Starting phenix.real_space_refine on Sun May 11 11:56:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6h_47565/05_2025/9e6h_47565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6h_47565/05_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_47565/05_2025/9e6h_47565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6h_47565/05_2025/9e6h_47565.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6h_47565/05_2025/9e6h_47565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6h_47565/05_2025/9e6h_47565.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.30, per 1000 atoms: 0.53 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: 2.94 Conformation dependent library (CDL) restraints added in 904.5 milliseconds 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: 1.12 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: 2.58 Time building geometry restraints manager: 3.15 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.690 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (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 TRP 0.011 0.001 TRP D 262 HIS 0.003 0.001 HIS B 174 PHE 0.008 0.001 PHE C 102 TYR 0.005 0.001 TYR C 165 ARG 0.002 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00057 ( 1) link_TRANS : angle 0.09356 ( 3) link_NAG-ASN : bond 0.00181 ( 16) link_NAG-ASN : angle 1.81767 ( 48) 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_ALPHA1-3 : bond 0.00315 ( 8) link_ALPHA1-3 : angle 0.88750 ( 24) hydrogen bonds : bond 0.12265 ( 320) hydrogen bonds : angle 6.24159 ( 1032) SS BOND : bond 0.08370 ( 2) SS BOND : angle 1.67655 ( 4) covalent geometry : bond 0.01399 ( 8305) covalent geometry : angle 0.92380 (11391) *********************** 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 : 0.956 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: 1.4022 time to fit residues: 209.4476 Evaluate side-chains 99 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 81 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 B 128 GLN C 50 GLN D 62 GLN D 171 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.064696 restraints weight = 13728.104| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.73 r_work: 0.2660 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8352 Z= 0.256 Angle : 0.909 18.892 11530 Z= 0.387 Chirality : 0.056 0.340 1426 Planarity : 0.005 0.045 1409 Dihedral : 18.830 103.795 1919 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.83 % Allowed : 9.05 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 970 helix: -2.12 (0.64), residues: 24 sheet: 0.93 (0.25), residues: 464 loop : 0.02 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 262 HIS 0.003 0.001 HIS B 257 PHE 0.017 0.002 PHE A 98 TYR 0.014 0.002 TYR B 121 ARG 0.007 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.17092 ( 3) link_NAG-ASN : bond 0.00297 ( 16) link_NAG-ASN : angle 2.72749 ( 48) link_ALPHA1-6 : bond 0.01400 ( 4) link_ALPHA1-6 : angle 2.20436 ( 12) link_BETA1-4 : bond 0.02630 ( 16) link_BETA1-4 : angle 6.22280 ( 48) link_ALPHA1-3 : bond 0.00800 ( 8) link_ALPHA1-3 : angle 3.21912 ( 24) hydrogen bonds : bond 0.04273 ( 320) hydrogen bonds : angle 5.15652 ( 1032) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.24035 ( 4) covalent geometry : bond 0.00567 ( 8305) covalent geometry : angle 0.78446 (11391) *********************** 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 117 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.944 Fit side-chains REVERT: A 65 ARG cc_start: 0.8588 (ptm-80) cc_final: 0.8327 (ptm-80) REVERT: A 147 ASP cc_start: 0.8163 (t0) cc_final: 0.7911 (t0) REVERT: A 269 GLU cc_start: 0.7705 (pp20) cc_final: 0.7415 (pp20) REVERT: B 52 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: B 65 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.7736 (ptm160) REVERT: B 107 LYS cc_start: 0.8466 (tttp) cc_final: 0.8252 (tttm) REVERT: B 147 ASP cc_start: 0.8251 (t0) cc_final: 0.7875 (t0) REVERT: B 269 GLU cc_start: 0.8080 (pm20) cc_final: 0.7848 (pm20) REVERT: C 52 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8536 (pt0) REVERT: C 65 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.7611 (ptm160) REVERT: C 67 