Starting phenix.real_space_refine on Thu Jul 2 07:29:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbx_64935/07_2026/9vbx_64935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbx_64935/07_2026/9vbx_64935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vbx_64935/07_2026/9vbx_64935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbx_64935/07_2026/9vbx_64935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vbx_64935/07_2026/9vbx_64935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbx_64935/07_2026/9vbx_64935.map" } resolution = 2.4 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= 0.004 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 Ca 4 9.91 5 Mn 4 7.51 5 C 4712 2.51 5 N 1200 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7453 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "B" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "C" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "D" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1805 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Chain: "b" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'FUC': 1, 'GAL': 1, 'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 1, ' MN': 1} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 1.91, per 1000 atoms: 0.26 Number of scatterers: 7453 At special positions: 0 Unit cell: (80.51, 88.81, 83.83, 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) Mn 4 24.99 Ca 4 19.99 O 1533 8.00 N 1200 7.00 C 4712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-2 " MAN a 1 " - " NAG a 2 " " MAN b 1 " - " NAG b 2 " " MAN c 1 " - " NAG c 2 " " MAN d 1 " - " NAG d 2 " BETA1-3 " NAG a 2 " - " FUC a 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG b 2 " - " FUC b 3 " " NAG c 2 " - " FUC c 3 " " NAG d 2 " - " FUC d 3 " BETA1-4 " NAG a 2 " - " GAL a 4 " " NAG b 2 " - " GAL b 4 " " NAG c 2 " - " GAL c 4 " " NAG d 2 " - " GAL d 4 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 416.1 milliseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 12 sheets defined 6.5% alpha, 58.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.697A pdb=" N PHE A 105 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.697A pdb=" N PHE B 105 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.696A pdb=" N PHE C 105 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.697A pdb=" N PHE D 105 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 210 through 214 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.778A pdb=" N TRP A 246 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR A 66 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER A 244 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A 68 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 242 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 70 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER A 240 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 72 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 238 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 74 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 236 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 76 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN A 234 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B 234 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE B 76 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 236 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE B 74 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER B 238 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 72 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER B 240 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 70 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR B 242 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE B 68 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER B 244 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR B 66 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP B 246 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 22 removed outlier: 5.101A pdb=" N VAL A 221 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 18 through 22 removed outlier: 5.101A pdb=" N VAL A 221 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 166 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 22 removed outlier: 5.100A pdb=" N VAL B 221 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 5.100A pdb=" N VAL B 221 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 166 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'C' and resid 203 through 208 removed outlier: 6.778A pdb=" N TRP C 246 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 66 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER C 244 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE C 68 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 242 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR C 70 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER C 240 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 72 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER C 238 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE C 74 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 236 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE C 76 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN C 234 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASN D 234 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 76 " --> pdb=" O ASN D 234 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL D 236 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE D 74 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER D 238 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE D 72 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER D 240 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR D 70 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR D 242 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE D 68 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER D 244 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR D 66 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP D 246 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 18 through 22 removed outlier: 5.100A pdb=" N VAL C 221 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 22 removed outlier: 5.100A pdb=" N VAL C 221 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL C 166 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 22 removed outlier: 5.100A pdb=" N VAL D 221 " --> pdb=" O TYR D 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 22 removed outlier: 5.100A pdb=" N VAL D 221 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 166 " --> pdb=" O ILE D 157 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1032 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: 1.25 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 1180 1.28 - 1.35: 1139 1.35 - 1.42: 965 1.42 - 1.48: 1292 1.48 - 1.55: 3032 Bond restraints: 7608 Sorted by residual: bond pdb=" N TYR B 147 " pdb=" CA TYR B 147 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.21e+00 bond pdb=" N TYR D 147 " pdb=" CA TYR D 147 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.26e-02 6.30e+03 8.01e+00 bond pdb=" N TYR C 147 " pdb=" CA TYR C 147 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.26e-02 6.30e+03 7.71e+00 bond pdb=" N SER C 200 " pdb=" CA SER C 200 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.64e+00 bond pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.26e-02 6.30e+03 6.59e+00 ... (remaining 7603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 9749 1.75 - 3.50: 588 3.50 - 5.25: 41 5.25 - 7.01: 26 7.01 - 8.76: 4 Bond angle restraints: 10408 Sorted by residual: angle pdb=" N GLU D 60 " pdb=" CA GLU D 60 " pdb=" C GLU D 60 " ideal model delta sigma weight residual 109.07 103.19 5.88 1.52e+00 4.33e-01 1.50e+01 angle pdb=" N GLU B 60 " pdb=" CA GLU B 60 " pdb=" C GLU B 60 " ideal model delta sigma weight residual 109.07 103.23 5.84 1.52e+00 4.33e-01 1.47e+01 angle pdb=" N GLU A 60 " pdb=" CA GLU A 60 " pdb=" C GLU A 60 " ideal model delta sigma weight residual 109.07 103.25 5.82 1.52e+00 4.33e-01 1.47e+01 angle pdb=" N GLU C 60 " pdb=" CA GLU C 60 " pdb=" C GLU C 60 " ideal model delta sigma weight residual 109.07 103.26 5.81 1.52e+00 4.33e-01 1.46e+01 angle pdb=" N GLY B 87 " pdb=" CA GLY B 87 " pdb=" C GLY B 87 " ideal model delta sigma weight residual 110.38 115.68 -5.30 1.42e+00 4.96e-01 1.39e+01 ... (remaining 10403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 4199 16.13 - 32.25: 310 32.25 - 48.38: 83 48.38 - 64.51: 12 64.51 - 80.63: 12 Dihedral angle restraints: 4616 sinusoidal: 1916 harmonic: 2700 Sorted by residual: dihedral pdb=" CA ALA D 89 " pdb=" C ALA D 89 " pdb=" N PHE D 90 " pdb=" CA PHE D 90 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA A 89 " pdb=" C ALA A 89 " pdb=" N PHE A 90 " pdb=" CA PHE A 90 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA B 89 " pdb=" C ALA B 89 " pdb=" N PHE B 90 " pdb=" CA PHE B 90 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 679 0.047 - 0.093: 392 0.093 - 0.140: 115 0.140 - 0.186: 33 0.186 - 0.233: 5 Chirality restraints: 1224 Sorted by residual: chirality pdb=" C1 NAG d 2 " pdb=" O2 MAN d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.81e+01 chirality pdb=" C1 NAG a 2 " pdb=" O2 MAN a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.79e+01 chirality pdb=" C1 NAG b 2 " pdb=" O2 MAN b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.59e+01 ... (remaining 1221 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " 0.038 2.00e-02 2.50e+03 3.13e-02 1.22e+01 pdb=" C7 NAG b 2 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " 0.037 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" C7 NAG a 2 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " -0.049 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " -0.037 