Starting phenix.real_space_refine on Wed Aug 5 14:09:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjv_39351/08_2026/8yjv_39351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjv_39351/08_2026/8yjv_39351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yjv_39351/08_2026/8yjv_39351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjv_39351/08_2026/8yjv_39351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yjv_39351/08_2026/8yjv_39351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjv_39351/08_2026/8yjv_39351.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 404 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 61 5.16 5 C 6057 2.51 5 N 1667 2.21 5 O 2089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9938 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "D" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2779 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1946 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "B" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1938 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 2.05, per 1000 atoms: 0.21 Number of scatterers: 9938 At special positions: 0 Unit cell: (108.73, 107.07, 105.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 64 15.00 O 2089 8.00 N 1667 7.00 C 6057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 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 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 296.5 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 31.9% alpha, 24.2% beta 12 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.243A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.132A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.796A pdb=" N TYR D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 27' Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.536A pdb=" N ASN D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 118 Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 134 through 149 Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.698A pdb=" N SER D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.894A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 256 through 262 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 317 through 334 removed outlier: 3.802A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.818A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 222 Proline residue: A 220 - end of helix No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.096A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.682A pdb=" N ALA B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 61 removed outlier: 4.924A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG C 5 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.779A pdb=" N MET C 68 " --> pdb=" O TRP C 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.527A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.027A pdb=" N LYS D 345 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 204 through 208 Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 21 Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.755A pdb=" N ALA D 174 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AB1, first strand: chain 'A' and resid 66 through 71 removed outlier: 7.288A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 251 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.735A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 160 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.904A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 30 Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 40 removed outlier: 3.728A pdb=" N LEU B 251 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 235 " --> pdb=" O LEU B 251 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2315 1.33 - 1.45: 2144 1.45 - 1.57: 5536 1.57 - 1.69: 127 1.69 - 1.81: 98 Bond restraints: 10220 Sorted by residual: bond pdb=" C3' DT E 3 " pdb=" O3' DT E 3 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.22e+01 bond pdb=" C1' DT E 8 " pdb=" N1 DT E 8 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" C3' DT J 1 " pdb=" C2' DT J 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DA E 28 " pdb=" O3' DA E 28 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" C3' DT E 22 " pdb=" C2' DT E 22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 13772 3.19 - 6.38: 248 6.38 - 9.58: 39 9.58 - 12.77: 7 12.77 - 15.96: 2 Bond angle restraints: 14068 Sorted by residual: angle pdb=" C ALA C 242 " pdb=" N ASP C 243 " pdb=" CA ASP C 243 " ideal model delta sigma weight residual 121.54 135.01 -13.47 1.91e+00 2.74e-01 4.97e+01 angle pdb=" CA PRO B 106 " pdb=" N PRO B 106 " pdb=" CD