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7913 (mp0) REVERT: C 72 GLN cc_start: 0.8704 (mm-40) cc_final: 0.7304 (mp10) REVERT: C 107 LYS cc_start: 0.8479 (tttp) cc_final: 0.8259 (tttm) REVERT: C 147 ASP cc_start: 0.8311 (t0) cc_final: 0.7984 (t0) REVERT: C 269 GLU cc_start: 0.8034 (pm20) cc_final: 0.7784 (pm20) REVERT: D 65 ARG cc_start: 0.8574 (ptm-80) cc_final: 0.8353 (ptm-80) REVERT: D 147 ASP cc_start: 0.8218 (t0) cc_final: 0.7936 (t0) REVERT: D 269 GLU cc_start: 0.7814 (pp20) cc_final: 0.7501 (pp20) outliers start: 7 outliers final: 3 residues processed: 114 average time/residue: 1.3188 time to fit residues: 159.0548 Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain D residue 31 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.0020 chunk 2 optimal weight: 4.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.061584 restraints weight = 13977.027| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.96 r_work: 0.2576 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8352 Z= 0.210 Angle : 0.842 18.270 11530 Z= 0.357 Chirality : 0.055 0.315 1426 Planarity : 0.004 0.047 1409 Dihedral : 17.511 106.772 1917 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.60 % Allowed : 10.24 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 970 helix: -1.96 (0.72), residues: 24 sheet: 0.92 (0.26), residues: 470 loop : 0.18 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 262 HIS 0.002 0.001 HIS C 257 PHE 0.015 0.002 PHE B 161 TYR 0.014 0.002 TYR B 121 ARG 0.004 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00012 ( 1) link_TRANS : angle 0.15732 ( 3) link_NAG-ASN : bond 0.00290 ( 16) link_NAG-ASN : angle 2.51428 ( 48) link_ALPHA1-6 : bond 0.01548 ( 4) link_ALPHA1-6 : angle 1.59796 ( 12) link_BETA1-4 : bond 0.02400 ( 16) link_BETA1-4 : angle 6.12275 ( 48) link_ALPHA1-3 : bond 0.00915 ( 8) link_ALPHA1-3 : angle 2.74952 ( 24) hydrogen bonds : bond 0.03983 ( 320) hydrogen bonds : angle 4.85853 ( 1032) SS BOND : bond 0.00031 ( 2) SS BOND : angle 0.16152 ( 4) covalent geometry : bond 0.00457 ( 8305) covalent geometry : angle 0.71690 (11391) *********************** 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 107 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.902 Fit side-chains REVERT: A 147 ASP cc_start: 0.8332 (t0) cc_final: 0.8050 (t0) REVERT: A 269 GLU cc_start: 0.7730 (pp20) cc_final: 0.7391 (pp20) REVERT: B 65 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7996 (ttp-110) REVERT: B 67 GLU cc_start: 0.7867 (mp0) cc_final: 0.6857 (mp0) REVERT: B 72 GLN cc_start: 0.8683 (mm110) cc_final: 0.7991 (mm110) REVERT: B 121 TYR cc_start: 0.9278 (p90) cc_final: 0.9077 (p90) REVERT: B 147 ASP cc_start: 0.8356 (t0) cc_final: 0.7944 (t0) REVERT: B 269 GLU cc_start: 0.8062 (pm20) cc_final: 0.7816 (pm20) REVERT: C 65 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8255 (ttp-110) REVERT: C 107 LYS cc_start: 0.8522 (tttp) cc_final: 0.8313 (tttm) REVERT: C 121 TYR cc_start: 0.9285 (p90) cc_final: 0.9075 (p90) REVERT: C 147 ASP cc_start: 0.8431 (t0) cc_final: 0.8055 (t0) REVERT: C 269 GLU cc_start: 0.8007 (pm20) cc_final: 0.7771 (pm20) REVERT: D 147 ASP cc_start: 0.8330 (t0) cc_final: 0.8064 (t0) REVERT: D 269 GLU cc_start: 0.7728 (pp20) cc_final: 0.7322 (pp20) outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 1.5355 time to fit residues: 167.5288 Evaluate side-chains 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.0370 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.057270 restraints weight = 13774.473| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.97 r_work: 0.2640 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3159 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= 0.219 Angle : 0.862 18.323 11530 Z= 0.365 Chirality : 0.057 0.335 1426 Planarity : 0.004 0.047 1409 Dihedral : 16.133 106.015 1917 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.31 % Allowed : 10.60 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 970 helix: -1.86 (0.82), residues: 24 sheet: 0.89 (0.26), residues: 470 loop : 0.26 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 190 HIS 0.002 0.001 HIS C 257 PHE 0.016 0.002 PHE A 98 TYR 0.009 0.001 TYR A 165 