Starting phenix.real_space_refine on Wed Jul 30 14:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l6u_23208/07_2025/7l6u_23208.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l6u_23208/07_2025/7l6u_23208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l6u_23208/07_2025/7l6u_23208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l6u_23208/07_2025/7l6u_23208.map" model { file = "/net/cci-nas-00/data/ceres_data/7l6u_23208/07_2025/7l6u_23208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l6u_23208/07_2025/7l6u_23208.cif" } resolution = 3.3 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= 0.003 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8255 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Time building chain proxies: 7.60, per 1000 atoms: 0.60 Number of scatterers: 12675 At special positions: 0 Unit cell: (92.064, 93.16, 121.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2275 8.00 N 2115 7.00 C 8255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 38.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS A 54 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.541A pdb=" N THR A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS B 54 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.541A pdb=" N THR B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS C 54 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.541A pdb=" N THR C 321 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS D 54 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.664A pdb=" N ASN D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 253 removed outlier: 3.832A pdb=" N PHE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.541A pdb=" N THR D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 237 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.541A pdb=" N THR E 321 " --> pdb=" O ILE E 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 14 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 143 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B 14 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER B 143 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 14 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER C 143 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 14 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER D 143 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL E 14 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER E 143 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1905 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: 3.81 Time building geometry restraints manager: 3.63 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: 3037 1.33 - 1.45: 2787 1.45 - 1.57: 7141 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 13015 Sorted by residual: bond pdb=" C VAL A 58 " pdb=" N GLU A 59 " ideal model delta sigma weight residual 1.332 1.221 0.112 1.40e-02 5.10e+03 6.36e+01 bond pdb=" C VAL C 58 " pdb=" N GLU C 59 " ideal model delta sigma weight residual 1.332 1.222 0.111 1.40e-02 5.10e+03 6.23e+01 bond pdb=" C VAL D 58 " pdb=" N GLU D 59 " ideal model delta sigma weight residual 1.332 1.222 0.110 1.40e-02 5.10e+03 6.19e+01 bond pdb=" C VAL E 58 " pdb=" N GLU E 59 " ideal model delta sigma weight residual 1.332 1.223 0.110 1.40e-02 5.10e+03 6.13e+01 bond pdb=" C VAL B 58 " pdb=" N GLU B 59 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.40e-02 5.10e+03 6.11e+01 ... (remaining 13010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17049 1.66 - 3.31: 519 3.31 - 4.97: 112 4.97 - 6.62: 50 6.62 - 8.28: 5 Bond angle restraints: 17735 Sorted by residual: angle pdb=" N VAL A 291 " pdb=" CA VAL A 291 " pdb=" C VAL A 291 " ideal model delta sigma weight residual 113.71 107.58 6.13 9.50e-01 1.11e+00 4.17e+01 angle pdb=" N VAL B 291 " pdb=" CA VAL B 291 " pdb=" C VAL B 291 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.12e+01 angle pdb=" N VAL E 291 " pdb=" CA VAL E 291 " pdb=" C VAL E 291 " ideal model delta sigma weight residual 113.71 107.62 6.09 9.50e-01 1.11e+00 4.11e+01 angle pdb=" N VAL D 291 " pdb=" CA VAL D 291 " pdb=" C VAL D 291 " ideal model delta sigma weight residual 113.71 107.63 6.08 9.50e-01 1.11e+00 4.10e+01 angle pdb=" N VAL C 291 " pdb=" CA VAL C 291 " pdb=" C VAL C 291 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 ... (remaining 17730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 6653 15.94 - 31.89: 751 31.89 - 47.83: 175 47.83 - 63.78: 26 63.78 - 79.72: 10 Dihedral angle restraints: 7615 sinusoidal: 3060 harmonic: 4555 Sorted by residual: dihedral pdb=" CA GLN C 182 " pdb=" C GLN C 182 " pdb=" N PRO C 183 " pdb=" CA PRO C 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN A 182 " pdb=" C GLN A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN D 182 " pdb=" C GLN D 182 " pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1519 0.059 - 0.117: 396 0.117 - 0.176: 55 0.176 - 0.235: 0 0.235 - 0.293: 5 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CA GLU B 59 " pdb=" N GLU B 59 " pdb=" C GLU B 59 " pdb=" CB GLU B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1972 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 59 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLU A 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU A 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN B 60 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU E 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU E 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN E 60 " -0.021 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4737 2.87 - 3.38: 11474 3.38 - 3.89: 19850 3.89 - 4.39: 22253 4.39 - 4.90: 40341 Nonbonded interactions: 98655 Sorted by model distance: nonbonded pdb=" OH TYR D 33 " pdb=" O VAL D 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR E 33 " pdb=" O VAL E 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 33 " pdb=" O VAL A 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR B 33 " pdb=" O VAL B 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR C 33 " pdb=" O VAL C 127 " model vdw 2.366 3.040 ... (remaining 98650 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.520 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.350 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.112 13015 Z= 0.391 Angle : 0.786 8.281 17735 Z= 0.454 Chirality : 0.054 0.293 1975 Planarity : 0.005 0.070 2260 Dihedral : 14.086 79.721 4675 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.72 % Allowed : 0.79 % Favored : 98.49 % 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: -1.06 (0.22), residues: 1545 helix: 0.42 (0.22), residues: 515 sheet: -0.18 (0.26), residues: 480 loop : -2.25 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 160 HIS 0.003 0.001 HIS D 285 PHE 0.025 0.002 PHE B 247 TYR 0.021 0.002 TYR A 248 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.13090 ( 615) hydrogen bonds : angle 5.88600 ( 1905) covalent geometry : bond 0.00905 (13015) covalent geometry : angle 0.78587 (17735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.495 Fit side-chains REVERT: A 142 PHE cc_start: 0.6837 (t80) cc_final: 0.6603 (t80) REVERT: B 138 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: B 142 PHE cc_start: 0.6826 (t80) cc_final: 0.6556 (t80) REVERT: C 142 PHE cc_start: 0.7021 (t80) cc_final: 0.6643 (t80) REVERT: D 142 PHE cc_start: 0.6975 (t80) cc_final: 0.6681 (t80) REVERT: E 138 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: E 142 PHE cc_start: 0.6831 (t80) cc_final: 0.6586 (t80) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 0.3121 time to fit residues: 50.3840 Evaluate side-chains 90 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 138 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130206 restraints weight = 14312.560| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.20 r_work: 0.3636 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13015 Z= 0.145 Angle : 0.608 7.164 17735 Z= 0.314 Chirality : 0.047 0.156 1975 Planarity : 0.004 0.054 2260 Dihedral : 5.996 55.209 1731 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.29 % Allowed : 4.10 % Favored : 95.61 % 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 (0.22), residues: 1545 helix: 0.90 (0.23), residues: 535 sheet: 0.21 (0.26), residues: 480 loop : -2.07 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 43 HIS 0.004 0.001 HIS E 285 PHE 0.029 0.001 PHE E 247 TYR 0.016 0.001 TYR A 248 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 615) hydrogen bonds : angle 4.39843 ( 1905) covalent geometry : bond 0.00335 (13015) covalent geometry : angle 0.60797 (17735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 1.502 Fit side-chains REVERT: A 142 PHE cc_start: 0.7214 (t80) cc_final: 0.6864 (t80) REVERT: B 113 ASP cc_start: 0.7702 (m-30) cc_final: 0.7335 (p0) REVERT: B 138 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: B 142 PHE cc_start: 0.7312 (t80) cc_final: 0.6792 (t80) REVERT: B 248 TYR cc_start: 0.8685 (t80) cc_final: 0.8421 (t80) REVERT: C 113 ASP cc_start: 0.7682 (m-30) cc_final: 0.7266 (p0) REVERT: C 142 PHE cc_start: 0.7473 (t80) cc_final: 0.6848 (t80) REVERT: D 86 ASP cc_start: 0.8574 (t0) cc_final: 0.8260 (t0) REVERT: D 142 PHE cc_start: 0.7453 (t80) cc_final: 0.6913 (t80) REVERT: E 113 ASP cc_start: 0.7991 (m-30) cc_final: 0.7652 (p0) REVERT: E 138 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: E 142 PHE cc_start: 0.7367 (t80) cc_final: 0.6914 (t80) outliers start: 4 outliers final: 1 residues processed: 120 average time/residue: 0.2649 time to fit residues: 46.1960 Evaluate side-chains 94 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 138 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 103 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 81 optimal weight: 0.0020 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 89 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN C 89 ASN D 89 ASN D 138 GLN D 285 HIS E 89 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.160326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126645 restraints weight = 14527.170| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.21 r_work: 0.3591 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13015 Z= 0.213 Angle : 0.634 7.144 17735 Z= 0.324 Chirality : 0.048 0.157 1975 Planarity : 0.004 0.049 2260 Dihedral : 5.345 59.260 1716 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.65 % Allowed : 8.49 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1545 helix: 0.84 (0.23), residues: 535 sheet: 0.39 (0.27), residues: 485 loop : -2.22 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 224 HIS 0.004 0.001 HIS E 285 PHE 0.022 0.002 PHE D 247 TYR 0.017 0.002 TYR A 248 ARG 0.001 0.000 ARG E 163 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 615) hydrogen bonds : angle 4.38354 ( 1905) covalent geometry : bond 0.00532 (13015) covalent geometry : angle 0.63450 (17735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.369 Fit side-chains REVERT: A 285 HIS cc_start: 0.6859 (t70) cc_final: 0.6420 (t-90) REVERT: B 113 ASP cc_start: 0.7745 (m-30) cc_final: 0.7320 (p0) REVERT: B 138 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8299 (tm-30) REVERT: B 142 PHE cc_start: 0.7355 (t80) cc_final: 0.6874 (t80) REVERT: C 142 PHE cc_start: 0.7507 (t80) cc_final: 0.6807 (t80) REVERT: C 285 HIS cc_start: 0.6790 (t70) cc_final: 0.6428 (t-90) REVERT: D 86 ASP cc_start: 0.8715 (t0) cc_final: 0.8350 (t0) REVERT: D 142 PHE cc_start: 0.7488 (t80) cc_final: 0.6968 (t80) REVERT: E 138 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: E 142 PHE cc_start: 0.7352 (t80) cc_final: 0.6866 (t80) outliers start: 9 outliers final: 3 residues processed: 112 average time/residue: 0.2941 time to fit residues: 47.0187 Evaluate side-chains 93 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN D 138 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.173881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.141418 restraints weight = 14781.642| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.18 r_work: 0.3574 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13015 Z= 0.269 Angle : 0.678 7.051 17735 Z= 0.349 Chirality : 0.050 0.184 1975 Planarity : 0.005 0.048 2260 Dihedral : 5.490 58.096 1716 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.08 % Allowed : 11.44 % Favored : 87.48 % 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: -0.63 (0.22), residues: 1545 helix: 0.73 (0.22), residues: 535 sheet: 0.31 (0.26), residues: 485 loop : -2.34 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 43 HIS 0.004 0.001 HIS E 285 PHE 0.022 0.002 PHE B 247 TYR 0.017 0.002 TYR A 248 ARG 0.003 0.000 ARG E 286 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 615) hydrogen bonds : angle 4.48189 ( 1905) covalent geometry : bond 0.00675 (13015) covalent geometry : angle 0.67773 (17735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.471 Fit side-chains REVERT: A 285 HIS cc_start: 