PRO B 106 " ideal model delta sigma weight residual 112.00 104.02 7.98 1.40e+00 5.10e-01 3.25e+01 angle pdb=" C ALA B 242 " pdb=" N ASP B 243 " pdb=" CA ASP B 243 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" C3' DT E 3 " pdb=" O3' DT E 3 " pdb=" P DT E 4 " ideal model delta sigma weight residual 119.70 125.58 -5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" CA LEU D 275 " pdb=" CB LEU D 275 " pdb=" CG LEU D 275 " ideal model delta sigma weight residual 116.30 132.26 -15.96 3.50e+00 8.16e-02 2.08e+01 ... (remaining 14063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 5746 35.35 - 70.69: 402 70.69 - 106.04: 17 106.04 - 141.39: 1 141.39 - 176.73: 1 Dihedral angle restraints: 6167 sinusoidal: 2933 harmonic: 3234 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual 93.00 153.33 -60.33 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASP A 150 " pdb=" C ASP A 150 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ILE B 241 " pdb=" C ILE B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1280 0.073 - 0.145: 290 0.145 - 0.218: 40 0.218 - 0.290: 6 0.290 - 0.363: 3 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CG LEU B 72 " pdb=" CB LEU B 72 " pdb=" CD1 LEU B 72 " pdb=" CD2 LEU B 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU B 235 " pdb=" CB LEU B 235 " pdb=" CD1 LEU B 235 " pdb=" CD2 LEU B 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1616 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 234 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 214 " -0.019 2.00e-02 2.50e+03 2.60e-02 1.18e+01 pdb=" CG PHE B 214 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE B 214 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 214 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE B 214 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 214 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 214 " 0.018 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE C 214 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE C 214 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE C 214 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 214 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 214 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 214 " 0.001 2.00e-02 2.50e+03 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2804 2.83 - 3.35: 8286 3.35 - 3.87: 17788 3.87 - 4.38: 19625 4.38 - 4.90: 33050 Nonbonded interactions: 81553 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.317 3.040 nonbonded pdb=" O THR B 216 " pdb=" OG1 THR B 219 " model vdw 2.338 3.040 nonbonded pdb=" OG SER D 197 " pdb=" OP2 DA E 14 " model vdw 2.342 3.040 nonbonded pdb=" O ASN B 71 " pdb=" OG SER B 74 " model vdw 2.355 3.040 nonbonded pdb=" N GLY D 2 " pdb=" OD1 ASP D 179 " model vdw 2.383 3.120 ... (remaining 81548 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' and resid 2 through 253) selection = chain 'B' selection = (chain 'C' and resid 2 through 253) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.120 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.007 0.099 10222 Z= 0.416 Angle : 1.122 15.960 14072 Z= 0.684 Chirality : 0.062 0.363 1619 Planarity : 0.008 0.103 1591 Dihedral : 20.737 176.732 4063 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 0.73 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.21), residues: 1103 helix: -2.47 (0.22), residues: 308 sheet: -2.02 (0.26), residues: 335 loop : -2.42 (0.22), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 5 TYR 0.030 0.003 TYR A 249 PHE 0.059 0.005 PHE B 214 TRP 0.051 0.005 TRP D 274 HIS 0.016 0.002 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.42 (10220) covalent geometry : angle 1.12180 / 0.68 (14068) SS BOND : bond 0.00067 / 0.03 ( 2) SS BOND : angle 1.35529 / 1.10 ( 4) hydrogen bonds : bond 0.20225 / 13.64 ( 449) hydrogen bonds : angle 10.17809 / 7.04 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.284 Fit side-chains REVERT: C 53 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7393 (mtm180) REVERT: C 97 ASP cc_start: 0.4939 (p0) cc_final: 0.4469 (p0) REVERT: C 244 MET cc_start: 0.8524 (mtp) cc_final: 0.8228 (mtp) REVERT: D 21 ASN cc_start: 0.7825 (m110) cc_final: 0.7594 (m110) REVERT: A 199 MET cc_start: 0.5303 (ttm) cc_final: 0.4907 (ttm) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.0823 time to fit residues: 18.8019 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 100 optimal weight: 0.9980 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.160818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123608 restraints weight = 13135.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127341 restraints weight = 7702.