ARG 0.004 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00016 ( 1) link_TRANS : angle 0.15713 ( 3) link_NAG-ASN : bond 0.00306 ( 16) link_NAG-ASN : angle 2.65502 ( 48) link_ALPHA1-6 : bond 0.01507 ( 4) link_ALPHA1-6 : angle 1.75784 ( 12) link_BETA1-4 : bond 0.02401 ( 16) link_BETA1-4 : angle 6.13189 ( 48) link_ALPHA1-3 : bond 0.00854 ( 8) link_ALPHA1-3 : angle 3.01056 ( 24) hydrogen bonds : bond 0.03924 ( 320) hydrogen bonds : angle 4.79784 ( 1032) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.17480 ( 4) covalent geometry : bond 0.00480 ( 8305) covalent geometry : angle 0.73629 (11391) *********************** 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 113 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.861 Fit side-chains REVERT: A 65 ARG cc_start: 0.8716 (ptm-80) cc_final: 0.8475 (ptm-80) REVERT: A 147 ASP cc_start: 0.8487 (t0) cc_final: 0.8178 (t0) REVERT: A 269 GLU cc_start: 0.7824 (pp20) cc_final: 0.7449 (pp20) REVERT: B 52 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8770 (pt0) REVERT: B 121 TYR cc_start: 0.9357 (p90) cc_final: 0.9112 (p90) REVERT: B 147 ASP cc_start: 0.8467 (t0) cc_final: 0.8144 (t0) REVERT: C 65 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8199 (ttp-110) REVERT: C 67 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7848 (mp0) REVERT: C 107 LYS cc_start: 0.8672 (tttp) cc_final: 0.8462 (tttm) REVERT: D 65 ARG cc_start: 0.8789 (ptm-80) cc_final: 0.8565 (ptm-80) REVERT: D 147 ASP cc_start: 0.8544 (t0) cc_final: 0.8223 (t0) REVERT: D 269 GLU cc_start: 0.7794 (pp20) cc_final: 0.7372 (pp20) outliers start: 11 outliers final: 4 residues processed: 108 average time/residue: 1.5267 time to fit residues: 173.2034 Evaluate side-chains 101 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 186 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 41 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.093232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.058671 restraints weight = 13617.619| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.96 r_work: 0.2679 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3205 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= 0.157 Angle : 0.838 18.279 11530 Z= 0.351 Chirality : 0.055 0.325 1426 Planarity : 0.004 0.046 1409 Dihedral : 15.494 107.006 1917 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.07 % Allowed : 12.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 970 helix: -1.89 (0.77), residues: 24 sheet: 0.93 (0.26), residues: 470 loop : 0.35 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 190 HIS 0.002 0.000 HIS B 257 PHE 0.017 0.001 PHE C 161 TYR 0.015 0.001 TYR B 74 ARG 0.011 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00048 ( 1) link_TRANS : angle 0.11520 ( 3) link_NAG-ASN : bond 0.00185 ( 16) link_NAG-ASN : angle 2.70666 ( 48) link_ALPHA1-6 : bond 0.01523 ( 4) link_ALPHA1-6 : angle 1.54129 ( 12) link_BETA1-4 : bond 0.02440 ( 16) link_BETA1-4 : angle 6.09872 ( 48) link_ALPHA1-3 : bond 0.00887 ( 8) link_ALPHA1-3 : angle 2.76671 ( 24) hydrogen bonds : bond 0.03448 ( 320) hydrogen bonds : angle 4.58344 ( 1032) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.11745 ( 4) covalent geometry : bond 0.00319 ( 8305) covalent geometry : angle 0.71024 (11391) *********************** 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 110 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.861 Fit side-chains REVERT: A 65 ARG cc_start: 0.8715 (ptm-80) cc_final: 0.8450 (ptm-80) REVERT: A 147 ASP cc_start: 0.8503 (t0) cc_final: 0.8157 (t0) REVERT: A 269 GLU cc_start: 0.7834 (pp20) cc_final: 0.7411 (pp20) REVERT: B 52 GLU cc_start: 0.8894 (pt0) cc_final: 0.8674 (pt0) REVERT: B 65 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8329 (ttp-110) REVERT: B 121 TYR cc_start: 0.9349 (p90) cc_final: 0.9110 (p90) REVERT: C 147 ASP cc_start: 0.8536 (t0) cc_final: 0.8202 (t0) REVERT: D 116 ASP cc_start: 0.7419 (m-30) cc_final: 0.7217 (m-30) REVERT: D 147 ASP cc_start: 0.8547 (t0) cc_final: 0.8229 (t0) REVERT: D 269 GLU cc_start: 0.7836 (pp20) cc_final: 0.7347 (pp20) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 1.4820 time to fit residues: 166.6669 Evaluate