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C7 NAG c 2 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " -0.028 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " 0.049 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " 0.008 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 72 2.47 - 3.08: 4957 3.08 - 3.69: 12198 3.69 - 4.29: 19117 4.29 - 4.90: 31434 Nonbonded interactions: 67778 Sorted by model distance: nonbonded pdb=" OD1 ASP A 149 " pdb="MN MN A 302 " model vdw 1.864 3.060 nonbonded pdb=" OD1 ASP C 149 " pdb="MN MN C 302 " model vdw 1.865 3.060 nonbonded pdb=" OD1 ASP D 149 " pdb="MN MN D 302 " model vdw 1.865 3.060 nonbonded pdb=" OD1 ASP B 149 " pdb="MN MN B 302 " model vdw 1.866 3.060 nonbonded pdb=" OD2 ASP C 140 " pdb="MN MN C 302 " model vdw 1.903 3.060 ... (remaining 67773 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.810 Find NCS groups from input model: 0.060 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.009 0.058 7620 Z= 0.415 Angle : 0.927 8.758 10444 Z= 0.528 Chirality : 0.062 0.233 1224 Planarity : 0.005 0.042 1300 Dihedral : 13.418 80.634 2872 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.74 (0.25), residues: 908 helix: None (None), residues: 0 sheet: 0.12 (0.24), residues: 420 loop : -1.03 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.012 0.002 TYR A 147 PHE 0.020 0.004 PHE C 6 TRP 0.012 0.003 TRP A 246 HIS 0.005 0.002 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.42 ( 7608) covalent geometry : angle 0.92830 / 0.53 (10408) hydrogen bonds : bond 0.09977 / 6.41 ( 324) hydrogen bonds : angle 6.60827 / 4.58 ( 1032) link_BETA1-2 : bond 0.00034 / 0.02 ( 4) link_BETA1-2 : angle 0.73827 / 0.47 ( 12) link_BETA1-3 : bond 0.00212 / 0.09 ( 4) link_BETA1-3 : angle 0.74986 / 0.45 ( 12) link_BETA1-4 : bond 0.00077 / 0.03 ( 4) link_BETA1-4 : angle 0.36410 / 0.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.4736 time to fit residues: 102.7007 Evaluate side-chains 168 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 73 ASN A 102 HIS A 133 ASN A 160 ASN A 173 GLN A 174 ASN B 23 HIS B 73 ASN B 102 HIS B 133 ASN B 160 ASN B 173 GLN B 174 ASN C 23 HIS C 73 ASN C 102 HIS C 133 ASN C 160 ASN C 173 GLN C 174 ASN D 23 HIS D 73 ASN D 102 HIS D 133 ASN D 160 ASN D 173 GLN D 174 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140628 restraints weight = 7365.797| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.64 r_work: 0.3392 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7620 Z= 0.150 Angle : 0.604 4.235 10444 Z= 0.340 Chirality : 0.047 0.161 1224 Planarity : 0.005 0.038 1300 Dihedral : 5.299 18.342 1300 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.59 % Allowed : 15.59 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -0.28 (0.27), residues: 908 helix: None (None), residues: 0 sheet: 0.45 (0.25), residues: 404 loop : -0.70 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 57 TYR 0.007 0.001 TYR A 184 PHE 0.015 0.002 PHE D 68 TRP 0.007 0.001 TRP A 246 HIS 0.004 0.001 HIS D 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 7608) covalent geometry : angle 0.59982 / 0.34 (10408) hydrogen bonds : bond 0.04383 / 2.83 ( 324) hydrogen bonds : angle 5.07048 / 3.49 ( 1032) link_BETA1-2 : bond 0.00487 / 0.22 ( 4) link_BETA1-2 : angle 1.16176 / 0.73 ( 12) link_BETA1-3 : bond 0.01042 / 0.46 ( 4) link_BETA1-3 : angle 1.26469 / 0.80 ( 12) link_BETA1-4 : bond 0.00457 / 0.20 ( 4) link_BETA1-4 : angle 1.58562 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7687 (mptp) cc_final: 0.6992 (mtpt) REVERT: B 176 LYS cc_start: 0.7685 (mptp) cc_final: 0.6964 (mtpt) REVERT: C 176 LYS cc_start: 0.7661 (mptp) cc_final: 0.6965 (mtpt) REVERT: D 176 LYS cc_start: 0.7686 (mptp) cc_final: 0.6987 (mtpt) outliers start: 29 outliers final: 15 residues processed: 197 average time/residue: 0.5264 time to fit residues: 110.0752 Evaluate side-chains 185 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 204 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135703 restraints weight = 7478.674| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.65 r_work: 0.3315 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7620 Z= 0.241 Angle : 0.636 4.685 10444 Z= 0.360 Chirality : 0.049 0.165 1224 Planarity : 0.005 0.041 1300 Dihedral : 5.284 16.996 1300 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.83 % Allowed : 14.73 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.04 (0.27), residues: 908 helix: None (None), residues: 0 sheet: 0.68 (0.26), residues: 404 loop : -0.49 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.008 0.001 TYR A 207 PHE 0.016 0.003 PHE A 6 TRP 0.005 0.001 TRP C 218 HIS 0.006 0.001 HIS C 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 ( 7608) covalent geometry : angle 0.63226 / 0.36 (10408) hydrogen bonds : bond 0.04847 / 3.12 ( 324) hydrogen bonds : angle 5.03575 / 3.46 ( 1032) link_BETA1-2 : bond 0.00487 / 0.22 ( 4) link_BETA1-2 : angle 1.12752 / 0.69 ( 