Starting phenix.real_space_refine on Sun Apr 5 19:17:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28yj_56971/04_2026/28yj_56971_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/28yj_56971/04_2026/28yj_56971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28yj_56971/04_2026/28yj_56971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28yj_56971/04_2026/28yj_56971.map" model { file = "/net/cci-nas-00/data/ceres_data/28yj_56971/04_2026/28yj_56971_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28yj_56971/04_2026/28yj_56971_trim.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 3956 2.51 5 N 1031 2.21 5 O 1241 1.98 5 H 5741 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12034 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4641 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 280} Chain: "B" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2222 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "C" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2629 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 162} Chain: "D" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2197 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 138} Chain: "E" 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: "F" 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: "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: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" 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: "K" 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: "L" 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 Time building chain proxies: 2.14, per 1000 atoms: 0.18 Number of scatterers: 12034 At special positions: 0 Unit cell: (73.36, 74.8272, 210.543, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 O 1241 8.00 N 1031 7.00 C 3956 6.00 H 5741 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 67 " distance=2.04 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 143 " distance=2.04 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 ALPHA1-3 " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " ALPHA1-6 " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG E 1 " - " ASN A 139 " " NAG F 1 " - " ASN A 150 " " NAG G 1 " - " ASN A 214 " " NAG H 1 " - " ASN B 214 " " NAG I 1 " - " ASN C 139 " " NAG J 1 " - " ASN C 150 " " NAG K 1 " - " ASN D 139 " " NAG L 1 " - " ASN D 150 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 370.3 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 18 sheets defined 7.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.657A pdb=" N ALA A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 4.540A pdb=" N ALA A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 4.539A pdb=" N ALA B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.537A pdb=" N ALA C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 136 through 144 removed outlier: 3.640A pdb=" N ALA D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 149 removed outlier: 6.513A pdb=" N GLU A 178 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N MET B 207 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS A 180 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG B 209 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 182 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY B 211 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL A 184 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 192 removed outlier: 6.548A pdb=" N ARG B 325 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL B 261 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N CYS B 327 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU B 259 " --> pdb=" O CYS B 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 211 removed outlier: 6.049A pdb=" N LEU A 203 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS C 180 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN A 205 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER C 182 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET A 207 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 184 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG A 209 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA C 186 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLY A 211 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 215 through 220 Processing sheet with