Starting phenix.real_space_refine on Mon Apr 28 20:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6h_47565/04_2025/9e6h_47565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6h_47565/04_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_47565/04_2025/9e6h_47565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6h_47565/04_2025/9e6h_47565.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6h_47565/04_2025/9e6h_47565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6h_47565/04_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-5669/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: 4.29, 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: 2.90 Conformation dependent library (CDL) restraints added in 949.2 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: 1.26 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: 3.26 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: 0.480 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.370 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- 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 : 0.765 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: 1.3970 time to fit residues: 208.5591 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 : 0.790 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.064697 restraints weight = 13728.113| |-----------------------------------------------------------------------------| 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 2.20434 ( 12) link_BETA1-4 : bond 0.02630 ( 16) link_BETA1-4 : angle 6.22278 ( 48) link_ALPHA1-3 : bond 0.00800 ( 8) link_ALPHA1-3 : angle 3.21909 ( 24) hydrogen bonds : bond 0.04273 ( 320) hydrogen bonds : angle 5.15652 ( 1032) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.24034 ( 4) covalent geometry : bond 0.00567 ( 8305) covalent geometry : angle 0.78445 (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 : 0.805 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: 0.8161 (t0) cc_final: 0.7910 (t0) REVERT: A 269 GLU cc_start: 0.7711 (pp20) cc_final: 0.7423 (pp20) REVERT: B 52 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8487 (pt0) REVERT: B 65 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.7734 (ptm160) REVERT: B 107 LYS cc_start: 0.8470 (tttp) cc_final: 0.8256 (tttm) REVERT: B 147 ASP cc_start: 0.8249 (t0) cc_final: 0.7873 (t0) REVERT: B 269 GLU cc_start: 0.8082 (pm20) cc_final: 0.7851 (pm20) REVERT: C 52 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: C 65 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.7608 (ptm160) REVERT: C 67 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7912 (mp0) REVERT: C 72 GLN cc_start: 0.8704 (mm-40) cc_final: 0.7306 (mp10) REVERT: C 107 LYS cc_start: 0.8482 (tttp) cc_final: 0.8262 (tttm) REVERT: C 147 ASP cc_start: 0.8311 (t0) cc_final: 0.7984 (t0) REVERT: C 269 GLU cc_start: 0.8035 (pm20) cc_final: 0.7785 (pm20) REVERT: D 65 ARG cc_start: 0.8574 (ptm-80) cc_final: 0.8353 (ptm-80) REVERT: D 147 ASP cc_start: 0.8217 (t0) cc_final: 0.7936 (t0) REVERT: D 269 GLU cc_start: 0.7816 (pp20) cc_final: 0.7505 (pp20) outliers start: 7 outliers final: 3 residues processed: 114 average time/residue: 1.3078 time to fit residues: 157.7145 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 : 0.863 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.0370 chunk 2 optimal weight: 4.