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129885 restraints weight = 5387.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131524 restraints weight = 4264.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132570 restraints weight = 3654.268| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10222 Z= 0.146 Angle : 0.645 8.205 14072 Z= 0.362 Chirality : 0.046 0.287 1619 Planarity : 0.005 0.085 1591 Dihedral : 21.698 175.084 1939 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.35 % Allowed : 6.85 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.22), residues: 1103 helix: -0.60 (0.27), residues: 311 sheet: -2.08 (0.26), residues: 326 loop : -2.17 (0.23), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 104 TYR 0.012 0.001 TYR A 114 PHE 0.032 0.002 PHE B 2 TRP 0.018 0.002 TRP D 274 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (10220) covalent geometry : angle 0.64450 / 0.36 (14068) SS BOND : bond 0.02108 / 1.11 ( 2) SS BOND : angle 0.86825 / 0.58 ( 4) hydrogen bonds : bond 0.05842 / 3.50 ( 449) hydrogen bonds : angle 7.23116 / 5.06 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.261 Fit side-chains REVERT: C 53 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7702 (mtm180) REVERT: C 97 ASP cc_start: 0.4909 (p0) cc_final: 0.4199 (p0) REVERT: C 214 PHE cc_start: 0.8593 (m-10) cc_final: 0.8348 (m-10) REVERT: C 244 MET cc_start: 0.8253 (mtp) cc_final: 0.8033 (ttm) REVERT: D 77 ASN cc_start: 0.7934 (m-40) cc_final: 0.7501 (m110) REVERT: B 131 GLN cc_start: 0.6489 (mm-40) cc_final: 0.6070 (mm-40) outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.0796 time to fit residues: 16.6163 Evaluate side-chains 125 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118081 restraints weight = 13237.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122347 restraints weight = 9299.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123374 restraints weight = 5743.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123742 restraints weight = 5172.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124148 restraints weight = 4882.055| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10222 Z= 0.220 Angle : 0.668 7.378 14072 Z= 0.365 Chirality : 0.048 0.321 1619 Planarity : 0.005 0.077 1591 Dihedral : 21.692 171.541 1939 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.08 % Allowed : 10.59 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.24), residues: 1103 helix: 0.19 (0.29), residues: 308 sheet: -2.02 (0.27), residues: 326 loop : -2.08 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 53 TYR 0.015 0.002 TYR D 83 PHE 0.035 0.002 PHE B 214 TRP 0.012 0.002 TRP D 274 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (10220) covalent geometry : angle 0.66818 / 0.37 (14068) SS BOND : bond 0.00244 / 0.13 ( 2) SS BOND : angle 1.24073 / 0.87 ( 4) hydrogen bonds : bond 0.05207 / 3.22 ( 449) hydrogen bonds : angle 6.84800 / 4.76 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.326 Fit side-chains REVERT: C 36 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: C 53 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7583 (mtm180) REVERT: C 97 ASP cc_start: 0.5019 (p0) cc_final: 0.4252 (p0) REVERT: C 244 MET cc_start: 0.8345 (mtp) cc_final: 0.7940 (ttm) REVERT: B 131 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6033 (mm110) REVERT: B 146 ARG cc_start: 0.7115 (ttt90) cc_final: 0.6901 (ttt90) outliers start: 20 outliers final: 13 residues processed: 140 average time/residue: 0.0751 time to fit residues: 15.7283 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 ASN D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS B 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118937 restraints weight = 13392.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122601 restraints weight = 7823.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125064 restraints weight = 5518.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126697 restraints weight = 4393.