id=AA8, first strand: chain 'A' and resid 278 through 279 removed outlier: 5.422A pdb=" N LEU A 259 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N CYS A 327 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL A 261 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 325 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AB1, first strand: chain 'B' and resid 215 through 220 Processing sheet with id=AB2, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 61 Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 83 through 87 Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 211 removed outlier: 5.952A pdb=" N LEU C 203 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N HIS D 180 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN C 205 " --> pdb=" O HIS D 180 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N SER D 182 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N MET C 207 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL D 184 " --> pdb=" O MET C 207 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG C 209 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ALA D 186 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY C 211 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 154 " --> pdb=" O TYR D 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 61 Processing sheet with id=AB8, first strand: chain 'D' and resid 73 through 74 Processing sheet with id=AB9, first strand: chain 'D' and resid 83 through 87 177 hydrogen bonds defined for protein. 447 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: 2.57 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 5741 1.02 - 1.22: 7 1.22 - 1.42: 2677 1.42 - 1.62: 3661 1.62 - 1.83: 88 Bond restraints: 12174 Sorted by residual: bond pdb=" ND2 ASN D 139 " pdb="HD21 ASN D 139 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" NE ARG C 209 " pdb=" HE ARG C 209 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C VAL C 200 " pdb=" N ASP C 201 " ideal model delta sigma weight residual 1.332 1.288 0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" C VAL A 200 " pdb=" N ASP A 201 " ideal model delta sigma weight residual 1.332 1.373 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N ASP A 201 " pdb=" CA ASP A 201 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.25e-02 6.40e+03 8.20e+00 ... (remaining 12169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21129 2.36 - 4.72: 622 4.72 - 7.07: 74 7.07 - 9.43: 20 9.43 - 11.79: 2 Bond angle restraints: 21847 Sorted by residual: angle pdb=" N HIS C 140 " pdb=" CA HIS C 140 " pdb=" C HIS C 140 " ideal model delta sigma weight residual 113.41 107.72 5.69 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N ASN D 139 " pdb=" CA ASN D 139 " pdb=" C ASN D 139 " ideal model delta sigma weight residual 113.28 118.56 -5.28 1.22e+00 6.72e-01 1.88e+01 angle pdb=" C ASN B 214 " pdb=" CA ASN B 214 " pdb=" CB ASN B 214 " ideal model delta sigma weight residual 109.84 116.38 -6.54 1.63e+00 3.76e-01 1.61e+01 angle pdb=" N ASP A 201 " pdb=" CA ASP A 201 " pdb=" C ASP A 201 " ideal model delta sigma weight residual 112.93 118.24 -5.31 1.33e+00 5.65e-01 1.59e+01 angle pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " pdb=" O2 BMA I 3 " ideal model delta sigma weight residual 108.40 120.19 -11.79 3.00e+00 1.11e-01 1.54e+01 ... (remaining 21842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 5693 21.16 - 42.32: 340 42.32 - 63.48: 101 63.48 - 84.63: 46 84.63 - 105.79: 34 Dihedral angle restraints: 6214 sinusoidal: 3600 harmonic: 2614 Sorted by residual: dihedral pdb=" CB CYS D 69 " pdb=" SG CYS D 69 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual -86.00 -130.97 44.97 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " pdb=" SG CYS C 78 " pdb=" CB CYS C 78 " ideal model delta sinusoidal sigma weight residual -86.00 -130.96 44.96 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS A 78 " pdb=" CB CYS A 78 " ideal model delta sinusoidal sigma weight residual -86.00 -130.95 44.95 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 6211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.324: 1031 0.324 - 0.648: 4 0.648 - 0.972: 3 0.972 - 1.297: 1 1.297 - 1.621: 2 Chirality restraints: 1041 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-02 2.50e+03 4.23e+03 chirality pdb=" C1 MAN I 6 " pdb=" O3 BMA I 3 " pdb=" C2 MAN I 6 " pdb=" O5 MAN