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.101786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.064062 restraints weight = 13880.194| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.87 r_work: 0.2625 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2458 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= 0.170 Angle : 0.823 18.377 11530 Z= 0.345 Chirality : 0.054 0.320 1426 Planarity : 0.004 0.045 1409 Dihedral : 17.594 106.684 1917 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.07 % Allowed : 9.76 % 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: 0.67 (0.28), residues: 970 helix: -1.82 (0.73), residues: 24 sheet: 0.96 (0.26), residues: 464 loop : 0.14 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 262 HIS 0.002 0.001 HIS C 257 PHE 0.015 0.002 PHE B 161 TYR 0.012 0.001 TYR C 74 ARG 0.007 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00047 ( 1) link_TRANS : angle 0.14695 ( 3) link_NAG-ASN : bond 0.00231 ( 16) link_NAG-ASN : angle 2.53476 ( 48) link_ALPHA1-6 : bond 0.01471 ( 4) link_ALPHA1-6 : angle 1.57122 ( 12) link_BETA1-4 : bond 0.02408 ( 16) link_BETA1-4 : angle 6.10212 ( 48) link_ALPHA1-3 : bond 0.00923 ( 8) link_ALPHA1-3 : angle 2.76889 ( 24) hydrogen bonds : bond 0.03665 ( 320) hydrogen bonds : angle 4.75157 ( 1032) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.14471 ( 4) covalent geometry : bond 0.00353 ( 8305) covalent geometry : angle 0.69434 (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 114 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.924 Fit side-chains REVERT: A 147 ASP cc_start: 0.8280 (t0) cc_final: 0.7925 (t0) REVERT: A 189 GLN cc_start: 0.9469 (OUTLIER) cc_final: 0.8976 (tt0) REVERT: A 269 GLU cc_start: 0.7730 (pp20) cc_final: 0.7407 (pp20) REVERT: B 52 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8536 (pt0) REVERT: B 65 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7856 (ttp-110) REVERT: B 67 GLU cc_start: 0.7686 (mp0) cc_final: 0.6503 (mp0) REVERT: B 72 GLN cc_start: 0.8623 (mm110) cc_final: 0.7786 (mp10) REVERT: B 147 ASP cc_start: 0.8302 (t0) cc_final: 0.7897 (t0) REVERT: B 269 GLU cc_start: 0.8029 (pm20) cc_final: 0.7763 (pm20) REVERT: C 50 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.9073 (mt0) REVERT: C 65 ARG cc_start: 0.8563 (ttp-110) cc_final: 0.7948 (ttp-110) REVERT: C 72 GLN cc_start: 0.8744 (mm-40) cc_final: 0.7700 (mm-40) REVERT: C 107 LYS cc_start: 0.8482 (tttp) cc_final: 0.8274 (tttm) REVERT: C 147 ASP cc_start: 0.8379 (t0) cc_final: 0.8015 (t0) REVERT: C 269 GLU cc_start: 0.7993 (pm20) cc_final: 0.7786 (pm20) REVERT: D 147 ASP cc_start: 0.8284 (t0) cc_final: 0.7973 (t0) REVERT: D 189 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.8964 (tt0) REVERT: D 269 GLU cc_start: 0.7722 (pp20) cc_final: 0.7334 (pp20) outliers start: 9 outliers final: 2 residues processed: 111 average time/residue: 1.4449 time to fit residues: 168.5448 Evaluate side-chains 107 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN 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 50 GLN Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.057399 restraints weight = 13714.667| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.86 r_work: 0.2595 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 8352 Z= 0.342 Angle : 0.924 18.313 11530 Z= 0.401 Chirality : 0.059 0.338 1426 Planarity : 0.005 0.050 1409 Dihedral : 16.483 105.024 1917 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.31 % Allowed : 10.36 % Favored : 88.33 % 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: 0.43 (0.28), residues: 970 helix: -2.15 (0.74), residues: 24 sheet: 0.69 (0.25), residues: 490 loop : 0.09 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 190 HIS 0.003 0.001 HIS D 174 PHE 0.020 0.002 PHE C 49 TYR 0.015 0.002 TYR B 121 ARG 0.004 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00025 ( 1) link_TRANS : angle 0.17257 ( 3) link_NAG-ASN : bond 0.00472 ( 16) link_NAG-ASN : angle 2.60419 ( 48) link_ALPHA1-6 : bond 0.01370 ( 4) link_ALPHA1-6 : angle 1.72134 ( 12) link_BETA1-4 : bond 0.02364 ( 16) link_BETA1-4 : angle 6.22490 ( 48) link_ALPHA1-3 : bond 0.00850 ( 8) link_ALPHA1-3 : angle 3.02560 ( 24) hydrogen bonds : bond 0.04738 ( 320) hydrogen bonds : angle 5.15039 ( 1032) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.30117 ( 4) covalent geometry : bond 0.00791 ( 8305) covalent geometry : angle 0.80579 (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 105 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.879 Fit side-chains REVERT: A 147 ASP cc_start: 0.8537 (t0) cc_final: 0.8245 (t0) REVERT: A 269 GLU cc_start: 0.7874 (pp20) cc_final: 0.7501 (pp20) REVERT: B 52 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8727 (pt0) REVERT: B 121 TYR cc_start: 0.9364 (p90) cc_final: 0.9146 (p90) REVERT: B 147 ASP cc_start: 0.8474 (t0) cc_final: 0.8122 (t0) REVERT: C 107 LYS cc_start: 0.8733 (tttp) cc_final: 0.8526 (tttm) REVERT: C 121 TYR cc_start: 0.9367 (p90) cc_final: 0.9147 (p90) REVERT: D 147 ASP cc_start: 0.8552 (t0) cc_final: 0.8258 (t0) REVERT: D 269 GLU cc_start: 0.7865 (pp20) cc_final: 0.7440 (pp20) outliers start: 11 outliers final: 4 residues processed: 101 average time/residue: 1.5150 time to fit residues: 160.6536 Evaluate side-chains 98 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 263 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 128 GLN C 50 GLN D 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.058067 restraints weight = 13601.489| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.93 r_work: 0.2665 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3310 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= 0.158 Angle : 0.850 18.309 11530 Z= 0.358 Chirality : 0.056 0.327 1426 Planarity : 0.004 0.046 1409 Dihedral : 15.757 107.152 1917 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.43 % Allowed : 11.79 % 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: 0.67 (0.28), residues: 970 helix: -1.99 (0.73), residues: 24 sheet: 0.83 (0.26), residues: 470 loop : 0.31 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 192 HIS 0.002 0.000 HIS B 257 PHE 0.016 0.002 PHE B 161 TYR 0.008 0.001 TYR D 165 ARG 0.011 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00043 ( 1) link_TRANS : angle 0.11004 ( 3) link_NAG-ASN : bond 0.00184 ( 16) link_NAG-ASN : angle 2.67617 ( 48) link_ALPHA1-6 : bond 0.01497 ( 4) link_ALPHA1-6 : angle 1.60732 ( 12) link_BETA1-4 : bond 0.02432 ( 16) link_BETA1-4 : angle 6.13033 ( 48) link_ALPHA1-3 : bond 0.00902 ( 8) link_ALPHA1-3 : angle 2.85890 ( 24) hydrogen bonds : bond 0.03591 ( 320) hydrogen bonds : angle 4.68286 ( 1032) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.08666 ( 4) covalent geometry : bond 0.00320 ( 8305) covalent geometry : angle 0.72248 (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 111 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.876 Fit side-chains REVERT: A 147 ASP cc_start: 0.8519 (t0) cc_final: 0.8168 (t0) REVERT: A 269 GLU cc_start: 0.7839 (pp20) cc_final: 0.7407 (pp20) REVERT: B 147 ASP cc_start: 0.8504 (t0) cc_final: 0.8158 (t0) REVERT: D 147 ASP cc_start: 0.8534 (t0) cc_final: 0.8203 (t0) REVERT: D 269 GLU cc_start: 0.7822 (pp20) cc_final: 0.7339 (pp20) outliers start: 12 outliers final: 3 residues processed: 106 average time/residue: 1.5812 time to fit residues: 175.7787 Evaluate side-chains 94 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 107 LYS 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: 0.0000 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9766 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.092769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.058029 restraints weight = 13640.844| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.98 r_work: 0.2665 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3357 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= 0.159 Angle : 0.852 18.267 11530 Z= 0.357 Chirality : 0.055 0.330 1426 Planarity : 0.004 0.045 1409 Dihedral : 15.015 106.860 1917 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.71 % Allowed : 12.26 % Favored : 87.02 % 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 (0.28), residues: 970 helix: -1.92 (0.74), residues: 24 sheet: 0.75 (0.26), residues: 453 loop : 0.43 (0.30), residues: 493 