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127802 restraints weight = 3770.825| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10222 Z= 0.155 Angle : 0.592 7.426 14072 Z= 0.328 Chirality : 0.045 0.324 1619 Planarity : 0.004 0.072 1591 Dihedral : 21.680 169.150 1939 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.45 % Allowed : 12.77 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.24), residues: 1103 helix: 0.46 (0.30), residues: 315 sheet: -2.10 (0.27), residues: 312 loop : -2.11 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 149 TYR 0.011 0.001 TYR D 83 PHE 0.026 0.002 PHE B 214 TRP 0.007 0.001 TRP A 28 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10220) covalent geometry : angle 0.59205 / 0.33 (14068) SS BOND : bond 0.00123 / 0.06 ( 2) SS BOND : angle 0.84719 / 0.54 ( 4) hydrogen bonds : bond 0.04684 / 2.82 ( 449) hydrogen bonds : angle 6.58394 / 4.58 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.329 Fit side-chains REVERT: C 28 TRP cc_start: 0.8267 (m100) cc_final: 0.8007 (m100) REVERT: C 53 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7623 (mtm180) REVERT: C 214 PHE cc_start: 0.8648 (m-10) cc_final: 0.8304 (m-10) REVERT: C 225 VAL cc_start: 0.8462 (t) cc_final: 0.8231 (p) REVERT: C 244 MET cc_start: 0.8281 (mtp) cc_final: 0.8010 (ttm) outliers start: 14 outliers final: 14 residues processed: 133 average time/residue: 0.0734 time to fit residues: 14.4711 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 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 = 0.3928 r_free = 0.3928 target = 0.153058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115443 restraints weight = 13431.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118931 restraints weight = 7899.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121294 restraints weight = 5661.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122865 restraints weight = 4525.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123528 restraints weight = 3917.484| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10222 Z= 0.226 Angle : 0.651 7.572 14072 Z= 0.353 Chirality : 0.047 0.335 1619 Planarity : 0.004 0.071 1591 Dihedral : 21.728 168.276 1939 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.70 % Allowed : 12.56 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.24), residues: 1103 helix: 0.52 (0.30), residues: 318 sheet: -2.23 (0.26), residues: 323 loop : -2.11 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 146 TYR 0.016 0.002 TYR D 83 PHE 0.025 0.002 PHE B 214 TRP 0.007 0.002 TRP B 28 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (10220) covalent geometry : angle 0.65059 / 0.35 (14068) SS BOND : bond 0.00108 / 0.05 ( 2) SS BOND : angle 1.16832 / 0.77 ( 4) hydrogen bonds : bond 0.04726 / 2.89 ( 449) hydrogen bonds : angle 6.55980 / 4.55 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.232 Fit side-chains REVERT: C 53 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7585 (mtm180) REVERT: C 225 VAL cc_start: 0.8503 (t) cc_final: 0.8276 (p) REVERT: C 244 MET cc_start: 0.8260 (mtp) cc_final: 0.7780 (mtp) REVERT: D 92 LEU cc_start: 0.7826 (mp) cc_final: 0.7581 (mp) outliers start: 26 outliers final: 19 residues processed: 141 average time/residue: 0.0740 time to fit residues: 15.3941 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118354 restraints weight = 13468.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122098 restraints weight = 7853.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124622 restraints weight = 5516.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126251 restraints weight = 4369.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127354 restraints weight = 3743.094| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10222 Z= 0.145 Angle : 0.584 7.665 14072 Z= 0.321 Chirality : 0.045 0.342 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.715 166.581 1939 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.66 % Allowed : 14.64 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.24), residues: 1103 helix: 0.73 (0.30), residues: 317 sheet: -2.13 (0.26), residues: 320 loop : -1.98 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.011 0.001 TYR B 250 PHE 0.026 0.002 PHE B 214 TRP 0.006 0.001 TRP A 28 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10220) covalent geometry : angle 0.58397 / 0.32 (14068) SS BOND : bond 0.00150 / 0.07 ( 2) SS BOND : angle 0.70650 / 0.44 ( 4) hydrogen bonds : bond 0.04322 / 2.61 ( 449) hydrogen bonds : angle 6.36710 / 4.41 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.265 Fit side-chains REVERT: C 28 TRP cc_start: 0.8296 (m100) cc_final: 0.8022 (m100) REVERT: C 53 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7639 (mtm180) REVERT: C 214 PHE cc_start: 0.8581 (m-10) cc_final: 0.8258 (m-10) REVERT: C 244 MET cc_start: 0.8174 (mtp) cc_final: 0.7650 (ttp) REVERT: D 92 LEU cc_start: 0.7815 (mp) cc_final: 0.7587 (mp) REVERT: D 327 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6496 (ptt180) outliers start: 16 outliers final: 12 residues processed: 133 average time/residue: 0.0802 time to fit residues: 15.4685 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117482 restraints weight = 13329.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121159 restraints weight = 7780.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123596 restraints weight = 5482.