I 6 " both_signs ideal model delta sigma weight residual False 2.40 1.43 0.97 2.00e-02 2.50e+03 2.33e+03 chirality pdb=" C1 MAN I 5 " pdb=" O3 MAN I 4 " pdb=" C2 MAN I 5 " pdb=" O5 MAN I 5 " both_signs ideal model delta sigma weight residual False 2.40 1.71 0.69 2.00e-02 2.50e+03 1.21e+03 ... (remaining 1038 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.299 2.00e-02 2.50e+03 2.59e-01 8.36e+02 pdb=" C7 NAG H 1 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.245 2.00e-02 2.50e+03 2.04e-01 5.22e+02 pdb=" C7 NAG I 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.340 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.181 2.00e-02 2.50e+03 1.55e-01 3.01e+02 pdb=" C7 NAG K 2 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.256 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.141 2.00e-02 2.50e+03 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 198 2.12 - 2.74: 20108 2.74 - 3.36: 31847 3.36 - 3.98: 40041 3.98 - 4.60: 62275 Nonbonded interactions: 154469 Sorted by model distance: nonbonded pdb=" OE1 GLU D 138 " pdb=" H GLU D 138 " model vdw 1.497 2.450 nonbonded pdb="HE22 GLN C 149 " pdb=" HH TYR C 187 " model vdw 1.649 2.100 nonbonded pdb=" OG SER D 155 " pdb="HG22 VAL D 184 " model vdw 1.827 2.620 nonbonded pdb=" H TYR A 187 " pdb=" HD1 TYR A 187 " model vdw 1.843 2.100 nonbonded pdb=" O LEU A 203 " pdb=" H GLU C 178 " model vdw 1.857 2.450 ... (remaining 154464 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 11.960 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: 0.070 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.006 0.213 6481 Z= 0.326 Angle : 1.368 30.960 8830 Z= 0.629 Chirality : 0.111 1.621 1041 Planarity : 0.016 0.259 1091 Dihedral : 18.920 105.792 2798 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.75 % Allowed : 3.75 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.29), residues: 744 helix: 0.43 (0.88), residues: 35 sheet: 0.27 (0.32), residues: 236 loop : -0.14 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 108 TYR 0.008 0.001 TYR A 256 PHE 0.026 0.003 PHE C 131 TRP 0.002 0.001 TRP B 265 HIS 0.008 0.002 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 6433) covalent geometry : angle 1.08149 ( 8707) SS BOND : bond 0.00329 ( 21) SS BOND : angle 1.46618 ( 42) hydrogen bonds : bond 0.10045 ( 177) hydrogen bonds : angle 8.46670 ( 447) link_ALPHA1-3 : bond 0.02908 ( 2) link_ALPHA1-3 : angle 6.23573 ( 6) link_ALPHA1-6 : bond 0.03824 ( 1) link_ALPHA1-6 : angle 5.12700 ( 3) link_BETA1-4 : bond 0.02781 ( 16) link_BETA1-4 : angle 7.31603 ( 48) link_NAG-ASN : bond 0.07739 ( 8) link_NAG-ASN : angle 11.85164 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.5727 (mtm) cc_final: 0.5184 (mtm) REVERT: A 96 VAL cc_start: 0.7185 (t) cc_final: 0.6711 (t) REVERT: C 135 LEU cc_start: 0.8919 (tp) cc_final: 0.8686 (tp) REVERT: D 94 MET cc_start: 0.8983 (mtm) cc_final: 0.8706 (mpp) REVERT: D 135 LEU cc_start: 0.6853 (tp) cc_final: 0.6192 (tp) REVERT: D 187 TYR cc_start: 0.1201 (m-80) cc_final: -0.0102 (t80) outliers start: 5 outliers final: 1 residues processed: 89 average time/residue: 0.1808 time to fit residues: 20.6830 Evaluate side-chains 56 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS C 55 HIS C 112 HIS C 116 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.051230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.041372 restraints weight = 183364.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.042919 restraints weight = 94253.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.044006 restraints weight = 59161.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.044726 restraints weight = 42324.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.045213 restraints weight = 33405.745| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6481 Z= 0.176 Angle : 0.893 13.122 8830 Z= 0.387 Chirality : 0.053 0.451 1041 Planarity : 0.004 0.038 1091 Dihedral : 15.193 75.960 1350 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.29), residues: 744 helix: -0.18 (0.74), residues: 42 sheet: -0.02 (0.34), residues: 220 loop : -0.22 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.008 0.001 TYR D 156 PHE 0.011 0.001 PHE A 131 TRP 0.002 0.001 TRP A 265 HIS 0.014 0.002 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6433) covalent geometry : angle 0.76073 ( 8707) SS BOND : bond 0.00175 ( 21) SS BOND : angle 