Starting phenix.real_space_refine on Wed Sep 17 10:14:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6h_47565/09_2025/9e6h_47565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6h_47565/09_2025/9e6h_47565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6h_47565/09_2025/9e6h_47565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6h_47565/09_2025/9e6h_47565.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6h_47565/09_2025/9e6h_47565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6h_47565/09_2025/9e6h_47565.cif" } resolution = 2.84 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= 0.018 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 4 7.51 5 S 4 5.16 5 C 5122 2.51 5 N 1230 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8106 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1883 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D, G, I, K, H, J, L Time building chain proxies: 1.68, per 1000 atoms: 0.21 Number of scatterers: 8106 At special positions: 0 Unit cell: (97.65, 84.63, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 Ca 4 19.99 S 4 16.00 O 1742 8.00 N 1230 7.00 C 5122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS C 272 " distance=2.11 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS D 272 " distance=1.95 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 E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " 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 A 301 " - " ASN A 90 " " NAG A 302 " - " ASN A 220 " " NAG B 301 " - " ASN B 90 " " NAG B 302 " - " ASN B 220 " " NAG C 301 " - " ASN C 90 " " NAG C 302 " - " ASN C 220 " " NAG D 301 " - " ASN D 90 " " NAG D 302 " - " ASN D 220 " " NAG E 1 " - " ASN A 142 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN B 142 " " NAG H 1 " - " ASN B 208 " " NAG I 1 " - " ASN C 142 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 142 " " NAG L 1 " - " ASN D 208 " TRANS " ALA B 274 " - " ASP B 273 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 414.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 4.5% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.685A pdb=" N ILE A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL A 254 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.685A pdb=" N ILE B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL B 254 " --> pdb=" O PRO B 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.686A pdb=" N ILE C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL C 254 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.686A pdb=" N ILE D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.645A pdb=" N VAL D 254 " --> pdb=" O PRO D 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 229 removed outlier: 4.509A pdb=" N GLY A 196 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 106 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 261 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL A 105 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL A 259 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS A 107 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS A 257 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS D 257 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 107 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL D 259 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL D 105 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 261 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL D 106 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY D 196 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL A 242 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL A 242 " --> pdb=" O TYR A 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 117 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 118 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A 186 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'B' and resid 222 through 229 removed outlier: 4.509A pdb=" N GLY B 196 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 106 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 261 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 105 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL B 259 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS B 107 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS B 257 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS C 257 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS C 107 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL C 259 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 105 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 261 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 106 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY C 196 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL B 242 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL B 242 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 117 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 118 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 186 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB2, first strand: chain 'C' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL C 242 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL C 242 " --> pdb=" O TYR C 81 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 117 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 118 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 186 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL D 242 " --> pdb=" O TYR D 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 47 through 51 removed outlier: 5.251A pdb=" N VAL D 242 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 117 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 118 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 186 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 66 through 67 392 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: 1.40 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1310 1.31 - 1.43: 2329 1.43 - 1.56: 4662 1.56 - 1.68: 0 1.68 - 1.81: 4 Bond restraints: 8305 Sorted by residual: bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.490 -0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C7 NAG G 1 " pdb=" N2 NAG G 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C7 NAG H 1 " pdb=" N2 NAG H 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C7 NAG K 1 " pdb=" N2 NAG K 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C7 NAG I 1 " pdb=" N2 NAG I 1 " ideal model delta sigma weight residual 1.346 1.489 -0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 8300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 10930 2.27 - 4.54: 374 4.54 - 6.81: 70 6.81 - 9.08: 13 9.08 - 11.35: 4 Bond angle restraints: 11391 Sorted by residual: angle pdb=" C3 NAG E 2 " pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 107.29 118.64 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3 NAG K 2 " pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 107.29 118.63 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3 NAG I 2 " pdb=" C4 NAG I 2 " pdb=" O4 NAG I 2 " ideal model delta sigma weight residual 107.29 118.61 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C3 NAG G 2 " pdb=" C4 NAG G 2 " pdb=" O4 NAG G 2 " ideal model delta sigma weight residual 107.29 118.61 -11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C2 NAG J 1 " pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 110.06 117.81 -7.75 3.00e+00 1.11e-01 6.67e+00 ... (remaining 11386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.21: 5021 23.21 - 46.42: 213 46.42 - 69.63: 40 69.63 - 92.85: 60 92.85 - 116.06: 36 Dihedral angle restraints: 5370 sinusoidal: 2520 harmonic: 2850 Sorted by residual: dihedral pdb=" C2 MAN J 4 " pdb=" C1 MAN J 4 " pdb=" O5 MAN J 4 " pdb=" C5 MAN J 4 " ideal model delta sinusoidal sigma weight residual -57.62 58.44 -116.06 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C2 MAN F 4 " pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual -57.62 58.41 -116.03 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C2 MAN L 4 " pdb=" C1 MAN L 4 " pdb=" O5 MAN L 4 " pdb=" C5 MAN L 4 " ideal model delta sinusoidal sigma weight residual -57.62 58.41 -116.03 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 5367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 989 0.043 - 0.086: 258 