side-chains 103 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 D residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.058304 restraints weight = 13652.387| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.94 r_work: 0.2668 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3324 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= 0.173 Angle : 0.854 18.252 11530 Z= 0.358 Chirality : 0.055 0.330 1426 Planarity : 0.004 0.046 1409 Dihedral : 14.740 106.249 1917 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.71 % Allowed : 12.74 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 970 helix: -1.84 (0.79), residues: 24 sheet: 0.84 (0.26), residues: 458 loop : 0.49 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 190 HIS 0.002 0.001 HIS B 257 PHE 0.017 0.002 PHE C 161 TYR 0.009 0.001 TYR C 121 ARG 0.014 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00032 ( 1) link_TRANS : angle 0.11267 ( 3) link_NAG-ASN : bond 0.00223 ( 16) link_NAG-ASN : angle 2.73029 ( 48) link_ALPHA1-6 : bond 0.01539 ( 4) link_ALPHA1-6 : angle 1.43211 ( 12) link_BETA1-4 : bond 0.02431 ( 16) link_BETA1-4 : angle 6.10417 ( 48) link_ALPHA1-3 : bond 0.00852 ( 8) link_ALPHA1-3 : angle 2.79272 ( 24) hydrogen bonds : bond 0.03526 ( 320) hydrogen bonds : angle 4.56391 ( 1032) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.14794 ( 4) covalent geometry : bond 0.00366 ( 8305) covalent geometry : angle 0.72860 (11391) *********************** 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 102 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8696 (ptm-80) cc_final: 0.8425 (ptm-80) REVERT: A 147 ASP cc_start: 0.8511 (t0) cc_final: 0.8162 (t0) REVERT: A 269 GLU cc_start: 0.7807 (pp20) cc_final: 0.7347 (pp20) REVERT: B 121 TYR cc_start: 0.9335 (p90) cc_final: 0.9098 (p90) REVERT: C 65 ARG cc_start: 0.8817 (ttp-110) cc_final: 0.8589 (ttp-110) REVERT: D 147 ASP cc_start: 0.8585 (t0) cc_final: 0.8252 (t0) REVERT: D 269 GLU cc_start: 0.7871 (pp20) cc_final: 0.7375 (pp20) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 1.5248 time to fit residues: 160.1025 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 : 0.901 ------------------------------------------------------------------------------- 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 263 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.093274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.061470 restraints weight = 13736.431| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.71 r_work: 0.2561 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3463 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= 0.171 Angle : 0.850 18.243 11530 Z= 0.356 Chirality : 0.054 0.329 1426 Planarity : 0.004 0.046 1409 Dihedral : 13.999 105.835 1917 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.60 % Allowed : 13.10 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 970 helix: -1.79 (0.80), residues: 24 sheet: 0.79 (0.26), residues: 453 loop : 0.49 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 190 HIS 0.002 0.000 HIS C 257 PHE 0.018 0.002 PHE B 161 TYR 0.009 0.001 TYR C 121 ARG 0.013 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00037 ( 1) link_TRANS : angle 0.10234 ( 3) link_NAG-ASN : bond 0.00209 ( 16) link_NAG-ASN : angle 2.70969 ( 48) link_ALPHA1-6 : bond 0.01572 ( 4) link_ALPHA1-6 : angle 1.22290 ( 12) link_BETA1-4 : bond 0.02443 ( 16) link_BETA1-4 : angle 6.12060 ( 48) link_ALPHA1-3 : bond 0.00849 ( 8) link_ALPHA1-3 : angle 2.71276 ( 24) hydrogen bonds : bond 0.03514 ( 320) hydrogen bonds : angle 4.51986 ( 1032) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.15839 ( 4) covalent geometry : bond 0.00360 ( 8305) covalent geometry : angle 0.72497 (11391) *********************** 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 100 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8463 (t0) cc_final: 0.8097 (t0) REVERT: A 269 GLU cc_start: 0.7723 (pp20) cc_final: 0.7254 (pp20) REVERT: B 121 TYR cc_start: 0.9215 (p90) cc_final: 0.8993 (p90) REVERT: C 112 ASP cc_start: 0.9011 (m-30) cc_final: 0.8666 (p0) REVERT: D 147 ASP cc_start: 0.8501 (t0) cc_final: 0.8117 (t0) REVERT: D 269 GLU cc_start: 