1.08988 ( 42) hydrogen bonds : bond 0.05512 ( 177) hydrogen bonds : angle 7.56048 ( 447) link_ALPHA1-3 : bond 0.01639 ( 2) link_ALPHA1-3 : angle 1.85290 ( 6) link_ALPHA1-6 : bond 0.00127 ( 1) link_ALPHA1-6 : angle 2.01802 ( 3) link_BETA1-4 : bond 0.01205 ( 16) link_BETA1-4 : angle 4.99178 ( 48) link_NAG-ASN : bond 0.00469 ( 8) link_NAG-ASN : angle 5.52165 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.5208 (mtm) cc_final: 0.4953 (mtm) REVERT: B 245 MET cc_start: 0.8675 (tpp) cc_final: 0.8039 (tpt) REVERT: C 135 LEU cc_start: 0.8852 (tp) cc_final: 0.8396 (tp) REVERT: D 135 LEU cc_start: 0.7005 (tp) cc_final: 0.6380 (tp) REVERT: D 187 TYR cc_start: 0.1094 (m-80) cc_final: -0.0303 (t80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1499 time to fit residues: 12.3312 Evaluate side-chains 50 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 HIS C 116 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.049886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.039965 restraints weight = 187018.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.041461 restraints weight = 97547.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.042535 restraints weight = 62054.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.043214 restraints weight = 44952.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.043680 restraints weight = 35941.880| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6481 Z= 0.201 Angle : 0.865 12.431 8830 Z= 0.374 Chirality : 0.051 0.352 1041 Planarity : 0.004 0.035 1091 Dihedral : 10.289 64.118 1350 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.29), residues: 744 helix: 0.25 (0.81), residues: 42 sheet: -0.39 (0.34), residues: 228 loop : -0.25 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.010 0.001 TYR B 315 PHE 0.016 0.002 PHE B 206 TRP 0.004 0.001 TRP A 265 HIS 0.009 0.002 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6433) covalent geometry : angle 0.75348 ( 8707) SS BOND : bond 0.00300 ( 21) SS BOND : angle 0.74857 ( 42) hydrogen bonds : bond 0.04340 ( 177) hydrogen bonds : angle 7.12032 ( 447) link_ALPHA1-3 : bond 0.01723 ( 2) link_ALPHA1-3 : angle 2.16463 ( 6) link_ALPHA1-6 : bond 0.00158 ( 1) link_ALPHA1-6 : angle 1.71622 ( 3) link_BETA1-4 : bond 0.01241 ( 16) link_BETA1-4 : angle 4.52325 ( 48) link_NAG-ASN : bond 0.00300 ( 8) link_NAG-ASN : angle 5.06497 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8704 (tpp) cc_final: 0.8424 (tpp) REVERT: D 187 TYR cc_start: 0.1088 (m-80) cc_final: -0.0532 (t80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1351 time to fit residues: 11.1845 Evaluate side-chains 45 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.047268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.037919 restraints weight = 192191.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.039314 restraints weight = 99503.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.040253 restraints weight = 63204.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.040856 restraints weight = 46285.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.041307 restraints weight = 37440.158| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 6481 Z= 0.367 Angle : 1.029 12.909 8830 Z= 0.463 Chirality : 0.052 0.292 1041 Planarity : 0.006 0.045 1091 Dihedral : 12.303 67.041 1350 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.15 % Allowed : 3.45 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.28), residues: 744 helix: -1.30 (0.63), residues: 49 sheet: -1.03 (0.32), residues: 234 loop : -0.95 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 97 TYR 0.025 0.002 TYR D 185 PHE 0.028 0.003 PHE B 206 TRP 0.008 0.002 TRP A 265 HIS 0.011 0.003 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 6433) covalent geometry : angle 0.93285 ( 8707) SS BOND : bond 0.00492 ( 21) SS BOND : angle 1.05260 ( 42) hydrogen bonds : bond 0.04797 ( 177) hydrogen bonds : angle 7.24840 ( 447) link_ALPHA1-3 : bond 0.01120 ( 2) link_ALPHA1-3 : angle 2.40200 ( 6) link_ALPHA1-6 : bond 0.00092 ( 1) link_ALPHA1-6 : angle 3.54592 ( 3) link_BETA1-4 : bond 0.01194 ( 16) link_BETA1-4 : angle 4.41052 ( 48) link_NAG-ASN : bond 0.00996 ( 8) link_NAG-ASN : angle 5.48164 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8206 (tmm) cc_final: 0.7847 (tmm) REVERT: D 94 MET cc_start: 0.8350 (mpp) cc_final: 0.8074 (mpp) REVERT: D 187 TYR cc_start: 0.1576 (m-80) cc_final: -0.0341 (t80) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.1515 time to fit residues: 9.9657 Evaluate side-chains 41 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.048588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.038552 restraints weight = 186233.