0.6917 (t70) cc_final: 0.6569 (t-90) REVERT: B 113 ASP cc_start: 0.7724 (m-30) cc_final: 0.7309 (p0) REVERT: B 138 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8422 (tm-30) REVERT: C 142 PHE cc_start: 0.7468 (t80) cc_final: 0.6793 (t80) REVERT: C 285 HIS cc_start: 0.6772 (t70) cc_final: 0.6452 (t-90) REVERT: D 86 ASP cc_start: 0.8685 (t0) cc_final: 0.8337 (t0) REVERT: E 138 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8504 (tm-30) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.2683 time to fit residues: 40.2096 Evaluate side-chains 92 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.174980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140880 restraints weight = 14906.189| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.08 r_work: 0.3684 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13015 Z= 0.119 Angle : 0.561 6.508 17735 Z= 0.287 Chirality : 0.045 0.144 1975 Planarity : 0.004 0.045 2260 Dihedral : 4.922 58.816 1716 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.15 % Allowed : 11.65 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1545 helix: 1.13 (0.23), residues: 535 sheet: 0.57 (0.26), residues: 485 loop : -2.19 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 224 HIS 0.006 0.001 HIS E 285 PHE 0.020 0.001 PHE B 247 TYR 0.016 0.001 TYR C 248 ARG 0.002 0.000 ARG D 65 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 615) hydrogen bonds : angle 3.90881 ( 1905) covalent geometry : bond 0.00286 (13015) covalent geometry : angle 0.56148 (17735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.489 Fit side-chains REVERT: A 285 HIS cc_start: 0.7120 (t70) cc_final: 0.6666 (t-90) REVERT: B 113 ASP cc_start: 0.7960 (m-30) cc_final: 0.7485 (p0) REVERT: B 138 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: C 285 HIS cc_start: 0.7075 (t70) cc_final: 0.6651 (t-90) REVERT: D 86 ASP cc_start: 0.8858 (t0) cc_final: 0.8515 (t0) REVERT: D 93 MET cc_start: 0.8418 (ttm) cc_final: 0.8093 (ttp) REVERT: D 138 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: E 138 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: E 185 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7441 (tp-100) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 0.2559 time to fit residues: 49.2836 Evaluate side-chains 110 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 128 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN C 103 ASN ** E 138 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 = 0.4027 r_free = 0.4027 target = 0.164902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131131 restraints weight = 14584.744| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.23 r_work: 0.3637 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13015 Z= 0.136 Angle : 0.565 6.701 17735 Z= 0.288 Chirality : 0.045 0.146 1975 Planarity : 0.004 0.044 2260 Dihedral : 4.915 58.933 1716 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.44 % Allowed : 12.16 % Favored : 86.40 % 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: -0.06 (0.23), residues: 1545 helix: 1.15 (0.23), residues: 535 sheet: 0.78 (0.26), residues: 480 loop : -2.12 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 43 HIS 0.003 0.001 HIS E 285 PHE 0.017 0.001 PHE B 247 TYR 0.022 0.001 TYR C 248 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 615) hydrogen bonds : angle 3.89682 ( 1905) covalent geometry : bond 0.00329 (13015) covalent geometry : angle 0.56487 (17735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.387 Fit side-chains REVERT: A 285 HIS cc_start: 0.6972 (t70) cc_final: 0.6685 (t-90) REVERT: B 113 ASP cc_start: 0.7711 (m-30) cc_final: 0.7352 (p0) REVERT: B 138 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: C 285 HIS cc_start: 0.6838 (t70) cc_final: 0.6597 (t-90) REVERT: D 86 ASP cc_start: 0.8738 (t0) cc_final: 0.8354 (t0) REVERT: D 93 MET cc_start: 0.8244 (ttm) cc_final: 0.7904 (ttp) REVERT: D 138 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: E 59 GLU cc_start: 0.8824 (tp30) cc_final: 0.8567 (mm-30) REVERT: E 138 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8323 (tm-30) REVERT: E 185 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7359 (tp-100) outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 0.2640 time to fit residues: 46.1197 Evaluate side-chains 111 