 time to fit residues: 69.1885 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 : 0.717 ------------------------------------------------------------------------------- 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 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 A residue 193 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 98 ASN 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 249 ILE 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 94 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 100 LEU 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: 2.9990 chunk 32 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 0.0040 chunk 42 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.154030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118620 restraints weight = 12089.554| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.28 r_work: 0.3282 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7510 Z= 0.139 Angle : 0.678 14.703 10278 Z= 0.315 Chirality : 0.044 0.175 1174 Planarity : 0.005 0.054 1283 Dihedral : 6.472 52.457 1286 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.35 % Allowed : 27.26 % Favored : 67.39 % 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: 0.83 (0.28), residues: 874 helix: 2.72 (0.42), residues: 150 sheet: 0.89 (0.29), residues: 288 loop : -0.46 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.006 0.001 HIS B 59 PHE 0.021 0.001 PHE C 62 TYR 0.027 0.002 TYR A 205 ARG 0.007 0.000 ARG B 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 8) link_NAG-ASN : angle 3.97705 ( 24) link_ALPHA1-6 : bond 0.01703 ( 1) link_ALPHA1-6 : angle 1.31797 ( 3) link_BETA1-4 : bond 0.01193 ( 7) link_BETA1-4 : angle 4.30233 ( 21) hydrogen bonds : bond 0.04245 ( 275) hydrogen bonds : angle 4.83016 ( 747) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.98938 ( 16) covalent geometry : bond 0.00313 ( 7486) covalent geometry : angle 0.62020 (10214) *********************** 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: 42 poor density : 211 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8457 (m) cc_final: 0.8209 (p) REVERT: A 168 TYR cc_start: 0.7948 (p90) cc_final: 0.7661 (p90) REVERT: A 179 LEU cc_start: 0.8442 (mt) cc_final: 0.7951 (mp) REVERT: A 180 GLU cc_start: 0.8123 (tp30) cc_final: 0.7868 (tp30) REVERT: A 183 LEU cc_start: 0.8377 (mm) cc_final: 0.8043 (mp) REVERT: A 210 MET cc_start: 0.7931 (mmm) cc_final: 0.7663 (mmm) REVERT: A 214 GLU cc_start: 0.7204 (pp20) cc_final: 0.6662 (pp20) REVERT: B 45 THR cc_start: 0.8270 (m) cc_final: 0.8008 (p) REVERT: B 54 CYS cc_start: 0.7885 (t) cc_final: 0.7592 (t) REVERT: B 64 TYR cc_start: 0.8648 (m-80) cc_final: 0.8424 (m-80) REVERT: B 114 ASN cc_start: 0.8244 (t0) cc_final: 0.8029 (t0) REVERT: B 116 TYR cc_start: 0.8477 (t80) cc_final: 0.8145 (t80) REVERT: B 146 TRP cc_start: 0.7108 (p90) cc_final: 0.6554 (p90) REVERT: B 249 ILE cc_start: 0.5669 (OUTLIER) cc_final: 0.5455 (mt) REVERT: C 133 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7400 (mt-10) REVERT: C 209 THR cc_start: 0.8372 (p) cc_final: 0.8144 (p) REVERT: D 43 LEU cc_start: 0.8501 (mt) cc_final: 0.8059 (mp) REVERT: D 154 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7876 (mt0) outliers start: 42 outliers final: 28 residues processed: 223 average time/residue: 0.2368 time to fit residues: 66.8470 Evaluate side-chains 242 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 59 HIS 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 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 249 ILE 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 85 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 100 LEU 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 84 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.154486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119288 restraints weight = 