0.086 - 0.128: 127 0.128 - 0.171: 36 0.171 - 0.214: 16 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 208 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN D 208 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1423 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 217 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO D 218 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 218 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 218 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 217 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO C 218 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 218 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 218 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 217 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 218 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.021 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 144 2.65 - 3.21: 7488 3.21 - 3.77: 11924 3.77 - 4.34: 17372 4.34 - 4.90: 29334 Nonbonded interactions: 66262 Sorted by model distance: nonbonded pdb=" O3 NAG G 2 " pdb=" O5 BMA G 3 " model vdw 2.087 3.040 nonbonded pdb=" O3 NAG E 2 " pdb=" O5 BMA E 3 " model vdw 2.087 3.040 nonbonded pdb=" O3 NAG I 2 " pdb=" O5 BMA I 3 " model vdw 2.088 3.040 nonbonded pdb=" O3 NAG K 2 " pdb=" O5 BMA K 3 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU C 156 " pdb="MN MN C 304 " model vdw 2.142 2.320 ... (remaining 66257 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 'A' selection = (chain 'B' and (resid 30 through 273 or resid 301 through 304)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.760 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.014 0.144 8352 Z= 0.701 Angle : 0.989 15.853 11530 Z= 0.396 Chirality : 0.054 0.214 1426 Planarity : 0.005 0.038 1409 Dihedral : 19.320 116.057 3525 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.47 (0.27), residues: 970 helix: -2.66 (0.57), residues: 24 sheet: 0.83 (0.25), residues: 464 loop : 0.04 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 65 TYR 0.005 0.001 TYR C 165 PHE 0.008 0.001 PHE C 102 TRP 0.011 0.001 TRP D 262 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.01399 ( 8305) covalent geometry : angle 0.92380 (11391) SS BOND : bond 0.08370 ( 2) SS BOND : angle 1.67655 ( 4) hydrogen bonds : bond 0.12265 ( 320) hydrogen bonds : angle 6.24159 ( 1032) link_ALPHA1-3 : bond 0.00315 ( 8) link_ALPHA1-3 : angle 0.88750 ( 24) link_ALPHA1-6 : bond 0.00504 ( 4) link_ALPHA1-6 : angle 1.04193 ( 12) link_BETA1-4 : bond 0.01519 ( 16) link_BETA1-4 : angle 5.31466 ( 48) link_NAG-ASN : bond 0.00181 ( 16) link_NAG-ASN : angle 1.81767 ( 48) link_TRANS : bond 0.00057 ( 1) link_TRANS : angle 0.09356 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: B 107 LYS cc_start: 0.8325 (tttp) cc_final: 0.8099 (tttm) REVERT: C 72 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8132 (mm-40) REVERT: C 107 LYS cc_start: 0.8499 (tttp) cc_final: 0.8257 (tttm) REVERT: D 48 LEU cc_start: 0.8854 (mt) cc_final: 0.8626 (mt) REVERT: D 89 ASP cc_start: 0.7689 (t0) cc_final: 0.7427 (t0) outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.6948 time to fit residues: 103.4314 Evaluate side-chains 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0470 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN B 128 GLN C 50 GLN D 62 GLN D 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.070306 restraints weight = 13650.870| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.76 r_work: 0.2779 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8352 Z= 0.175 Angle : 0.863 19.454 11530 Z= 0.361 Chirality : 0.053 0.301 1426 Planarity : 0.005 0.042 1409 Dihedral : 19.031 105.918 1919 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.95 % Allowed : 8.10 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.59 (0.27), residues: 970 helix: -2.13 (0.63), residues: 24 sheet: 0.95 (0.25), residues: 464 loop : 0.05 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 65 TYR 0.012 0.001 TYR B 165 PHE 0.014 0.002 PHE A 98 TRP 0.012 0.001 TRP A 262 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8305) covalent geometry : angle 0.72590 (11391) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.18713 ( 4) hydrogen bonds : bond 0.03690 ( 320) hydrogen bonds : angle 4.99527 ( 1032) link_ALPHA1-3 : bond 0.00825 ( 8) link_ALPHA1-3 : angle 3.09363 ( 24) link_ALPHA1-6 : bond 0.01197 ( 4) link_ALPHA1-6 : angle 1.98072 ( 12) link_BETA1-4 : bond 0.02515 ( 16) link_BETA1-4 : angle 6.35062 ( 48) link_NAG-ASN : bond 0.00252 ( 16) link_NAG-ASN : angle 2.80246 ( 48) link_TRANS : bond 0.00034 ( 1) link_TRANS : angle 0.16023 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.307 Fit side-chains REVERT: A 147 ASP cc_start: 0.7996 (t0) cc_final: 0.7740 (t0) REVERT: A 189 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.8929 (tt0) REVERT: A 269 GLU cc_start: 0.7731 (pp20) cc_final: 0.7522 (pp20) REVERT: B 52 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8618 (mt-10) REVERT: B 65 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.7682 (ptm160) REVERT: B 72 GLN cc_start: 0.8109 (mm110) cc_final: 0.7445 (mm110) REVERT: B 107 LYS cc_start: 0.8351 (tttp) cc_final: 0.8149 (tttm) REVERT: B 147 ASP cc_start: 0.8146 (t0) cc_final: 0.7805 (t0) REVERT: B 269 GLU cc_start: 0.8031 (pm20) cc_final: 0.7810 (pm20) REVERT: C 65 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.7396 (ptm160) REVERT: C 67 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7873 (mp0) REVERT: C 72 GLN cc_start: 0.8621 (mm-40) cc_final: 0.7394 (mp10) REVERT: C 107 LYS cc_start: 0.8388 (tttp) cc_final: 0.8178 (tttm) REVERT: C 147 ASP cc_start: 0.8239 (t0) cc_final: 0.7940 (t0) REVERT: D 48 LEU cc_start: 0.9093 (mt) cc_final: 0.8893 (mt) REVERT: D 147 ASP cc_start: 0.8051 (t0) cc_final: 0.7781 (t0) REVERT: D 189 GLN cc_start: 0.9445 (OUTLIER) cc_final: 0.8831 (tt0) REVERT: D 269 GLU cc_start: 0.7750 (pp20) cc_final: 0.7477 (pp20) outliers start: 8 outliers final: 3 residues processed: 112 average time/residue: 0.6428 time to fit residues: 75.9873 Evaluate side-chains 100 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 171 ASN C 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.093710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.058901 restraints weight = 13587.237| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.97 r_work: 0.2562 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8352 Z= 0.220 Angle : 0.851 18.085 11530 Z= 0.365 Chirality : 0.056 0.327 1426 Planarity : 0.004 0.046 1409 Dihedral : 17.270 105.362 1917 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.07 % Allowed : 9.88 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.66 (0.28), residues: 970 helix: -1.86 (0.74), residues: 24 sheet: 0.89 (0.25), residues: 470 loop : 0.20 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 65 TYR 0.016 0.002 TYR B 121 PHE 0.016 0.002 PHE A 98 TRP 0.016 0.002 TRP D 262 HIS 0.003 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 8305) covalent geometry : angle 0.73010 (11391) SS BOND : bond 0.00070 ( 2) SS BOND : angle 0.20675 ( 4) hydrogen bonds : bond 0.04134 ( 320) hydrogen bonds : angle 4.91140 ( 1032) link_ALPHA1-3 : bond 0.00940 ( 8) link_ALPHA1-3 : angle 2.79146 ( 24) link_ALPHA1-6 : bond 0.01541 ( 4) link_ALPHA1-6 : angle 1.50308 ( 12) link_BETA1-4 : bond 0.02376 ( 16) link_BETA1-4 : angle 6.04907 ( 48) link_NAG-ASN : bond 0.00341 ( 16) link_NAG-ASN : angle 2.49850 ( 48) link_TRANS : bond 0.00023 ( 1) link_TRANS : angle 0.16259 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.382 Fit side-chains REVERT: A 147 ASP cc_start: 0.8288 (t0) cc_final: 0.8006 (t0) REVERT: A 269 GLU cc_start: 0.7751 (pp20) cc_final: 0.7345 (pp20) REVERT: B 52 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8852 (mt-10) REVERT: B 65 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8097 (ttp-110) REVERT: B 67 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 72 GLN cc_start: 0.8490 (mm110) cc_final: 0.7692 (mm-40) REVERT: B 107 LYS cc_start: 0.8539 (tttp) cc_final: 0.8335 (tttm) REVERT: B 121 TYR cc_start: 0.9280 (p90) cc_final: 0.9068 (p90) REVERT: B 134 VAL cc_start: 0.9025 (p) cc_final: 0.8797 (t) REVERT: B 147 ASP cc_start: 0.8319 (t0) cc_final: 0.7865 (t0) REVERT: B 269 GLU cc_start: 0.8020 (pm20) cc_final: 0.7754 (pm20) REVERT: C 52 