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** E 138 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 = 0.3993 r_free = 0.3993 target = 0.161864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128088 restraints weight = 14533.742| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.22 r_work: 0.3601 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13015 Z= 0.193 Angle : 0.604 6.484 17735 Z= 0.309 Chirality : 0.047 0.156 1975 Planarity : 0.004 0.043 2260 Dihedral : 5.078 58.134 1716 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.80 % Allowed : 12.52 % Favored : 85.68 % 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: -0.20 (0.22), residues: 1545 helix: 1.05 (0.23), residues: 535 sheet: 0.58 (0.26), residues: 490 loop : -2.14 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 224 HIS 0.004 0.001 HIS D 285 PHE 0.017 0.002 PHE B 247 TYR 0.017 0.001 TYR C 248 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 615) hydrogen bonds : angle 4.08596 ( 1905) covalent geometry : bond 0.00482 (13015) covalent geometry : angle 0.60351 (17735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.355 Fit side-chains REVERT: A 285 HIS cc_start: 0.6977 (t70) cc_final: 0.6728 (t-90) REVERT: B 113 ASP cc_start: 0.7711 (m-30) cc_final: 0.7300 (p0) REVERT: B 138 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: C 285 HIS cc_start: 0.6885 (t70) cc_final: 0.6580 (t-90) REVERT: D 86 ASP cc_start: 0.8776 (t0) cc_final: 0.8391 (t0) REVERT: D 93 MET cc_start: 0.8345 (ttm) cc_final: 0.8024 (ttm) REVERT: D 138 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8288 (tm-30) REVERT: E 138 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: E 185 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7413 (tp-100) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.2825 time to fit residues: 46.6922 Evaluate side-chains 110 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 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 = 0.4014 r_free = 0.4014 target = 0.163939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130082 restraints weight = 14506.049| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.23 r_work: 0.3627 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13015 Z= 0.151 Angle : 0.572 6.394 17735 Z= 0.293 Chirality : 0.046 0.148 1975 Planarity : 0.004 0.043 2260 Dihedral : 4.933 57.706 1716 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.65 % Allowed : 13.02 % Favored : 85.32 % 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: -0.03 (0.22), residues: 1545 helix: 1.19 (0.23), residues: 535 sheet: 0.83 (0.26), residues: 480 loop : -2.17 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.004 0.001 HIS E 285 PHE 0.018 0.001 PHE B 247 TYR 0.018 0.001 TYR C 248 ARG 0.002 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 615) hydrogen bonds : angle 3.95987 ( 1905) covalent geometry : bond 0.00372 (13015) covalent geometry : angle 0.57213 (17735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 1.527 Fit side-chains REVERT: A 285 HIS cc_start: 0.6918 (t70) cc_final: 0.6687 (t-90) REVERT: B 113 ASP cc_start: 0.7639 (m-30) cc_final: 0.7265 (p0) REVERT: B 138 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: B 285 HIS cc_start: 0.6797 (t70) cc_final: 0.6381 (t-90) REVERT: C 285 HIS cc_start: 0.6782 (t70) cc_final: 0.6539 (t-90) REVERT: D 86 ASP cc_start: 0.8808 (t0) cc_final: 0.8397 (t0) REVERT: D 93 MET cc_start: 0.8291 (ttm) cc_final: 0.7949 (ttp) REVERT: D 138 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: E 59 GLU cc_start: 0.8943 (tp30) cc_final: 0.8711 (mm-30) REVERT: E 138 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8459 (tm-30) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.2734 time to fit residues: 45.4251 Evaluate side-chains 113 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 4 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 154 optimal weight: 30.0000 chunk 122 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.173996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142428 restraints weight = 14561.097| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.12 r_work: 0.3615 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13015 Z= 0.167 Angle : 0.580 6.408 17735 Z= 0.296 Chirality : 0.046 0.150 1975 Planarity : 0.004 0.042 2260 