12) link_BETA1-3 : bond 0.00880 / 0.41 ( 4) link_BETA1-3 : angle 1.61797 / 0.99 ( 12) link_BETA1-4 : bond 0.00506 / 0.23 ( 4) link_BETA1-4 : angle 1.35409 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.331 Fit side-chains REVERT: A 176 LYS cc_start: 0.7772 (mptp) cc_final: 0.7009 (mtpt) REVERT: A 189 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8626 (mtmm) REVERT: B 176 LYS cc_start: 0.7762 (mptp) cc_final: 0.7016 (mtpt) REVERT: B 189 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8705 (mtmm) REVERT: C 176 LYS cc_start: 0.7774 (mptp) cc_final: 0.7008 (mtpt) REVERT: C 189 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8677 (mtmm) REVERT: D 176 LYS cc_start: 0.7786 (mptp) cc_final: 0.7029 (mtpt) REVERT: D 189 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8665 (mtmm) outliers start: 39 outliers final: 24 residues processed: 175 average time/residue: 0.5613 time to fit residues: 103.9906 Evaluate side-chains 180 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 189 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140880 restraints weight = 7412.065| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.63 r_work: 0.3428 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7620 Z= 0.129 Angle : 0.544 4.206 10444 Z= 0.306 Chirality : 0.045 0.150 1224 Planarity : 0.004 0.038 1300 Dihedral : 4.888 16.294 1300 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.58 % Allowed : 15.59 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.09 (0.27), residues: 908 helix: None (None), residues: 0 sheet: 0.81 (0.28), residues: 356 loop : -0.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 57 TYR 0.007 0.001 TYR D 52 PHE 0.015 0.002 PHE D 68 TRP 0.003 0.001 TRP C 218 HIS 0.002 0.001 HIS C 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 7608) covalent geometry : angle 0.54041 / 0.31 (10408) hydrogen bonds : bond 0.03852 / 2.51 ( 324) hydrogen bonds : angle 4.68717 / 3.22 ( 1032) link_BETA1-2 : bond 0.00403 / 0.19 ( 4) link_BETA1-2 : angle 0.84823 / 0.52 ( 12) link_BETA1-3 : bond 0.00975 / 0.45 ( 4) link_BETA1-3 : angle 1.26758 / 0.79 ( 12) link_BETA1-4 : bond 0.00550 / 0.25 ( 4) link_BETA1-4 : angle 1.28976 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.304 Fit side-chains REVERT: A 176 LYS cc_start: 0.7849 (mptp) cc_final: 0.7168 (mtpt) REVERT: B 176 LYS cc_start: 0.7841 (mptp) cc_final: 0.7174 (mtpt) REVERT: C 176 LYS cc_start: 0.7862 (mptp) cc_final: 0.7185 (mtpt) REVERT: D 176 LYS cc_start: 0.7852 (mptp) cc_final: 0.7185 (mtpt) REVERT: D 189 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8699 (mttp) outliers start: 37 outliers final: 15 residues processed: 188 average time/residue: 0.5455 time to fit residues: 108.8350 Evaluate side-chains 184 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 189 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.165037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138284 restraints weight = 7532.498| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.65 r_work: 0.3372 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7620 Z= 0.184 Angle : 0.577 4.410 10444 Z= 0.325 Chirality : 0.046 0.152 1224 Planarity : 0.005 0.039 1300 Dihedral : 5.010 16.226 1300 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.59 % Allowed : 18.07 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.11 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.77 (0.26), residues: 396 loop : -0.47 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 57 TYR 0.008 0.001 TYR B 52 PHE 0.015 0.002 PHE C 6 TRP 0.003 0.001 TRP C 246 HIS 0.004 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 7608) covalent geometry : angle 0.57303 / 0.32 (10408) hydrogen bonds : bond 0.04238 / 2.74 ( 324) hydrogen bonds : angle 4.77408 / 3.28 ( 1032) link_BETA1-2 : bond 0.00357 / 0.16 ( 4) link_BETA1-2 : angle 0.94753 / 0.59 ( 12) link_BETA1-3 : bond 0.00932 / 0.43 ( 4) link_BETA1-3 : angle 1.57858 / 0.97 ( 12) link_BETA1-4 : bond 0.00519 / 0.24 ( 4) link_BETA1-4 : angle 1.33111 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.294 Fit side-chains REVERT: A 176 LYS cc_start: 0.7891 (mptp) cc_final: 0.7179 (mtpt) REVERT: B 176 LYS cc_start: 0.7885 (mptp) cc_final: 0.7191 (mtpt) REVERT: C 176 LYS cc_start: 0.7897 (mptp) cc_final: 0.7189 (mtpt) REVERT: D 176 LYS cc_start: 0.7900 (mptp) cc_final: 0.7197 (mtpt) REVERT: D 189 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8727 (mttp) outliers start: 29 outliers final: 16 residues processed: 186 average time/residue: 0.5571 time to fit residues: 109.7005 Evaluate side-chains 183 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 189 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN C 28 ASN D 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.167531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141197 restraints weight = 7482.935| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.65 r_work: 0.3394 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7620 