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8835 (pt0) REVERT: C 65 ARG cc_start: 0.8666 (ttp-110) cc_final: 0.8360 (ttp-110) REVERT: C 72 GLN cc_start: 0.8696 (mm-40) cc_final: 0.7780 (mm-40) REVERT: C 112 ASP cc_start: 0.9124 (m-30) cc_final: 0.8724 (p0) REVERT: C 147 ASP cc_start: 0.8409 (t0) cc_final: 0.8024 (t0) REVERT: D 147 ASP cc_start: 0.8294 (t0) cc_final: 0.8052 (t0) REVERT: D 269 GLU cc_start: 0.7746 (pp20) cc_final: 0.7277 (pp20) outliers start: 9 outliers final: 4 residues processed: 110 average time/residue: 0.7404 time to fit residues: 85.4212 Evaluate side-chains 104 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.059054 restraints weight = 13977.042| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.02 r_work: 0.2680 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8352 Z= 0.175 Angle : 0.841 18.372 11530 Z= 0.352 Chirality : 0.055 0.333 1426 Planarity : 0.004 0.046 1409 Dihedral : 15.910 106.094 1917 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.71 % Allowed : 11.43 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.78 (0.29), residues: 970 helix: -1.75 (0.78), residues: 24 sheet: 0.96 (0.26), residues: 470 loop : 0.31 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 65 TYR 0.013 0.001 TYR C 121 PHE 0.016 0.002 PHE D 98 TRP 0.008 0.001 TRP B 190 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8305) covalent geometry : angle 0.71355 (11391) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.13752 ( 4) hydrogen bonds : bond 0.03609 ( 320) hydrogen bonds : angle 4.65575 ( 1032) link_ALPHA1-3 : bond 0.00873 ( 8) link_ALPHA1-3 : angle 2.90721 ( 24) link_ALPHA1-6 : bond 0.01520 ( 4) link_ALPHA1-6 : angle 1.71624 ( 12) link_BETA1-4 : bond 0.02454 ( 16) link_BETA1-4 : angle 6.08989 ( 48) link_NAG-ASN : bond 0.00222 ( 16) link_NAG-ASN : angle 2.68028 ( 48) link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.13723 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.276 Fit side-chains REVERT: A 147 ASP cc_start: 0.8416 (t0) cc_final: 0.8142 (t0) REVERT: A 269 GLU cc_start: 0.7804 (pp20) cc_final: 0.7446 (pp20) REVERT: B 65 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8134 (ptm160) REVERT: B 147 ASP cc_start: 0.8440 (t0) cc_final: 0.8015 (t0) REVERT: C 65 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.7891 (ttp-110) REVERT: C 67 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7960 (mp0) REVERT: C 73 GLN cc_start: 0.9051 (pm20) cc_final: 0.8849 (pm20) REVERT: C 147 ASP cc_start: 0.8482 (t0) cc_final: 0.8170 (t0) REVERT: D 147 ASP cc_start: 0.8476 (t0) cc_final: 0.8170 (t0) REVERT: D 269 GLU cc_start: 0.7807 (pp20) cc_final: 0.7392 (pp20) outliers start: 6 outliers final: 7 residues processed: 100 average time/residue: 0.7432 time to fit residues: 77.9480 Evaluate side-chains 106 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.059082 restraints weight = 13722.845| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.91 r_work: 0.2693 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8352 Z= 0.172 Angle : 0.838 18.268 11530 Z= 0.351 Chirality : 0.055 0.326 1426 Planarity : 0.004 0.045 1409 Dihedral : 15.416 106.211 1917 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.95 % Allowed : 11.55 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.85 (0.29), residues: 970 helix: -1.86 (0.74), residues: 24 sheet: 0.97 (0.26), residues: 470 loop : 0.40 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 65 TYR 0.009 0.001 TYR C 121 PHE 0.015 0.002 PHE B 161 TRP 0.007 0.001 TRP C 190 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8305) covalent geometry : angle 0.71108 (11391) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.12282 ( 4) hydrogen bonds : bond 0.03561 ( 320) hydrogen bonds : angle 4.60363 ( 1032) link_ALPHA1-3 : bond 0.00883 ( 8) link_ALPHA1-3 : angle 2.80420 ( 24) link_ALPHA1-6 : bond 0.01504 ( 4) link_ALPHA1-6 : angle 1.52950 ( 12) link_BETA1-4 : bond 0.02432 ( 16) link_BETA1-4 : angle 6.08725 ( 48) link_NAG-ASN : bond 0.00218 ( 16) link_NAG-ASN : angle 2.68498 ( 48) link_TRANS : bond 0.00028 ( 1) link_TRANS : angle 0.13688 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.250 Fit side-chains REVERT: A 147 ASP cc_start: 0.8454 (t0) cc_final: 0.8128 (t0) REVERT: A 269 GLU cc_start: 0.7833 (pp20) cc_final: 0.7414 (pp20) REVERT: B 65 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8291 (ttp-110) REVERT: B 147 ASP cc_start: 0.8457 (t0) cc_final: 0.8125 (t0) REVERT: C 52 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8754 (pt0) REVERT: C 147 ASP cc_start: 0.8497 (t0) cc_final: 0.8182 (t0) REVERT: D 147 ASP cc_start: 0.8504 (t0) cc_final: 0.8188 (t0) REVERT: D 269 GLU cc_start: 0.7807 (pp20) cc_final: 0.7365 (pp20) outliers start: 8 outliers final: 6 residues processed: 104 average time/residue: 0.7263 time to fit residues: 79.2296 Evaluate side-chains 104 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.061327 restraints weight = 13804.656| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.71 r_work: 0.2547 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8352 Z= 0.188 Angle : 0.853 18.212 11530 Z= 0.359 Chirality : 0.055 0.329 1426 Planarity : 0.004 0.047 1409 Dihedral : 14.555 105.730 1917 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 11.67 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.84 (0.29), residues: 970 helix: -2.01 (0.73), residues: 24 sheet: 0.93 (0.26), residues: 470 loop : 0.45 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 65 TYR 0.010 0.001 TYR B 121 PHE 0.018 0.002 PHE C 161 TRP 0.008 0.001 TRP C 190 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8305) covalent geometry : angle 0.72865 (11391) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.18539 ( 4) hydrogen bonds : bond 0.03664 ( 320) hydrogen bonds : angle 4.60219 ( 1032) link_ALPHA1-3 : bond 0.00845 ( 8) link_ALPHA1-3 : angle 2.77252 ( 24) link_ALPHA1-6 : bond 0.01520 ( 4) link_ALPHA1-6 : angle 1.37194 ( 12) link_BETA1-4 : bond 0.02415 ( 16) link_BETA1-4 : angle 6.09737 ( 48) link_NAG-ASN : bond 0.00239 ( 16) link_NAG-ASN : angle 2.68610 ( 48) link_TRANS : bond 0.00018 ( 1) link_TRANS : angle 0.12305 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.314 Fit side-chains REVERT: A 147 ASP cc_start: 0.8429 (t0) cc_final: 0.8050 (t0) REVERT: A 269 GLU cc_start: 0.7764 (pp20) cc_final: 0.7320 (pp20) REVERT: B 65 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8220 (ttp-110) REVERT: B 67 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7638 (mp0) REVERT: C 65 ARG cc_start: 0.8722 (ttp-110) cc_final: 0.8201 (ttp-110) REVERT: C 67 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7740 (mp0) REVERT: D 147 ASP cc_start: 0.8488 (t0) cc_final: 0.8143 (t0) REVERT: D 269 GLU cc_start: 0.7788 (pp20) cc_final: 0.7276 (pp20) outliers start: 13 outliers final: 4 residues processed: 108 average time/residue: 0.7369 time to fit residues: 83.3700 Evaluate side-chains 98 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.059560 restraints weight = 13672.345| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.81 r_work: 0.2642 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8352 Z= 0.221 Angle : 0.875 18.238 11530 Z= 0.370 Chirality : 0.056 0.334 1426 Planarity : 0.004 0.048 1409 Dihedral : 13.825 105.073 1917 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.83 % Allowed : 12.26 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.76 (0.29), residues: 970 helix: -2.18 (0.72), residues: 24 sheet: 0.87 (0.26), residues: 453 loop : 0.42 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 65 TYR 0.010 0.001 TYR C 121 PHE 0.017 0.002 PHE C 161 TRP 0.010 0.001 TRP B 190 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8305) covalent geometry : angle 0.75198 (11391) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.25826 ( 4) hydrogen bonds : bond 0.03887 ( 320) hydrogen bonds : angle 4.70072 ( 1032) link_ALPHA1-3 : bond 0.00823 ( 8) link_ALPHA1-3 : angle 2.81340 ( 24) link_ALPHA1-6 : bond 0.01526 ( 4) link_ALPHA1-6 : angle 1.19437 ( 12) link_BETA1-4 : bond 0.02418 ( 16) link_BETA1-4 : angle 6.17372 ( 48) link_NAG-ASN : bond 0.00278 ( 16) link_NAG-ASN : angle 2.67972 ( 48) link_TRANS : bond 0.00002 ( 1) link_TRANS : angle 0.12847 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.322 Fit side-chains REVERT: A 269 GLU cc_start: 0.7809 (pp20) cc_final: 0.7345 (pp20) REVERT: B 65 ARG cc_start: 0.8751 (ttp-110) cc_final: 0.8296 (ttp-110) REVERT: B 67 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8261 (mm-30) REVERT: C 65 ARG cc_start: 0.8805 (ttp-110) cc_final: 0.8470 (ttp-110) REVERT: C 67 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8264 (mm-30) REVERT: C 112 ASP cc_start: 0.9005 (m-30) cc_final: 0.8661 (p0) REVERT: D 147 ASP cc_start: 0.8580 (t0) cc_final: 0.8204 (t0) REVERT: D 269 GLU cc_start: 0.7858 (pp20) cc_final: 0.7356 (pp20) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 0.7595 time to fit residues: 77.0787 Evaluate side-chains 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.061613 restraints weight = 13643.480| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.69 r_work: 0.2570 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8352 Z= 0.145 Angle : 0.842 18.236 11530 Z= 0.354 Chirality : 0.054 0.331 1426 Planarity : 0.004 0.045 1409 Dihedral : 13.374 106.017 1917 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.24 % Allowed : 12.62 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.81 (0.29), residues: 970 helix: -2.07 (0.74), residues: 24 sheet: 0.82 (0.26), residues: 460 loop : 0.56 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 65 TYR 0.010 0.001 TYR B 74 PHE 0.016 0.001 PHE B 161 TRP 0.006 0.001 TRP B 190 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8305) covalent geometry : angle 0.71703 (11391) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.12076 ( 4) hydrogen bonds : bond 0.03348 ( 320) hydrogen bonds : angle 4.47286 ( 1032) link_ALPHA1-3 : bond 0.00850 ( 8) link_ALPHA1-3 : angle 2.62699 ( 24) link_ALPHA1-6 : bond 0.01538 ( 4) link_ALPHA1-6 : angle 0.99296 ( 12) link_BETA1-4 : bond 0.02440 ( 16) link_BETA1-4 : angle 6.11258 ( 48) link_NAG-ASN : bond 0.00147 ( 16) link_NAG-ASN : angle 2.70990 ( 48) link_TRANS : bond 0.00040 ( 1) link_TRANS : angle 0.11704 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8490 (t0) cc_final: 0.8114 (t0) REVERT: A 269 GLU cc_start: 0.7737 (pp20) cc_final: 0.7265 (pp20) REVERT: B 52 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 67 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7646 (mp0) REVERT: C 65 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8456 (ttp-110) REVERT: C 112 ASP cc_start: 0.9017 (m-30) cc_final: 0.8669 (p0) REVERT: D 147 ASP cc_start: 0.8505 (t0) cc_final: 0.8120 (t0) REVERT: D 269 GLU cc_start: 0.7755 (pp20) cc_final: 0.7236 (pp20) outliers start: 2 outliers final: 3 residues processed: 93 average time/residue: 0.7839 time to fit residues: 76.0899 Evaluate side-chains 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.0270 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.061756 restraints weight = 13759.478| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.72 r_work: 0.2564 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8352 Z= 0.145 Angle : 0.836 18.220 11530 Z= 0.351 Chirality : 0.053 0.329 1426 Planarity : 0.004 0.045 1409 Dihedral : 13.121 105.663 1917 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.12 % Allowed : 13.10 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.82 (0.29), residues: 970 helix: -2.01 (0.74), residues: 24 sheet: 0.82 (0.26), residues: 458 loop : 0.55 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 65 TYR 0.007 0.001 TYR C 121 PHE 0.017 0.001 PHE C 161 TRP 0.006 0.001 TRP B 190 HIS 0.002 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8305) covalent geometry : angle 0.70997 (11391) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.10708 ( 4) hydrogen bonds : bond 0.03259 ( 320) hydrogen bonds : angle 4.43132 ( 1032) link_ALPHA1-3 : bond 0.00826 ( 8) link_ALPHA1-3 : angle 2.58313 ( 24) link_ALPHA1-6 : bond 0.01520 ( 4) link_ALPHA1-6 : angle 0.92448 ( 12) link_BETA1-4 : bond 0.02435 ( 16) link_BETA1-4 : angle 6.10799 ( 48) link_NAG-ASN : bond 0.00151 ( 16) link_NAG-ASN : angle 2.74095 ( 48) link_TRANS : bond 0.00035 ( 1) link_TRANS : angle 0.13632 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.320 Fit side-chains REVERT: A 269 GLU cc_start: 0.7734 (pp20) cc_final: 0.7255 (pp20) REVERT: B 52 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8568 (mt-10) REVERT: B 65 