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 0.001 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 0.11955 ( 3) link_NAG-ASN : bond 0.00208 ( 16) link_NAG-ASN : angle 2.76578 ( 48) link_ALPHA1-6 : bond 0.01527 ( 4) link_ALPHA1-6 : angle 1.50451 ( 12) link_BETA1-4 : bond 0.02429 ( 16) link_BETA1-4 : angle 6.10321 ( 48) link_ALPHA1-3 : bond 0.00859 ( 8) link_ALPHA1-3 : angle 2.79212 ( 24) hydrogen bonds : bond 0.03466 ( 320) hydrogen bonds : angle 4.57176 ( 1032) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.11677 ( 4) covalent geometry : bond 0.00328 ( 8305) covalent geometry : angle 0.72578 (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 99 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.822 Fit side-chains REVERT: A 147 ASP cc_start: 0.8526 (t0) cc_final: 0.8159 (t0) REVERT: A 269 GLU cc_start: 0.7823 (pp20) cc_final: 0.7369 (pp20) REVERT: B 189 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8911 (tt0) REVERT: D 147 ASP cc_start: 0.8593 (t0) cc_final: 0.8265 (t0) REVERT: D 269 GLU cc_start: 0.7856 (pp20) cc_final: 0.7365 (pp20) outliers start: 6 outliers final: 5 residues processed: 97 average time/residue: 1.6164 time to fit residues: 164.2026 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 : 0.900 ------------------------------------------------------------------------------- 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 189 GLN 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: 5.9990 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 0.0010 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.093069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.061075 restraints weight = 13703.837| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.73 r_work: 0.2548 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3501 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= 0.165 Angle : 0.851 18.267 11530 Z= 0.356 Chirality : 0.054 0.329 1426 Planarity : 0.004 0.049 1409 Dihedral : 14.140 106.097 1917 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 (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 (0.29), residues: 970 helix: -2.13 (0.69), residues: 24 sheet: 0.72 (0.26), residues: 455 loop : 0.45 (0.30), residues: 491 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 0.018 0.001 PHE B 161 TYR 0.011 0.001 TYR C 121 ARG 0.016 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00046 ( 1) link_TRANS : angle 0.09840 ( 3) link_NAG-ASN : bond 0.00213 ( 16) link_NAG-ASN : angle 2.75215 ( 48) link_ALPHA1-6 : bond 0.01580 ( 4) link_ALPHA1-6 : angle 1.28225 ( 12) link_BETA1-4 : bond 0.02440 ( 16) link_BETA1-4 : angle 6.11482 ( 48) link_ALPHA1-3 : bond 0.00856 ( 8) link_ALPHA1-3 : angle 2.71183 ( 24) hydrogen bonds : bond 0.03468 ( 320) hydrogen bonds : angle 4.49115 ( 1032) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.15500 ( 4) covalent geometry : bond 0.00344 ( 8305) covalent geometry : angle 0.72511 (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 103 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.881 Fit side-chains REVERT: A 147 ASP cc_start: 0.8489 (t0) cc_final: 0.8121 (t0) REVERT: A 269 GLU cc_start: 0.7751 (pp20) cc_final: 0.7274 (pp20) REVERT: B 147 ASP cc_start: 0.8496 (t0) cc_final: 0.8154 (t0) REVERT: B 189 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8865 (tt0) REVERT: C 112 ASP cc_start: 0.9015 (m-30) cc_final: 0.8670 (p0) REVERT: C 147 ASP cc_start: 0.8533 (t0) cc_final: 0.8152 (t0) REVERT: D 147 ASP cc_start: 0.8517 (t0) cc_final: 0.8155 (t0) REVERT: D 269 GLU cc_start: 0.7781 (pp20) cc_final: 0.7300 (pp20) outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 1.5967 time to fit residues: 167.9096 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 : 0.900 ------------------------------------------------------------------------------- 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 189 