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.039956 restraints weight = 98911.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.040908 restraints weight = 63869.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.041626 restraints weight = 47304.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.042087 restraints weight = 38099.251| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6481 Z= 0.151 Angle : 0.774 12.210 8830 Z= 0.340 Chirality : 0.049 0.319 1041 Planarity : 0.004 0.034 1091 Dihedral : 10.607 59.315 1350 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.15 % Allowed : 1.05 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.29), residues: 744 helix: -0.71 (0.70), residues: 49 sheet: -1.14 (0.32), residues: 233 loop : -0.64 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.008 0.001 TYR B 229 PHE 0.027 0.002 PHE A 131 TRP 0.005 0.001 TRP A 265 HIS 0.010 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6433) covalent geometry : angle 0.68000 ( 8707) SS BOND : bond 0.00193 ( 21) SS BOND : angle 0.82285 ( 42) hydrogen bonds : bond 0.03942 ( 177) hydrogen bonds : angle 6.74586 ( 447) link_ALPHA1-3 : bond 0.01609 ( 2) link_ALPHA1-3 : angle 1.83463 ( 6) link_ALPHA1-6 : bond 0.00389 ( 1) link_ALPHA1-6 : angle 1.27942 ( 3) link_BETA1-4 : bond 0.01149 ( 16) link_BETA1-4 : angle 3.85921 ( 48) link_NAG-ASN : bond 0.00317 ( 8) link_NAG-ASN : angle 4.56542 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8273 (tmm) cc_final: 0.7904 (tmm) REVERT: D 187 TYR cc_start: 0.1543 (m-80) cc_final: -0.0438 (t80) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.1480 time to fit residues: 9.9772 Evaluate side-chains 43 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.047996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.038082 restraints weight = 191228.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.039536 restraints weight = 101186.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.040545 restraints weight = 65310.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.041199 restraints weight = 47864.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.041646 restraints weight = 38741.858| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6481 Z= 0.153 Angle : 0.738 11.457 8830 Z= 0.323 Chirality : 0.047 0.286 1041 Planarity : 0.004 0.032 1091 Dihedral : 10.022 59.968 1350 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.15 % Allowed : 1.05 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.29), residues: 744 helix: -0.58 (0.71), residues: 49 sheet: -1.13 (0.32), residues: 231 loop : -0.57 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.006 0.001 TYR B 315 PHE 0.016 0.001 PHE B 206 TRP 0.004 0.001 TRP A 265 HIS 0.012 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6433) covalent geometry : angle 0.64665 ( 8707) SS BOND : bond 0.00330 ( 21) SS BOND : angle 0.92487 ( 42) hydrogen bonds : bond 0.03640 ( 177) hydrogen bonds : angle 6.50906 ( 447) link_ALPHA1-3 : bond 0.01527 ( 2) link_ALPHA1-3 : angle 1.67840 ( 6) link_ALPHA1-6 : bond 0.00397 ( 1) link_ALPHA1-6 : angle 1.40731 ( 3) link_BETA1-4 : bond 0.01083 ( 16) link_BETA1-4 : angle 3.73270 ( 48) link_NAG-ASN : bond 0.00260 ( 8) link_NAG-ASN : angle 4.29197 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8708 (tpp) cc_final: 0.8425 (tpp) REVERT: B 217 MET cc_start: 0.8388 (tmm) cc_final: 0.8040 (tmm) REVERT: C 113 LEU cc_start: 0.9401 (mp) cc_final: 0.9163 (mp) REVERT: D 187 TYR cc_start: 0.1499 (m-80) cc_final: -0.0252 (t80) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.1370 time to fit residues: 9.8695 Evaluate side-chains 45 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 52 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.048517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.038663 restraints weight = 184842.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.040079 restraints weight = 97632.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.041071 restraints weight = 62965.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.041768 restraints weight = 46267.