Z= 0.129 Angle : 0.538 4.126 10444 Z= 0.302 Chirality : 0.045 0.145 1224 Planarity : 0.004 0.040 1300 Dihedral : 4.791 15.935 1300 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.09 % Allowed : 18.81 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.17 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.83 (0.28), residues: 356 loop : -0.35 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 57 TYR 0.008 0.001 TYR B 142 PHE 0.015 0.002 PHE A 68 TRP 0.003 0.001 TRP B 246 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 7608) covalent geometry : angle 0.53471 / 0.30 (10408) hydrogen bonds : bond 0.03719 / 2.43 ( 324) hydrogen bonds : angle 4.62034 / 3.18 ( 1032) link_BETA1-2 : bond 0.00377 / 0.17 ( 4) link_BETA1-2 : angle 0.81166 / 0.51 ( 12) link_BETA1-3 : bond 0.00974 / 0.45 ( 4) link_BETA1-3 : angle 1.40046 / 0.87 ( 12) link_BETA1-4 : bond 0.00545 / 0.25 ( 4) link_BETA1-4 : angle 1.30837 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.388 Fit side-chains REVERT: B 86 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8447 (t70) REVERT: D 189 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8639 (mttp) outliers start: 25 outliers final: 13 residues processed: 191 average time/residue: 0.5310 time to fit residues: 107.6903 Evaluate side-chains 189 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.165967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139205 restraints weight = 7521.999| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.65 r_work: 0.3386 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7620 Z= 0.169 Angle : 0.573 4.170 10444 Z= 0.320 Chirality : 0.046 0.151 1224 Planarity : 0.004 0.039 1300 Dihedral : 4.959 16.086 1300 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.22 % Allowed : 18.07 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.17 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.77 (0.26), residues: 396 loop : -0.39 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 57 TYR 0.008 0.001 TYR B 52 PHE 0.015 0.002 PHE C 6 TRP 0.004 0.001 TRP A 218 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 7608) covalent geometry : angle 0.56814 / 0.32 (10408) hydrogen bonds : bond 0.04057 / 2.64 ( 324) hydrogen bonds : angle 4.70871 / 3.24 ( 1032) link_BETA1-2 : bond 0.00304 / 0.14 ( 4) link_BETA1-2 : angle 0.91773 / 0.56 ( 12) link_BETA1-3 : bond 0.00901 / 0.41 ( 4) link_BETA1-3 : angle 1.61775 / 1.00 ( 12) link_BETA1-4 : bond 0.00526 / 0.24 ( 4) link_BETA1-4 : angle 1.35962 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.317 Fit side-chains REVERT: A 86 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8478 (t70) REVERT: A 176 LYS cc_start: 0.7911 (mptp) cc_final: 0.7214 (mtpt) REVERT: B 86 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8505 (t70) REVERT: B 176 LYS cc_start: 0.7909 (mptp) cc_final: 0.7217 (mtpt) REVERT: C 86 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8480 (t70) REVERT: C 176 LYS cc_start: 0.7919 (mptp) cc_final: 0.7208 (mtpt) REVERT: D 86 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8506 (t70) REVERT: D 176 LYS cc_start: 0.7922 (mptp) cc_final: 0.7226 (mtpt) REVERT: D 189 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8668 (mttp) outliers start: 26 outliers final: 16 residues processed: 182 average time/residue: 0.5582 time to fit residues: 107.5530 Evaluate side-chains 189 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 133 ASN D 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.166393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139628 restraints weight = 7625.949| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.67 r_work: 0.3372 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7620 Z= 0.159 Angle : 0.567 4.480 10444 Z= 0.316 Chirality : 0.046 0.154 1224 Planarity : 0.004 0.039 1300 Dihedral : 4.916 16.098 1300 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.72 % Allowed : 19.31 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.20 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.91 (0.28), residues: 356 loop : -0.38 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 57 TYR 0.008 0.001 TYR D 147 PHE 0.014 0.002 PHE B 6 TRP 0.004 0.001 TRP A 246 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 7608) covalent geometry : angle 0.56248 / 0.32 (10408) hydrogen bonds : bond 0.03932 / 2.56 ( 324) hydrogen bonds : angle 4.68421 / 3.22 ( 1032) link_BETA1-2 : bond 0.00335 / 0.15 ( 4) link_BETA1-2 : angle 0.81811 / 0.51 ( 12) link_BETA1-3 : bond 0.00963 / 0.44 ( 4) link_BETA1-3 : angle 1.54008 / 0.95 ( 12) link_BETA1-4 : bond 0.00489 / 0.22 ( 4) link_BETA1-4 : angle 1.41314 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.286 Fit side-chains REVERT: A 86 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8492 (t70) REVERT: B 86 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8434 (t70) REVERT: D 86 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8487 (t70) REVERT: D 189 