Dihedral : 4.972 58.423 1716 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.73 % Allowed : 13.17 % Favored : 85.11 % 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: -0.07 (0.22), residues: 1545 helix: 1.16 (0.23), residues: 535 sheet: 0.82 (0.26), residues: 480 loop : -2.20 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 224 HIS 0.004 0.001 HIS E 285 PHE 0.017 0.001 PHE B 247 TYR 0.017 0.001 TYR C 248 ARG 0.002 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 615) hydrogen bonds : angle 3.99889 ( 1905) covalent geometry : bond 0.00412 (13015) covalent geometry : angle 0.57989 (17735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.465 Fit side-chains REVERT: A 285 HIS cc_start: 0.6941 (t70) cc_final: 0.6716 (t-90) REVERT: B 113 ASP cc_start: 0.7635 (m-30) cc_final: 0.7279 (p0) REVERT: B 138 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: B 285 HIS cc_start: 0.6794 (t70) cc_final: 0.6562 (t-90) REVERT: D 86 ASP cc_start: 0.8804 (t0) cc_final: 0.8414 (t0) REVERT: D 93 MET cc_start: 0.8329 (ttm) cc_final: 0.7978 (ttp) REVERT: D 138 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: E 138 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8510 (tm-30) outliers start: 24 outliers final: 21 residues processed: 114 average time/residue: 0.2637 time to fit residues: 43.6676 Evaluate side-chains 113 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 148 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 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 = 0.4037 r_free = 0.4037 target = 0.166059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132329 restraints weight = 14400.205| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.22 r_work: 0.3654 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13015 Z= 0.120 Angle : 0.547 6.589 17735 Z= 0.279 Chirality : 0.045 0.143 1975 Planarity : 0.004 0.043 2260 Dihedral : 4.758 57.989 1716 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.58 % Allowed : 13.45 % Favored : 84.96 % 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: 0.18 (0.23), residues: 1545 helix: 1.38 (0.23), residues: 535 sheet: 0.98 (0.26), residues: 480 loop : -2.11 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 43 HIS 0.002 0.001 HIS E 285 PHE 0.017 0.001 PHE D 247 TYR 0.019 0.001 TYR C 248 ARG 0.003 0.000 ARG C 286 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 615) hydrogen bonds : angle 3.80684 ( 1905) covalent geometry : bond 0.00286 (13015) covalent geometry : angle 0.54700 (17735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.778 Fit side-chains REVERT: A 285 HIS cc_start: 0.6932 (t70) cc_final: 0.6693 (t-90) REVERT: B 113 ASP cc_start: 0.7576 (m-30) cc_final: 0.7234 (p0) REVERT: B 138 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: B 285 HIS cc_start: 0.6809 (t70) cc_final: 0.6590 (t-90) REVERT: D 86 ASP cc_start: 0.8771 (t0) cc_final: 0.8362 (t0) REVERT: D 93 MET cc_start: 0.8219 (ttm) cc_final: 0.7899 (ttp) REVERT: D 138 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: E 138 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8332 (tm-30) outliers start: 22 outliers final: 15 residues processed: 117 average time/residue: 0.2680 time to fit residues: 45.8052 Evaluate side-chains 111 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146144 restraints weight = 14555.309| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.16 r_work: 0.3662 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13015 Z= 0.112 Angle : 0.537 6.263 17735 Z= 0.273 Chirality : 0.044 0.140 1975 Planarity : 0.004 0.041 2260 Dihedral : 4.669 59.516 1716 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.29 % Allowed : 13.96 % Favored : 84.75 % 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: 0.25 (0.23), residues: 1545 helix: 1.48 (0.23), residues: 535 sheet: 1.16 (0.26), residues: 460 loop : -2.14 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 43 HIS 0.002 0.000 HIS C 284 PHE 0.016 0.001 PHE D 247 TYR 0.024 0.001 TYR C 248 ARG 0.001 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 615) hydrogen bonds : angle 3.71764 ( 1905) covalent geometry : bond 0.00266 (13015) covalent geometry : angle 0.53699 (17735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.21 seconds wall clock time: 93 minutes 31.44 seconds (5611.44 seconds total)