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.042185 restraints weight = 37291.027| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6481 Z= 0.110 Angle : 0.690 11.857 8830 Z= 0.302 Chirality : 0.048 0.309 1041 Planarity : 0.003 0.032 1091 Dihedral : 8.982 53.093 1350 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.15 % Allowed : 0.90 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.30), residues: 744 helix: -0.41 (0.73), residues: 48 sheet: -1.04 (0.34), residues: 222 loop : -0.50 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.006 0.001 TYR B 229 PHE 0.013 0.001 PHE D 130 TRP 0.003 0.001 TRP A 265 HIS 0.011 0.001 HIS A 180 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 6433) covalent geometry : angle 0.60338 ( 8707) SS BOND : bond 0.00140 ( 21) SS BOND : angle 0.79007 ( 42) hydrogen bonds : bond 0.03413 ( 177) hydrogen bonds : angle 6.25714 ( 447) link_ALPHA1-3 : bond 0.01708 ( 2) link_ALPHA1-3 : angle 1.63492 ( 6) link_ALPHA1-6 : bond 0.00528 ( 1) link_ALPHA1-6 : angle 1.39231 ( 3) link_BETA1-4 : bond 0.01155 ( 16) link_BETA1-4 : angle 3.55017 ( 48) link_NAG-ASN : bond 0.00344 ( 8) link_NAG-ASN : angle 3.97376 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8655 (tpp) cc_final: 0.8353 (tpp) REVERT: B 217 MET cc_start: 0.8328 (tmm) cc_final: 0.7688 (tmm) REVERT: C 207 MET cc_start: 0.7929 (ttt) cc_final: 0.7546 (ttm) REVERT: D 187 TYR cc_start: 0.1721 (m-80) cc_final: -0.0176 (t80) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.1281 time to fit residues: 9.2742 Evaluate side-chains 43 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.048126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.038304 restraints weight = 185206.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.039701 restraints weight = 97636.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.040648 restraints weight = 62981.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.041332 restraints weight = 46711.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.041793 restraints weight = 37696.604| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6481 Z= 0.139 Angle : 0.694 11.291 8830 Z= 0.305 Chirality : 0.047 0.345 1041 Planarity : 0.004 0.033 1091 Dihedral : 8.779 53.047 1350 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.30), residues: 744 helix: -0.74 (0.69), residues: 49 sheet: -1.08 (0.34), residues: 222 loop : -0.50 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 97 TYR 0.007 0.001 TYR C 187 PHE 0.010 0.001 PHE D 130 TRP 0.004 0.001 TRP A 265 HIS 0.012 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6433) covalent geometry : angle 0.60873 ( 8707) SS BOND : bond 0.00174 ( 21) SS BOND : angle 0.61632 ( 42) hydrogen bonds : bond 0.03442 ( 177) hydrogen bonds : angle 6.22952 ( 447) link_ALPHA1-3 : bond 0.01592 ( 2) link_ALPHA1-3 : angle 1.58975 ( 6) link_ALPHA1-6 : bond 0.00358 ( 1) link_ALPHA1-6 : angle 1.40965 ( 3) link_BETA1-4 : bond 0.01075 ( 16) link_BETA1-4 : angle 3.55257 ( 48) link_NAG-ASN : bond 0.00304 ( 8) link_NAG-ASN : angle 3.98004 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8707 (tpp) cc_final: 0.8412 (tpp) REVERT: B 217 MET cc_start: 0.8295 (tmm) cc_final: 0.7666 (tmm) REVERT: C 207 MET cc_start: 0.7835 (ttt) cc_final: 0.7406 (ttm) REVERT: D 187 TYR cc_start: 0.1559 (m-80) cc_final: -0.0093 (t80) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1608 time to fit residues: 10.1691 Evaluate side-chains 41 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.0870 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.048484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.038576 restraints weight = 184390.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.040024 restraints weight = 97897.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.041028 restraints weight = 63030.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.041679 restraints weight = 46356.