Starting phenix.real_space_refine on Wed Jul 30 11:51:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f33_28830/07_2025/8f33_28830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f33_28830/07_2025/8f33_28830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f33_28830/07_2025/8f33_28830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f33_28830/07_2025/8f33_28830.map" model { file = "/net/cci-nas-00/data/ceres_data/8f33_28830/07_2025/8f33_28830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f33_28830/07_2025/8f33_28830.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 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: 12545 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D Time building chain proxies: 5.55, per 1000 atoms: 0.44 Number of scatterers: 12545 At special positions: 0 Unit cell: (86.724, 86.724, 123.516, 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 2250 8.00 N 2085 7.00 C 8180 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: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 34.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.875A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.726A pdb=" N ASP E 153 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 209 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 227 through 249 Processing helix chain 'E' and resid 260 through 287 removed outlier: 3.726A pdb=" N GLN E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 317 removed outlier: 3.615A pdb=" N ILE E 317 " --> pdb=" O CYS E 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.874A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.726A pdb=" N ASP D 153 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 209 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 227 through 249 Processing helix chain 'D' and resid 260 through 287 removed outlier: 3.726A pdb=" N GLN D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 317 removed outlier: 3.615A pdb=" N ILE D 317 " --> pdb=" O CYS D 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.875A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.726A pdb=" N ASP C 153 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 227 through 249 Processing helix chain 'C' and resid 260 through 287 removed outlier: 3.726A pdb=" N GLN C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 removed outlier: 3.615A pdb=" N ILE C 317 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.875A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.726A pdb=" N ASP B 153 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 209 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 227 through 249 Processing helix chain 'B' and resid 260 through 287 removed outlier: 3.726A pdb=" N GLN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.615A pdb=" N ILE B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.875A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.726A pdb=" N ASP A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 227 through 249 Processing helix chain 'A' and resid 260 through 287 removed outlier: 3.726A pdb=" N GLN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.615A pdb=" N ILE A 317 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.114A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.585A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.585A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.114A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.585A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.585A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.114A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.585A 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: 6.585A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.114A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.584A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.584A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.115A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.584A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.584A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1890 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: 4.26 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3991 1.34 - 1.46: 2739 1.46 - 1.57: 6100 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" CG1 ILE D 215 " pdb=" CD1 ILE D 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.13e+00 bond pdb=" CG1 ILE E 215 " pdb=" CD1 ILE E 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.12e+00 bond pdb=" CG1 ILE B 215 " pdb=" CD1 ILE B 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.10e+00 bond pdb=" CG1 ILE A 215 " pdb=" CD1 ILE A 215 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.09e+00 bond pdb=" CG1 ILE C 215 " pdb=" CD1 ILE C 215 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.08e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 16925 1.90 - 3.80: 542 3.80 - 5.69: 43 5.69 - 7.59: 20 7.59 - 9.49: 15 Bond angle restraints: 17545 Sorted by residual: angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 6810 17.22 - 34.45: 570 34.45 - 51.67: 125 51.67 - 68.90: 15 68.90 - 86.12: 10 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA PHE B 106 " pdb=" C PHE B 106 " pdb=" N LEU B 107 " pdb=" CA LEU B 107 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE C 106 " pdb=" C PHE C 106 " pdb=" N LEU C 107 " pdb=" CA LEU C 107 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE A 106 " pdb=" C PHE A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 163.03 16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1138 0.042 - 0.084: 572 0.084 - 0.126: 186 0.126 - 0.168: 32 0.168 - 0.210: 22 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE A 39 " pdb=" CA ILE A 39 " pdb=" CG1 ILE A 39 " pdb=" CG2 ILE A 39 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 206 " -0.013 2.00e-02 2.50e+03 1.27e-02 4.04e+00 pdb=" CG TRP B 206 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 206 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 206 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 206 