0.7762 (pp20) cc_final: 0.7277 (pp20) outliers start: 5 outliers final: 6 residues processed: 98 average time/residue: 1.5422 time to fit residues: 158.5843 Evaluate side-chains 101 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 116 ASP 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 5 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.061791 restraints weight = 13832.171| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.70 r_work: 0.2546 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3517 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= 0.165 Angle : 0.844 18.217 11530 Z= 0.353 Chirality : 0.054 0.330 1426 Planarity : 0.004 0.046 1409 Dihedral : 13.659 105.604 1917 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.95 % Allowed : 12.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 970 helix: -1.81 (0.79), residues: 24 sheet: 0.78 (0.26), residues: 458 loop : 0.49 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 190 HIS 0.002 0.000 HIS B 257 PHE 0.017 0.001 PHE B 161 TYR 0.008 0.001 TYR A 165 ARG 0.015 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 0.13967 ( 3) link_NAG-ASN : bond 0.00194 ( 16) link_NAG-ASN : angle 2.70819 ( 48) link_ALPHA1-6 : bond 0.01560 ( 4) link_ALPHA1-6 : angle 1.10180 ( 12) link_BETA1-4 : bond 0.02425 ( 16) link_BETA1-4 : angle 6.11569 ( 48) link_ALPHA1-3 : bond 0.00832 ( 8) link_ALPHA1-3 : angle 2.69752 ( 24) hydrogen bonds : bond 0.03472 ( 320) hydrogen bonds : angle 4.50549 ( 1032) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.14415 ( 4) covalent geometry : bond 0.00344 ( 8305) covalent geometry : angle 0.71856 (11391) *********************** 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 104 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.890 Fit side-chains REVERT: A 147 ASP cc_start: 0.8493 (t0) cc_final: 0.8111 (t0) REVERT: A 269 GLU cc_start: 0.7742 (pp20) cc_final: 0.7270 (pp20) REVERT: B 65 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8484 (ttp-110) REVERT: B 121 TYR cc_start: 0.9217 (p90) cc_final: 0.8988 (p90) REVERT: C 67 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7538 (mp0) REVERT: C 112 ASP cc_start: 0.9003 (m-30) cc_final: 0.8660 (p0) REVERT: D 147 ASP cc_start: 0.8520 (t0) cc_final: 0.8135 (t0) REVERT: D 269 GLU cc_start: 0.7776 (pp20) cc_final: 0.7284 (pp20) outliers start: 8 outliers final: 6 residues processed: 101 average time/residue: 1.5391 time to fit residues: 163.2910 Evaluate side-chains 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 263 SER Chi-restraints excluded: chain D residue 107 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.092699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.059263 restraints weight = 13754.750| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.83 r_work: 0.2521 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3695 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= 0.224 Angle : 0.868 18.214 11530 Z= 0.369 Chirality : 0.055 0.335 1426 Planarity : 0.004 0.047 1409 Dihedral : 13.174 104.515 1917 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.71 % Allowed : 12.74 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 970 helix: -1.87 (0.81), residues: 24 sheet: 0.71 (0.26), residues: 460 loop : 0.44 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 190 HIS 0.002 0.001 HIS A 174 PHE 0.017 0.002 PHE B 161 TYR 0.010 0.001 TYR C 121 ARG 0.012 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00004 ( 1) link_TRANS : angle 0.12689 ( 3) link_NAG-ASN : bond 0.00276 ( 16) link_NAG-ASN : angle 2.68745 ( 48) link_ALPHA1-6 : bond 0.01473 ( 4) link_ALPHA1-6 : angle 0.95531 ( 12) link_BETA1-4 : bond 0.02416 ( 16) link_BETA1-4 : angle 6.16560 ( 48) link_ALPHA1-3 : bond 0.00797 ( 8) link_ALPHA1-3 : angle 2.71781 ( 24) hydrogen bonds : bond 0.03879 ( 320) hydrogen bonds : angle 4.65960 ( 1032) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.30151 ( 4) covalent geometry : bond 0.00501 ( 8305) covalent geometry : angle 0.74544 (11391) *********************** 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 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.925 Fit side-chains REVERT: A 269 GLU cc_start: 