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125247 restraints weight = 4369.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126354 restraints weight = 3740.869| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10222 Z= 0.171 Angle : 0.600 9.256 14072 Z= 0.326 Chirality : 0.045 0.346 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.695 166.052 1939 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.60 % Allowed : 14.02 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.24), residues: 1103 helix: 0.83 (0.30), residues: 318 sheet: -2.16 (0.26), residues: 319 loop : -1.96 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.012 0.001 TYR D 83 PHE 0.026 0.002 PHE B 214 TRP 0.009 0.001 TRP D 274 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (10220) covalent geometry : angle 0.60009 / 0.33 (14068) SS BOND : bond 0.00133 / 0.06 ( 2) SS BOND : angle 0.86246 / 0.54 ( 4) hydrogen bonds : bond 0.04299 / 2.61 ( 449) hydrogen bonds : angle 6.32148 / 4.39 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.356 Fit side-chains REVERT: C 28 TRP cc_start: 0.8302 (m100) cc_final: 0.8034 (m100) REVERT: C 53 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7589 (mtm180) REVERT: C 214 PHE cc_start: 0.8601 (m-10) cc_final: 0.8227 (m-10) REVERT: C 244 MET cc_start: 0.8155 (mtp) cc_final: 0.7867 (ttm) REVERT: D 74 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7049 (mmt) REVERT: D 92 LEU cc_start: 0.7829 (mp) cc_final: 0.7611 (mp) REVERT: D 248 ASP cc_start: 0.6287 (m-30) cc_final: 0.5867 (t70) REVERT: D 327 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6521 (ptt180) REVERT: A 139 MET cc_start: 0.7694 (ptt) cc_final: 0.7367 (ptt) outliers start: 25 outliers final: 20 residues processed: 136 average time/residue: 0.0867 time to fit residues: 16.9890 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.153790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117008 restraints weight = 13338.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120508 restraints weight = 7847.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122880 restraints weight = 5558.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124482 restraints weight = 4422.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125334 restraints weight = 3788.954| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10222 Z= 0.160 Angle : 0.592 7.905 14072 Z= 0.322 Chirality : 0.045 0.356 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.687 164.046 1939 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 15.26 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.24), residues: 1103 helix: 0.84 (0.30), residues: 319 sheet: -2.11 (0.26), residues: 317 loop : -1.91 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.011 0.001 TYR B 250 PHE 0.025 0.002 PHE B 214 TRP 0.010 0.001 TRP D 274 HIS 0.007 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (10220) covalent geometry : angle 0.59168 / 0.32 (14068) SS BOND : bond 0.00136 / 0.06 ( 2) SS BOND : angle 0.81559 / 0.51 ( 4) hydrogen bonds : bond 0.04170 / 2.54 ( 449) hydrogen bonds : angle 6.24053 / 4.33 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: C 53 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7687 (mtm180) REVERT: C 214 PHE cc_start: 0.8611 (m-10) cc_final: 0.8280 (m-10) REVERT: C 244 MET cc_start: 0.8140 (mtp) cc_final: 0.7897 (ttm) REVERT: D 74 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7087 (mmt) REVERT: D 92 LEU cc_start: 0.7842 (mp) cc_final: 0.7636 (mp) REVERT: D 248 ASP cc_start: 0.6235 (m-30) cc_final: 0.5906 (t70) REVERT: D 327 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6564 (ptt180) REVERT: A 139 MET cc_start: 0.7671 (ptt) cc_final: 0.7287 (ptt) outliers start: 24 outliers final: 21 residues processed: 135 average time/residue: 0.0941 time to fit residues: 18.3062 Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117598 restraints weight = 13332.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121006 restraints weight = 7813.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123384 restraints weight = 5536.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125010 restraints weight = 4400.