12115.292| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.27 r_work: 0.3273 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1703 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= 0.130 Angle : 0.663 14.377 10278 Z= 0.308 Chirality : 0.043 0.176 1174 Planarity : 0.005 0.053 1283 Dihedral : 5.733 45.111 1283 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.71 % Allowed : 27.90 % Favored : 67.39 % 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 (0.28), residues: 874 helix: 2.71 (0.42), residues: 152 sheet: 0.99 (0.30), residues: 284 loop : -0.43 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 197 HIS 0.005 0.001 HIS B 167 PHE 0.015 0.001 PHE D 153 TYR 0.022 0.002 TYR A 205 ARG 0.004 0.000 ARG D 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 8) link_NAG-ASN : angle 3.88210 ( 24) link_ALPHA1-6 : bond 0.01304 ( 1) link_ALPHA1-6 : angle 1.35306 ( 3) link_BETA1-4 : bond 0.01138 ( 7) link_BETA1-4 : angle 4.20486 ( 21) hydrogen bonds : bond 0.04043 ( 275) hydrogen bonds : angle 4.74586 ( 747) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.94642 ( 16) covalent geometry : bond 0.00293 ( 7486) covalent geometry : angle 0.60721 (10214) *********************** 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 249 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: A 155 THR cc_start: 0.8442 (m) cc_final: 0.8233 (p) REVERT: A 179 LEU cc_start: 0.8470 (mt) cc_final: 0.8231 (mt) REVERT: A 180 GLU cc_start: 0.8137 (tp30) cc_final: 0.7853 (tp30) REVERT: A 210 MET cc_start: 0.7929 (mmm) cc_final: 0.7618 (mmm) REVERT: A 214 GLU cc_start: 0.7216 (pp20) cc_final: 0.6642 (pp20) REVERT: B 45 THR cc_start: 0.8274 (m) cc_final: 0.8015 (p) REVERT: B 54 CYS cc_start: 0.7914 (t) cc_final: 0.7618 (t) REVERT: B 64 TYR cc_start: 0.8600 (m-80) cc_final: 0.8389 (m-80) REVERT: B 84 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8356 (ptt180) REVERT: B 116 TYR cc_start: 0.8470 (t80) cc_final: 0.8144 (t80) REVERT: B 146 TRP cc_start: 0.7100 (p90) cc_final: 0.6544 (p90) REVERT: C 118 PHE cc_start: 0.8006 (m-80) cc_final: 0.7733 (m-80) REVERT: C 149 TRP cc_start: 0.8294 (p90) cc_final: 0.7792 (p90) REVERT: C 209 THR cc_start: 0.8373 (p) cc_final: 0.8144 (p) REVERT: D 43 LEU cc_start: 0.8480 (mt) cc_final: 0.8008 (mp) REVERT: D 154 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7900 (mt0) outliers start: 37 outliers final: 26 residues processed: 222 average time/residue: 0.2302 time to fit residues: 64.9919 Evaluate side-chains 236 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 123 GLU 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 59 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 161 LYS 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 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 107 THR Chi-restraints excluded: chain C residue 167 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 0.0030 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.9352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118574 restraints weight = 12001.192| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.28 r_work: 0.3280 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7510 Z= 0.159 Angle : 0.676 14.029 10278 Z= 0.316 Chirality : 0.044 0.176 1174 Planarity : 0.005 0.053 1283 Dihedral : 5.580 44.252 1283 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.84 % Allowed : 27.90 % 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: 0.88 (0.28), residues: 874 helix: 2.68 (0.41), residues: 152 sheet: 1.00 (0.30), residues: 283 loop : -0.45 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.006 0.001 HIS B 59 PHE 0.020 0.002 PHE D 153 TYR 0.020 0.002 TYR A 205 ARG 0.004 0.000 ARG D 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 8) link_NAG-ASN : angle 3.79909 ( 24) link_ALPHA1-6 : bond 0.01142 ( 1) link_ALPHA1-6 : angle 1.31176 ( 3) link_BETA1-4 : bond 0.01127 ( 7) link_BETA1-4 : angle 4.16168 ( 21) hydrogen bonds : bond 0.04160 ( 275) hydrogen bonds : angle 4.74682 ( 747) SS BOND : bond 0.00311 ( 8) SS BOND : angle 1.03538 ( 16) covalent geometry : bond 0.00359 ( 7486) covalent geometry : angle 0.62247 (10214) *********************** 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: 38 poor density : 207 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8436 (m) cc_final: 0.8229 (p) REVERT: A 180 GLU cc_start: 0.8232 (tp30) cc_final: 0.7941 (tp30) REVERT: A 210 MET cc_start: 0.7938 (mmm) cc_final: 0.7617 (mmm) REVERT: A 214 GLU cc_start: 0.7203 (pp20) cc_final: 0.6625 (pp20) REVERT: B 45 THR cc_start: 0.8267 (m) cc_final: 0.8001 (p) REVERT: B 54 CYS cc_start: 0.7908 (t) cc_final: 0.7608 (t) REVERT: B 64 TYR cc_start: 0.8585 (m-80) cc_final: 0.8342 (m-80) REVERT: B 84 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8380 (ptt180) REVERT: B 116 TYR cc_start: 0.8494 (t80) cc_final: 0.8140 (t80) REVERT: B 146 TRP cc_start: 0.7108 (p90) cc_final: 0.6555 (p90) REVERT: C 118 PHE cc_start: 0.8000 (m-80) cc_final: 0.7716 (m-80) REVERT: C 149 TRP cc_start: 0.8297 (p90) cc_final: 0.7717 (p90) REVERT: C 209 THR cc_start: 0.8362 (p) cc_final: 0.8141 (p) REVERT: D 43 LEU cc_start: 0.8476 (mt) cc_final: 0.7988 (mp) REVERT: D 149 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8375 (mtt180) REVERT: D 154 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7915 (mt0) outliers start: 38 outliers final: 29 residues processed: 220 average time/residue: 0.2335 time to fit residues: 65.0907 Evaluate side-chains 239 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 193 ILE Chi-restraints excluded: chain A residue 213 GLU 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 105 ILE Chi-restraints excluded: chain B residue 161 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 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 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: 0.1980 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 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 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 = 0.3970 r_free = 0.3970 target = 0.154317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118948 restraints weight = 12046.839| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.30 r_work: 0.3293 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1855 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= 0.139 Angle : 0.671 13.782 10278 Z= 0.312 Chirality : 0.044 0.186 1174 Planarity : 0.005 0.053 1283 Dihedral : 5.368 43.283 1283 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.20 % Allowed : 28.92 % 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: 0.92 (0.28), residues: 874 helix: 2.74 (0.42), residues: 152 sheet: 1.03 (0.30), residues: 282 loop : -0.44 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.006 0.001 HIS B 167 PHE 0.027 0.002 PHE C 62 TYR 0.019 0.002 TYR A 205 ARG 0.004 0.000 ARG D 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 8) link_NAG-ASN : angle 3.72696 ( 24) link_ALPHA1-6 : bond 0.01050 ( 1) link_ALPHA1-6 : angle 1.23855 ( 3) link_BETA1-4 : bond 0.01106 ( 7) link_BETA1-4 : angle 4.11589 ( 21) hydrogen bonds : bond 0.04002 ( 275) hydrogen bonds : angle 4.68721 ( 747) SS BOND : bond 0.00389 ( 8) SS BOND : angle 0.98422 ( 16) covalent geometry : bond 0.00314 ( 7486) covalent geometry : angle 0.61898 (10214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7888 (m-80) cc_final: 0.7631 (m-80) REVERT: A 120 VAL cc_start: 0.8225 (m) cc_final: 0.7992 (p) REVERT: A 155 THR cc_start: 0.8424 (m) cc_final: 0.8223 (p) REVERT: A 210 MET cc_start: 0.7925 (mmm) cc_final: 0.7585 (mmm) REVERT: A 214 GLU cc_start: 0.7221 (pp20) cc_final: 0.6643 (pp20) REVERT: B 45 THR cc_start: 0.8281 (m) cc_final: 0.8012 (p) REVERT: B 54 CYS cc_start: 0.7935 (t) cc_final: 0.7622 (t) REVERT: B 64 TYR cc_start: 0.8519 (m-80) cc_final: 