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8592 (mttp) outliers start: 22 outliers final: 16 residues processed: 186 average time/residue: 0.5346 time to fit residues: 105.5861 Evaluate side-chains 188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 HIS B 133 ASN D 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.168714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142430 restraints weight = 7492.035| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.65 r_work: 0.3477 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7620 Z= 0.123 Angle : 0.541 4.950 10444 Z= 0.299 Chirality : 0.045 0.152 1224 Planarity : 0.004 0.040 1300 Dihedral : 4.732 16.156 1300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.60 % Allowed : 19.31 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.25 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 1.00 (0.28), residues: 356 loop : -0.39 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.008 0.001 TYR B 52 PHE 0.015 0.002 PHE A 68 TRP 0.004 0.001 TRP A 246 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 7608) covalent geometry : angle 0.53686 / 0.30 (10408) hydrogen bonds : bond 0.03590 / 2.35 ( 324) hydrogen bonds : angle 4.56255 / 3.14 ( 1032) link_BETA1-2 : bond 0.00325 / 0.15 ( 4) link_BETA1-2 : angle 0.79912 / 0.49 ( 12) link_BETA1-3 : bond 0.00987 / 0.45 ( 4) link_BETA1-3 : angle 1.41443 / 0.87 ( 12) link_BETA1-4 : bond 0.00498 / 0.23 ( 4) link_BETA1-4 : angle 1.40000 / 0.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.286 Fit side-chains REVERT: A 86 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8383 (t70) REVERT: B 86 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8351 (t70) REVERT: D 189 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8635 (mttp) outliers start: 21 outliers final: 16 residues processed: 190 average time/residue: 0.4817 time to fit residues: 97.1670 Evaluate side-chains 192 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 83 optimal weight: 0.0050 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS C 23 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141789 restraints weight = 7472.630| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.66 r_work: 0.3496 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7620 Z= 0.134 Angle : 0.551 5.113 10444 Z= 0.304 Chirality : 0.045 0.154 1224 Planarity : 0.004 0.040 1300 Dihedral : 4.747 16.161 1300 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 20.92 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.25 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.99 (0.28), residues: 356 loop : -0.38 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 57 TYR 0.009 0.001 TYR D 147 PHE 0.014 0.002 PHE D 68 TRP 0.003 0.001 TRP D 218 HIS 0.003 0.001 HIS D 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 7608) covalent geometry : angle 0.54697 / 0.30 (10408) hydrogen bonds : bond 0.03668 / 2.39 ( 324) hydrogen bonds : angle 4.56220 / 3.14 ( 1032) link_BETA1-2 : bond 0.00324 / 0.15 ( 4) link_BETA1-2 : angle 0.83564 / 0.51 ( 12) link_BETA1-3 : bond 0.00997 / 0.46 ( 4) link_BETA1-3 : angle 1.48062 / 0.91 ( 12) link_BETA1-4 : bond 0.00480 / 0.22 ( 4) link_BETA1-4 : angle 1.39907 / 0.88 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.307 Fit side-chains REVERT: A 86 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8399 (t70) REVERT: B 86 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8355 (t70) outliers start: 19 outliers final: 16 residues processed: 189 average time/residue: 0.5185 time to fit residues: 104.0688 Evaluate side-chains 193 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.166105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139316 restraints weight = 7419.089| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.65 r_work: 0.3367 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7620 Z= 0.184 Angle : 0.593 4.838 10444 Z= 0.328 Chirality : 0.047 0.157 1224 Planarity : 0.005 0.039 1300 Dihedral : 4.974 15.876 1300 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.35 % Allowed : 20.79 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 0.20 (0.28), residues: 908 helix: None (None), residues: 0 sheet: 0.96 (0.28), residues: 356 loop : -0.43 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 57 TYR 0.009 0.001 TYR D 142 PHE 0.015 0.002 PHE B 6 TRP 0.003 0.001 TRP C 218 HIS 0.004 0.001 HIS D 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 7608) covalent geometry : angle 0.58841 / 0.33 (10408) hydrogen bonds : bond 0.04124 / 2.67 ( 324) hydrogen bonds : angle 4.74120 / 3.26 ( 1032) link_BETA1-2 : bond 0.00276 / 0.13 ( 4) link_BETA1-2 : angle 0.89566 / 0.55 ( 12) link_BETA1-3 : bond 0.01009 / 0.46 ( 4) link_BETA1-3 : angle 1.65033 / 1.02 ( 12) link_BETA1-4 : bond 0.00471 / 0.22 ( 4) link_BETA1-4 : angle 1.41272 / 0.89 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3350.32 seconds wall clock time: 58 minutes 3.70 seconds (3483.70 seconds total)