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.042133 restraints weight = 37686.553| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6481 Z= 0.104 Angle : 0.665 11.530 8830 Z= 0.292 Chirality : 0.047 0.342 1041 Planarity : 0.003 0.033 1091 Dihedral : 8.311 53.062 1350 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.30), residues: 744 helix: -0.76 (0.70), residues: 49 sheet: -1.03 (0.34), residues: 224 loop : -0.42 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.004 0.001 TYR B 229 PHE 0.012 0.001 PHE D 130 TRP 0.003 0.001 TRP A 265 HIS 0.010 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 6433) covalent geometry : angle 0.58219 ( 8707) SS BOND : bond 0.00137 ( 21) SS BOND : angle 0.62314 ( 42) hydrogen bonds : bond 0.03262 ( 177) hydrogen bonds : angle 6.07250 ( 447) link_ALPHA1-3 : bond 0.01697 ( 2) link_ALPHA1-3 : angle 1.73028 ( 6) link_ALPHA1-6 : bond 0.00421 ( 1) link_ALPHA1-6 : angle 1.31064 ( 3) link_BETA1-4 : bond 0.01113 ( 16) link_BETA1-4 : angle 3.42207 ( 48) link_NAG-ASN : bond 0.00407 ( 8) link_NAG-ASN : angle 3.82872 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.8647 (tpp) cc_final: 0.8350 (tpp) REVERT: C 207 MET cc_start: 0.7859 (ttt) cc_final: 0.7512 (ttm) REVERT: D 187 TYR cc_start: 0.1512 (m-80) cc_final: -0.0108 (t80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1662 time to fit residues: 10.7582 Evaluate side-chains 41 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.047531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.037724 restraints weight = 189487.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.039114 restraints weight = 101157.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.040059 restraints weight = 65356.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.040678 restraints weight = 48516.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.041113 restraints weight = 39623.562| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6481 Z= 0.179 Angle : 0.723 11.065 8830 Z= 0.319 Chirality : 0.046 0.259 1041 Planarity : 0.004 0.034 1091 Dihedral : 9.221 64.116 1350 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.29), residues: 744 helix: -1.11 (0.66), residues: 50 sheet: -1.04 (0.34), residues: 233 loop : -0.59 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 97 TYR 0.007 0.001 TYR A 243 PHE 0.011 0.001 PHE B 206 TRP 0.005 0.002 TRP A 265 HIS 0.008 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6433) covalent geometry : angle 0.64239 ( 8707) SS BOND : bond 0.00232 ( 21) SS BOND : angle 0.61628 ( 42) hydrogen bonds : bond 0.03363 ( 177) hydrogen bonds : angle 6.21789 ( 447) link_ALPHA1-3 : bond 0.01627 ( 2) link_ALPHA1-3 : angle 1.81880 ( 6) link_ALPHA1-6 : bond 0.00162 ( 1) link_ALPHA1-6 : angle 1.89092 ( 3) link_BETA1-4 : bond 0.01030 ( 16) link_BETA1-4 : angle 3.53196 ( 48) link_NAG-ASN : bond 0.00505 ( 8) link_NAG-ASN : angle 3.93981 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 MET cc_start: 0.6655 (mtp) cc_final: 0.6378 (mtp) REVERT: B 217 MET cc_start: 0.8266 (tmm) cc_final: 0.7978 (tmm) REVERT: D 187 TYR cc_start: 0.1293 (m-80) cc_final: -0.0173 (t80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1598 time to fit residues: 10.3868 Evaluate side-chains 41 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.048072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.038305 restraints weight = 182033.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.039697 restraints weight = 97044.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.040674 restraints weight = 62771.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.041243 restraints weight = 46222.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.041720 restraints weight = 37954.310| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6481 Z= 0.115 Angle : 0.671 11.519 8830 Z= 0.295 Chirality : 0.047 0.286 1041 Planarity : 0.003 0.033 1091 Dihedral : 8.637 55.918 1350 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.29), residues: 744 helix: -0.99 (0.68), residues: 49 sheet: -1.09 (0.35), residues: 220 loop : -0.59 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.006 0.001 TYR A 187 PHE 0.011 0.001 PHE D 130 TRP 0.003 0.001 TRP A 265 HIS 0.008 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6433) covalent geometry : angle 0.59271 ( 8707) SS BOND : bond 0.00143 ( 21) SS BOND : angle 0.61695 ( 42) hydrogen bonds : bond 0.03222 ( 177) hydrogen bonds : angle 6.06211 ( 447) link_ALPHA1-3 : bond 0.01677 ( 2) link_ALPHA1-3 : angle 1.88498 ( 6) link_ALPHA1-6 : bond 0.00390 ( 1) link_ALPHA1-6 : angle 1.37008 ( 3) link_BETA1-4 : bond 0.01091 ( 16) link_BETA1-4 : angle 3.38775 ( 48) link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 3.66043 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2327.04 seconds wall clock time: 40 minutes 26.18 seconds (2426.18 seconds total)