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.093768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.061821 restraints weight = 13855.786| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.77 r_work: 0.2560 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3565 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= 0.152 Angle : 0.836 18.262 11530 Z= 0.350 Chirality : 0.053 0.330 1426 Planarity : 0.004 0.046 1409 Dihedral : 13.239 105.403 1917 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.71 % Allowed : 12.38 % 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: 0.67 (0.29), residues: 970 helix: -2.17 (0.66), residues: 24 sheet: 0.71 (0.26), residues: 449 loop : 0.48 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 190 HIS 0.002 0.000 HIS C 257 PHE 0.018 0.001 PHE C 161 TYR 0.009 0.001 TYR B 121 ARG 0.015 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00038 ( 1) link_TRANS : angle 0.14889 ( 3) link_NAG-ASN : bond 0.00155 ( 16) link_NAG-ASN : angle 2.73260 ( 48) link_ALPHA1-6 : bond 0.01581 ( 4) link_ALPHA1-6 : angle 0.96402 ( 12) link_BETA1-4 : bond 0.02448 ( 16) link_BETA1-4 : angle 6.10670 ( 48) link_ALPHA1-3 : bond 0.00839 ( 8) link_ALPHA1-3 : angle 2.60919 ( 24) hydrogen bonds : bond 0.03278 ( 320) hydrogen bonds : angle 4.41126 ( 1032) SS BOND : bond 0.00076 ( 2) SS BOND : angle 0.12715 ( 4) covalent geometry : bond 0.00310 ( 8305) covalent geometry : angle 0.70918 (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 101 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.018 Fit side-chains REVERT: A 147 ASP cc_start: 0.8475 (t0) cc_final: 0.8105 (t0) REVERT: A 269 GLU cc_start: 0.7732 (pp20) cc_final: 0.7259 (pp20) REVERT: B 65 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.8346 (ttp-110) REVERT: C 112 ASP cc_start: 0.9005 (m-30) cc_final: 0.8645 (p0) REVERT: D 147 ASP cc_start: 0.8490 (t0) cc_final: 0.8111 (t0) REVERT: D 269 GLU cc_start: 0.7774 (pp20) cc_final: 0.7283 (pp20) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 1.8253 time to fit residues: 187.4153 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 : 0.913 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.092877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.060882 restraints weight = 13967.782| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.76 r_work: 0.2539 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3691 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= 0.175 Angle : 0.842 18.202 11530 Z= 0.356 Chirality : 0.053 0.331 1426 Planarity : 0.004 0.054 1409 Dihedral : 12.757 104.099 1917 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: 0.67 (0.29), residues: 970 helix: -2.06 (0.68), residues: 24 sheet: 0.71 (0.26), residues: 451 loop : 0.47 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 190 HIS 0.002 0.001 HIS B 257 PHE 0.017 0.001 PHE B 161 TYR 0.010 0.001 TYR A 250 ARG 0.016 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00023 ( 1) link_TRANS : angle 0.13863 ( 3) link_NAG-ASN : bond 0.00198 ( 16) link_NAG-ASN : angle 2.72149 ( 48) link_ALPHA1-6 : bond 0.01462 ( 4) link_ALPHA1-6 : angle 0.95212 ( 12) link_BETA1-4 : bond 0.02422 ( 16) link_BETA1-4 : angle 6.10816 ( 48) link_ALPHA1-3 : bond 0.00800 ( 8) link_ALPHA1-3 : angle 2.57938 ( 24) hydrogen bonds : bond 0.03506 ( 320) hydrogen bonds : angle 4.47308 ( 1032) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.23347 ( 4) covalent geometry : bond 0.00375 ( 8305) covalent geometry : angle 0.71759 (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 97 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.844 Fit side-chains REVERT: A 269 GLU cc_start: 0.7762 (pp20) cc_final: 0.7277 (pp20) REVERT: B 189 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8866 (tt0) REVERT: C 112 ASP cc_start: 0.9012 (m-30) cc_final: 0.8650 (p0) REVERT: D 147 ASP cc_start: 0.8514 (t0) cc_final: 0.8114 (t0) REVERT: D 269 GLU cc_start: 0.7792 (pp20) cc_final: 0.7297 (pp20) outliers start: 5 outliers final: 5 residues processed: 96 average time/residue: 1.6390 time to fit residues: 165.0201 Evaluate side-chains 95 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.092166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.060412 restraints weight = 13715.654| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.69 r_work: 0.2522 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3794 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= 0.189 Angle : 0.840 18.200 11530 Z= 0.360 Chirality : 0.053 0.333 1426 Planarity : 0.004 0.046 1409 Dihedral : 12.250 102.560 1917 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.71 % Allowed : 13.21 % Favored : 86.07 % 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 (0.29), residues: 970 helix: -1.99 (0.69), residues: 24 sheet: 0.70 (0.26), residues: 461 loop : 0.47 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 190 HIS 0.001 0.000 HIS D 257 PHE 0.014 0.001 PHE D 98 TYR 0.017 0.001 TYR D 74 ARG 0.014 0.001 ARG B 65 Details of bonding type rmsd link_TRANS : bond 0.00023 ( 1) link_TRANS : angle 0.13276 ( 3) link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 2.67482 ( 48) link_ALPHA1-6 : bond 0.01393 ( 4) link_ALPHA1-6 : angle 1.29291 ( 12) link_BETA1-4 : bond 0.02420 ( 16) link_BETA1-4 : angle 6.09358 ( 48) link_ALPHA1-3 : bond 0.00842 ( 8) link_ALPHA1-3 : angle 2.43479 ( 24) hydrogen bonds : bond 0.03661 ( 320) hydrogen bonds : angle 4.52643 ( 1032) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.56079 ( 4) covalent geometry : bond 0.00409 ( 8305) covalent geometry : angle 0.71697 (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: 6 poor density : 88 time to evaluate : 0.877 Fit side-chains REVERT: A 269 GLU cc_start: 0.7767 (pp20) cc_final: 0.7287 (pp20) REVERT: B 65 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8349 (ttp-110) REVERT: B 67 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 189 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8862 (tt0) REVERT: C 112 ASP cc_start: 0.9021 (m-30) cc_final: 0.8661 (p0) REVERT: D 147 ASP cc_start: 0.8531 (t0) cc_final: 0.8127 (t0) REVERT: D 269 GLU cc_start: 0.7802 (pp20) cc_final: 0.7294 (pp20) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 1.6877 time to fit residues: 162.4087 Evaluate side-chains 89 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.061172 restraints weight = 13893.540| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.68 r_work: 0.2538 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3883 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= 0.168 Angle : 0.831 18.219 11530 Z= 0.355 Chirality : 0.052 0.332 1426 Planarity : 0.004 0.045 1409 Dihedral : 11.691 100.130 1917 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.36 % Allowed : 14.05 % Favored : 85.60 % 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: -1.74 (0.74), residues: 24 sheet: 0.69 (0.26), residues: 449 loop : 0.49 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 190 HIS 0.001 0.000 HIS B 257 PHE 0.018 0.001 PHE B 161 TYR 0.010 0.001 TYR C 121 ARG 0.014 0.001 ARG C 65 Details of bonding type rmsd link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.27343 ( 3) link_NAG-ASN : bond 0.00149 ( 16) link_NAG-ASN : angle 2.69984 ( 48) link_ALPHA1-6 : bond 0.01237 ( 4) link_ALPHA1-6 : angle 1.80952 ( 12) link_BETA1-4 : bond 0.02427 ( 16) link_BETA1-4 : angle 6.08396 ( 48) link_ALPHA1-3 : bond 0.00835 ( 8) link_ALPHA1-3 : angle 2.37676 ( 24) hydrogen bonds : bond 0.03442 ( 320) hydrogen bonds : angle 4.45599 ( 1032) SS BOND : bond 0.00183 ( 2) SS BOND : angle 0.21514 ( 4) covalent geometry : bond 0.00355 ( 8305) covalent geometry : angle 0.70460 (11391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5405.05 seconds wall clock time: 94 minutes 12.12 seconds (5652.12 seconds total)