0.7763 (pp20) cc_final: 0.7284 (pp20) REVERT: B 121 TYR cc_start: 0.9283 (p90) cc_final: 0.9066 (p90) REVERT: B 189 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8892 (tt0) REVERT: D 147 ASP cc_start: 0.8603 (t0) cc_final: 0.8209 (t0) REVERT: D 269 GLU cc_start: 0.7812 (pp20) cc_final: 0.7304 (pp20) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 1.5761 time to fit residues: 152.2453 Evaluate side-chains 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 189 GLN Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.061165 restraints weight = 13736.938| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.73 r_work: 0.2545 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3740 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= 0.163 Angle : 0.840 18.227 11530 Z= 0.357 Chirality : 0.053 0.331 1426 Planarity : 0.004 0.046 1409 Dihedral : 12.754 104.955 1917 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.48 % Allowed : 13.69 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.29), residues: 970 helix: -1.75 (0.81), residues: 24 sheet: 0.74 (0.26), residues: 455 loop : 0.44 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 190 HIS 0.002 0.000 HIS C 257 PHE 0.017 0.001 PHE B 161 TYR 0.009 0.001 TYR C 121 ARG 0.016 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00037 ( 1) link_TRANS : angle 0.13188 ( 3) link_NAG-ASN : bond 0.00139 ( 16) link_NAG-ASN : angle 2.69553 ( 48) link_ALPHA1-6 : bond 0.01470 ( 4) link_ALPHA1-6 : angle 0.98619 ( 12) link_BETA1-4 : bond 0.02427 ( 16) link_BETA1-4 : angle 6.10591 ( 48) link_ALPHA1-3 : bond 0.00835 ( 8) link_ALPHA1-3 : angle 2.49675 ( 24) hydrogen bonds : bond 0.03446 ( 320) hydrogen bonds : angle 4.46656 ( 1032) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.25569 ( 4) covalent geometry : bond 0.00344 ( 8305) covalent geometry : angle 0.71609 (11391) ********************** 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 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.871 Fit side-chains REVERT: A 269 GLU cc_start: 0.7734 (pp20) cc_final: 0.7253 (pp20) REVERT: B 121 TYR cc_start: 0.9213 (p90) cc_final: 0.8991 (p90) REVERT: B 189 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8865 (tt0) REVERT: C 67 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7693 (mp0) REVERT: C 112 ASP cc_start: 0.9003 (m-30) cc_final: 0.8618 (p0) REVERT: D 147 ASP cc_start: 0.8520 (t0) cc_final: 0.8116 (t0) REVERT: D 269 GLU cc_start: 0.7790 (pp20) cc_final: 0.7279 (pp20) outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 1.6328 time to fit residues: 159.0368 Evaluate side-chains 92 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.092716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.061310 restraints weight = 13918.268| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.70 r_work: 0.2540 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3829 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= 0.167 Angle : 0.832 18.205 11530 Z= 0.356 Chirality : 0.052 0.332 1426 Planarity : 0.004 0.046 1409 Dihedral : 12.176 102.749 1917 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.36 % Allowed : 13.45 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.29), residues: 970 helix: -1.54 (0.84), residues: 24 sheet: 0.76 (0.26), residues: 460 loop : 0.47 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 190 HIS 0.001 0.001 HIS C 257 PHE 0.014 0.001 PHE A 98 TYR 0.012 0.001 TYR D 250 ARG 0.015 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00033 ( 1) link_TRANS : angle 0.13150 ( 3) link_NAG-ASN : bond 0.00191 ( 16) link_NAG-ASN : angle 2.73075 ( 48) link_ALPHA1-6 : bond 0.01369 ( 4) link_ALPHA1-6 : angle 1.39070 ( 12) link_BETA1-4 : bond 0.02424 ( 16) link_BETA1-4 : angle 6.07551 ( 48) link_ALPHA1-3 : bond 0.00831 ( 8) link_ALPHA1-3 : angle 2.39575 ( 24) hydrogen bonds : bond 0.03458 ( 320) hydrogen bonds : angle 4.46527 ( 1032) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.18998 ( 4) covalent geometry : bond 0.00352 ( 8305) covalent geometry : angle 0.70717 (11391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5134.26 seconds wall clock time: 89 minutes 16.83 seconds (5356.83 seconds total)