0.8274 (m-80) REVERT: B 84 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8377 (ptt180) REVERT: B 116 TYR cc_start: 0.8477 (t80) cc_final: 0.8124 (t80) REVERT: B 146 TRP cc_start: 0.7057 (p90) cc_final: 0.6513 (p90) REVERT: C 62 PHE cc_start: 0.8169 (m-80) cc_final: 0.7899 (m-10) REVERT: C 118 PHE cc_start: 0.7987 (m-80) cc_final: 0.7703 (m-80) REVERT: C 149 TRP cc_start: 0.8287 (p90) cc_final: 0.7707 (p90) REVERT: C 209 THR cc_start: 0.8361 (p) cc_final: 0.8105 (p) REVERT: D 43 LEU cc_start: 0.8432 (mt) cc_final: 0.7946 (mp) REVERT: D 149 ARG cc_start: 0.8573 (mtt180) cc_final: 0.8352 (mtt180) REVERT: D 154 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7939 (mt0) outliers start: 33 outliers final: 27 residues processed: 219 average time/residue: 0.2365 time to fit residues: 65.7434 Evaluate side-chains 234 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 59 HIS Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 161 LYS 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 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 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: 5.9990 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118730 restraints weight = 12241.776| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.31 r_work: 0.3285 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7510 Z= 0.152 Angle : 0.677 13.492 10278 Z= 0.317 Chirality : 0.044 0.186 1174 Planarity : 0.005 0.053 1283 Dihedral : 5.295 42.412 1283 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.20 % Allowed : 29.04 % 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 (0.28), residues: 874 helix: 2.73 (0.41), residues: 152 sheet: 1.01 (0.30), residues: 282 loop : -0.44 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 197 HIS 0.003 0.001 HIS D 150 PHE 0.027 0.002 PHE D 153 TYR 0.018 0.002 TYR A 205 ARG 0.004 0.000 ARG D 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 8) link_NAG-ASN : angle 3.65720 ( 24) link_ALPHA1-6 : bond 0.00979 ( 1) link_ALPHA1-6 : angle 1.21680 ( 3) link_BETA1-4 : bond 0.01101 ( 7) link_BETA1-4 : angle 4.09245 ( 21) hydrogen bonds : bond 0.04048 ( 275) hydrogen bonds : angle 4.68725 ( 747) SS BOND : bond 0.00330 ( 8) SS BOND : angle 1.10850 ( 16) covalent geometry : bond 0.00348 ( 7486) covalent geometry : angle 0.62660 (10214) *********************** 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 240 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7896 (m-80) cc_final: 0.7640 (m-80) REVERT: A 120 VAL cc_start: 0.8218 (m) cc_final: 0.7996 (p) REVERT: A 155 THR cc_start: 0.8430 (m) cc_final: 0.8229 (p) REVERT: A 210 MET cc_start: 0.7926 (mmm) cc_final: 0.7595 (mmm) REVERT: A 214 GLU cc_start: 0.7234 (pp20) cc_final: 0.6660 (pp20) REVERT: B 45 THR cc_start: 0.8292 (m) cc_final: 0.8013 (p) REVERT: B 54 CYS cc_start: 0.7929 (t) cc_final: 0.7623 (t) REVERT: B 64 TYR cc_start: 0.8531 (m-80) cc_final: 0.8288 (m-80) REVERT: B 116 TYR cc_start: 0.8478 (t80) cc_final: 0.8138 (t80) REVERT: B 146 TRP cc_start: 0.7056 (p90) cc_final: 0.6517 (p90) REVERT: C 118 PHE cc_start: 0.7987 (m-80) cc_final: 0.7749 (m-80) REVERT: C 149 TRP cc_start: 0.8284 (p90) cc_final: 0.7710 (p90) REVERT: C 209 THR cc_start: 0.8345 (p) cc_final: 0.8122 (p) REVERT: D 43 LEU cc_start: 0.8439 (mt) cc_final: 0.7951 (mp) REVERT: D 149 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8367 (mtt180) REVERT: D 154 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7933 (mt0) outliers start: 33 outliers final: 30 residues processed: 217 average time/residue: 0.2383 time to fit residues: 65.8713 Evaluate side-chains 238 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 161 LYS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.0030 chunk 38 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.155121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119740 restraints weight = 