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126009 restraints weight = 3771.156| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10222 Z= 0.152 Angle : 0.582 8.019 14072 Z= 0.317 Chirality : 0.044 0.364 1619 Planarity : 0.004 0.069 1591 Dihedral : 21.601 163.072 1939 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.70 % Allowed : 15.16 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1103 helix: 0.95 (0.30), residues: 318 sheet: -2.11 (0.26), residues: 318 loop : -1.86 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.010 0.001 TYR D 83 PHE 0.026 0.002 PHE B 214 TRP 0.010 0.001 TRP D 274 HIS 0.007 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10220) covalent geometry : angle 0.58226 / 0.32 (14068) SS BOND : bond 0.00157 / 0.07 ( 2) SS BOND : angle 0.78758 / 0.47 ( 4) hydrogen bonds : bond 0.04059 / 2.49 ( 449) hydrogen bonds : angle 6.18866 / 4.29 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: C 28 TRP cc_start: 0.8313 (m100) cc_final: 0.8022 (m100) REVERT: C 53 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7679 (mtm180) REVERT: C 214 PHE cc_start: 0.8598 (m-10) cc_final: 0.8263 (m-10) REVERT: D 74 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7026 (mmt) REVERT: D 248 ASP cc_start: 0.6288 (m-30) cc_final: 0.5925 (t70) REVERT: D 327 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6573 (ptt180) REVERT: A 139 MET cc_start: 0.7641 (ptt) cc_final: 0.7277 (ptt) outliers start: 26 outliers final: 22 residues processed: 135 average time/residue: 0.0863 time to fit residues: 16.7830 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.154599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117956 restraints weight = 13316.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121517 restraints weight = 7812.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123895 restraints weight = 5523.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125503 restraints weight = 4389.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126441 restraints weight = 3780.126| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10222 Z= 0.141 Angle : 0.581 8.045 14072 Z= 0.315 Chirality : 0.044 0.366 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.573 163.114 1939 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.70 % Allowed : 15.58 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.24), residues: 1103 helix: 0.95 (0.30), residues: 319 sheet: -2.08 (0.26), residues: 317 loop : -1.87 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.010 0.001 TYR B 250 PHE 0.025 0.002 PHE B 214 TRP 0.013 0.001 TRP D 274 HIS 0.008 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10220) covalent geometry : angle 0.58111 / 0.31 (14068) SS BOND : bond 0.00153 / 0.07 ( 2) SS BOND : angle 0.73392 / 0.43 ( 4) hydrogen bonds : bond 0.04044 / 2.46 ( 449) hydrogen bonds : angle 6.16031 / 4.27 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 28 TRP cc_start: 0.8302 (m100) cc_final: 0.8017 (m100) REVERT: C 53 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7696 (mtm180) REVERT: C 214 PHE cc_start: 0.8593 (m-10) cc_final: 0.8255 (m-10) REVERT: D 74 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7033 (mmt) REVERT: D 180 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7013 (mmp) REVERT: D 182 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7728 (t) REVERT: D 248 ASP cc_start: 0.6288 (m-30) cc_final: 0.5917 (t70) REVERT: D 327 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6576 (ptt180) REVERT: A 139 MET cc_start: 0.7633 (ptt) cc_final: 0.7268 (ptt) outliers start: 26 outliers final: 21 residues processed: 132 average time/residue: 0.0855 time to fit residues: 16.5184 Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.155470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118868 restraints weight = 13361.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122456 restraints weight = 7825.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124887 restraints weight = 5497.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126488 restraints weight = 4358.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127592 restraints weight = 3732.447| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10222 Z= 0.124 Angle : 0.569 8.061 14072 Z= 0.309 Chirality : 0.044 0.368 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.539 163.157 1939 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.18 % Allowed : 15.99 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.24), residues: 1103 helix: 1.00 (0.30), residues: 319 sheet: -2.10 (0.26), residues: 324 loop : -1.82 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 146 TYR 0.009 0.001 TYR B 250 PHE 0.025 0.001 PHE B 214 TRP 0.015 0.001 TRP D 274 HIS 0.008 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10220) covalent geometry : angle 0.56903 / 0.31 (14068) SS BOND : bond 0.00156 / 0.07 ( 2) SS BOND : angle 0.66942 / 0.38 ( 4) hydrogen bonds : bond 0.03992 / 2.41 ( 449) hydrogen bonds : angle 6.09435 / 4.22 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1682.45 seconds wall clock time: 29 minutes 47.67 seconds (1787.67 seconds total)