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.7944 (ttp-110) REVERT: B 67 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7663 (mp0) REVERT: C 65 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8427 (ttp-110) REVERT: C 67 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8095 (mm-30) REVERT: C 112 ASP cc_start: 0.9022 (m-30) cc_final: 0.8666 (p0) REVERT: D 147 ASP cc_start: 0.8512 (t0) cc_final: 0.8111 (t0) REVERT: D 269 GLU cc_start: 0.7775 (pp20) cc_final: 0.7280 (pp20) outliers start: 1 outliers final: 2 residues processed: 92 average time/residue: 0.8396 time to fit residues: 80.7141 Evaluate side-chains 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.061915 restraints weight = 13692.376| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.69 r_work: 0.2556 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8352 Z= 0.159 Angle : 0.828 18.202 11530 Z= 0.352 Chirality : 0.053 0.331 1426 Planarity : 0.004 0.046 1409 Dihedral : 12.341 103.583 1917 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.12 % Allowed : 13.10 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.75 (0.29), residues: 970 helix: -2.03 (0.75), residues: 24 sheet: 0.77 (0.26), residues: 463 loop : 0.51 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 65 TYR 0.013 0.001 TYR A 250 PHE 0.017 0.002 PHE B 161 TRP 0.007 0.001 TRP B 190 HIS 0.001 0.000 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8305) covalent geometry : angle 0.70271 (11391) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.20880 ( 4) hydrogen bonds : bond 0.03393 ( 320) hydrogen bonds : angle 4.40818 ( 1032) link_ALPHA1-3 : bond 0.00849 ( 8) link_ALPHA1-3 : angle 2.36340 ( 24) link_ALPHA1-6 : bond 0.01427 ( 4) link_ALPHA1-6 : angle 1.17716 ( 12) link_BETA1-4 : bond 0.02425 ( 16) link_BETA1-4 : angle 6.06162 ( 48) link_NAG-ASN : bond 0.00185 ( 16) link_NAG-ASN : angle 2.72738 ( 48) link_TRANS : bond 0.00033 ( 1) link_TRANS : angle 0.11367 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.292 Fit side-chains REVERT: A 269 GLU cc_start: 0.7716 (pp20) cc_final: 0.7249 (pp20) REVERT: B 65 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8228 (ttp-110) REVERT: B 67 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8298 (mm-30) REVERT: C 65 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8068 (ttp-110) REVERT: C 67 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7758 (mp0) REVERT: C 112 ASP cc_start: 0.9019 (m-30) cc_final: 0.8663 (p0) REVERT: D 147 ASP cc_start: 0.8533 (t0) cc_final: 0.8135 (t0) REVERT: D 269 GLU cc_start: 0.7790 (pp20) cc_final: 0.7295 (pp20) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.8289 time to fit residues: 78.7354 Evaluate side-chains 89 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN C 271 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.062816 restraints weight = 13664.034| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.69 r_work: 0.2583 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8352 Z= 0.148 Angle : 0.819 18.210 11530 Z= 0.348 Chirality : 0.052 0.330 1426 Planarity : 0.004 0.045 1409 Dihedral : 11.620 100.563 1917 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.36 % Allowed : 13.69 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.81 (0.29), residues: 970 helix: -1.88 (0.75), residues: 24 sheet: 0.81 (0.26), residues: 458 loop : 0.55 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 65 TYR 0.013 0.001 TYR B 74 PHE 0.014 0.001 PHE A 98 TRP 0.006 0.001 TRP B 190 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8305) covalent geometry : angle 0.69100 (11391) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.33723 ( 4) hydrogen bonds : bond 0.03182 ( 320) hydrogen bonds : angle 4.36068 ( 1032) link_ALPHA1-3 : bond 0.00835 ( 8) link_ALPHA1-3 : angle 2.32347 ( 24) link_ALPHA1-6 : bond 0.01262 ( 4) link_ALPHA1-6 : angle 1.79745 ( 12) link_BETA1-4 : bond 0.02437 ( 16) link_BETA1-4 : angle 6.06856 ( 48) link_NAG-ASN : bond 0.00132 ( 16) link_NAG-ASN : angle 2.72201 ( 48) link_TRANS : bond 0.00043 ( 1) link_TRANS : angle 0.12776 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.63 seconds wall clock time: 46 minutes 47.70 seconds (2807.70 seconds total)