12337.885| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.34 r_work: 0.3304 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1972 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= 0.122 Angle : 0.665 13.446 10278 Z= 0.311 Chirality : 0.044 0.187 1174 Planarity : 0.004 0.052 1283 Dihedral : 5.129 41.347 1283 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.69 % Allowed : 29.68 % Favored : 66.62 % 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: 2.83 (0.42), residues: 152 sheet: 0.97 (0.30), residues: 283 loop : -0.43 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.003 0.001 HIS B 59 PHE 0.030 0.002 PHE D 153 TYR 0.017 0.002 TYR A 205 ARG 0.004 0.000 ARG D 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 8) link_NAG-ASN : angle 3.62074 ( 24) link_ALPHA1-6 : bond 0.00948 ( 1) link_ALPHA1-6 : angle 1.18761 ( 3) link_BETA1-4 : bond 0.01123 ( 7) link_BETA1-4 : angle 4.04194 ( 21) hydrogen bonds : bond 0.03789 ( 275) hydrogen bonds : angle 4.61213 ( 747) SS BOND : bond 0.00345 ( 8) SS BOND : angle 1.03731 ( 16) covalent geometry : bond 0.00281 ( 7486) covalent geometry : angle 0.61548 (10214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7905 (m-80) cc_final: 0.7652 (m-80) REVERT: A 120 VAL cc_start: 0.8182 (m) cc_final: 0.7957 (p) REVERT: A 210 MET cc_start: 0.7867 (mmm) cc_final: 0.7522 (mmm) REVERT: A 214 GLU cc_start: 0.7230 (pp20) cc_final: 0.6645 (pp20) REVERT: B 45 THR cc_start: 0.8280 (m) cc_final: 0.7998 (p) REVERT: B 54 CYS cc_start: 0.7945 (t) cc_final: 0.7631 (t) REVERT: B 64 TYR cc_start: 0.8438 (m-80) cc_final: 0.8215 (m-80) REVERT: C 118 PHE cc_start: 0.7966 (m-80) cc_final: 0.7729 (m-80) REVERT: C 149 TRP cc_start: 0.8273 (p90) cc_final: 0.7774 (p90) REVERT: C 209 THR cc_start: 0.8353 (p) cc_final: 0.8125 (p) REVERT: D 43 LEU cc_start: 0.8370 (mt) cc_final: 0.7833 (mp) REVERT: D 149 ARG cc_start: 0.8572 (mtt180) cc_final: 0.8318 (mtt180) REVERT: D 154 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: D 224 LEU cc_start: 0.8651 (mt) cc_final: 0.8352 (tp) outliers start: 29 outliers final: 27 residues processed: 213 average time/residue: 0.2445 time to fit residues: 66.4964 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 : 0.796 ------------------------------------------------------------------------------- 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 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 53 LYS Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 161 LYS 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 28 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120030 restraints weight = 12018.588| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.28 r_work: 0.3309 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2011 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= 0.127 Angle : 0.665 13.034 10278 Z= 0.311 Chirality : 0.044 0.186 1174 Planarity : 0.005 0.052 1283 Dihedral : 5.062 40.574 1283 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.82 % Allowed : 29.55 % Favored : 66.62 % 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: 2.81 (0.41), residues: 152 sheet: 0.98 (0.30), residues: 283 loop : -0.43 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 197 HIS 0.004 0.001 HIS B 59 PHE 0.029 0.002 PHE D 153 TYR 0.017 0.002 TYR A 205 ARG 0.007 0.000 ARG D 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 8) link_NAG-ASN : angle 3.54041 ( 24) link_ALPHA1-6 : bond 0.00905 ( 1) link_ALPHA1-6 : angle 1.18707 ( 3) link_BETA1-4 : bond 0.01108 ( 7) link_BETA1-4 : angle 4.01468 ( 21) hydrogen bonds : bond 0.03755 ( 275) hydrogen bonds : angle 4.58315 ( 747) SS BOND : bond 0.00389 ( 8) SS BOND : angle 1.02928 ( 16) covalent geometry : bond 0.00292 ( 7486) covalent geometry : angle 0.61654 (10214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4232.59 seconds wall clock time: 73 minutes 55.62 seconds (4435.62 seconds total)