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 206 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.012 2.00e-02 2.50e+03 1.25e-02 3.93e+00 pdb=" CG TRP A 206 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 206 " -0.013 2.00e-02 2.50e+03 1.25e-02 3.93e+00 pdb=" CG TRP E 206 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP E 206 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 206 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 206 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 206 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 206 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 206 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 206 " -0.003 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4451 2.87 - 3.38: 10936 3.38 - 3.88: 21020 3.88 - 4.39: 23202 4.39 - 4.90: 42754 Nonbonded interactions: 102363 Sorted by model distance: nonbonded pdb=" O LEU D 225 " pdb=" NH2 ARG D 231 " model vdw 2.359 3.120 nonbonded pdb=" O LEU C 225 " pdb=" NH2 ARG C 231 " model vdw 2.360 3.120 nonbonded pdb=" O LEU A 225 " pdb=" NH2 ARG A 231 " model vdw 2.360 3.120 nonbonded pdb=" O LEU E 225 " pdb=" NH2 ARG E 231 " model vdw 2.360 3.120 nonbonded pdb=" O LEU B 225 " pdb=" NH2 ARG B 231 " model vdw 2.360 3.120 ... (remaining 102358 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: 0.09 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: 1.210 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.650 Find NCS groups from input model: 0.260 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:3.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.005 0.069 12880 Z= 0.231 Angle : 0.801 9.490 17545 Z= 0.425 Chirality : 0.056 0.210 1950 Planarity : 0.006 0.045 2235 Dihedral : 13.623 86.122 4620 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -1.40 (0.20), residues: 1525 helix: -0.47 (0.20), residues: 545 sheet: 0.83 (0.24), residues: 435 loop : -2.94 (0.22), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 206 HIS 0.002 0.001 HIS B 177 PHE 0.025 0.003 PHE B 247 TYR 0.023 0.003 TYR C 148 ARG 0.006 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.11683 ( 595) hydrogen bonds : angle 6.07368 ( 1890) covalent geometry : bond 0.00525 (12880) covalent geometry : angle 0.80137 (17545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.516 Fit side-chains REVERT: D 30 GLU cc_start: 0.5858 (tp30) cc_final: 0.5525 (mm-30) REVERT: A 30 GLU cc_start: 0.5801 (tp30) cc_final: 0.5458 (mm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2918 time to fit residues: 58.2029 Evaluate side-chains 97 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118275 restraints weight = 15174.703| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.79 r_work: 0.3166 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12880 Z= 0.184 Angle : 0.569 6.021 17545 Z= 0.295 Chirality : 0.048 0.145 1950 Planarity : 0.004 0.047 2235 Dihedral : 4.529 18.029 1690 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.65 % Allowed : 5.09 % Favored : 94.25 % 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: -0.71 (0.21), residues: 1525 helix: 0.47 (0.21), residues: 555 sheet: 0.95 (0.24), residues: 435 loop : -2.79 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 206 HIS 0.002 0.001 HIS C 177 PHE 0.035 0.002 PHE C 247 TYR 0.016 0.002 TYR C 245 ARG 0.002 0.000 ARG C 141 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 595) hydrogen bonds : angle 4.89920 ( 1890) covalent geometry : bond 0.00422 (12880) covalent geometry : angle 0.56908 (17545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 1.986 Fit side-chains REVERT: E 159 GLU cc_start: 0.7578 (pm20) cc_final: 0.6435 (tt0) REVERT: C 159 GLU cc_start: 0.7533 (pm20) cc_final: 0.6556 (tt0) REVERT: C 245 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.7835 (t80) REVERT: B 247 PHE cc_start: 0.5914 (p90) cc_final: 0.5274 (p90) REVERT: A 30 GLU cc_start: 0.5992 (tp30) cc_final: 0.5512 (mm-30) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.3998 time to fit residues: 61.6440 Evaluate side-chains 107 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 1 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 overall best weight: 3.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114838 restraints weight = 15445.493| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.79 r_work: 0.3128 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 12880 Z= 0.233 Angle : 0.612 9.632 17545 Z= 0.314 Chirality : 0.049 0.155 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.900 25.122 1690 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.31 % Allowed : 8.73 % Favored : 89.96 % 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: -0.48 (0.21), residues: 1525 helix: 0.66 (0.22), residues: 565 sheet: 0.92 (0.24), residues: 435 loop : -2.56 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 206 HIS 0.003 0.001 HIS E 177 PHE 0.033 0.002 PHE D 247 TYR 0.021 0.002 TYR C 245 ARG 0.004 0.000 ARG E 231 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 595) hydrogen bonds : angle 4.89397 ( 1890) covalent geometry : bond 0.00543 (12880) covalent geometry : angle 0.61183 (17545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.491 Fit side-chains REVERT: E 159 GLU cc_start: 0.7672 (pm20) cc_final: 0.6577 (tt0) REVERT: E 245 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8004 (t80) REVERT: E 247 PHE cc_start: 0.6356 (p90) cc_final: 0.5877 (p90) REVERT: D 245 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8014 (t80) REVERT: C 159 GLU cc_start: 0.7585 (pm20) cc_final: 0.6697 (tt0) REVERT: C 245 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8058 (t80) REVERT: B 245 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8008 (t80) REVERT: B 247 PHE cc_start: 0.6233 (p90) cc_final: 0.5756 (p90) REVERT: A 245 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.8035 (t80) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 0.2772 time to fit residues: 53.3964 Evaluate side-chains 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.151498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116971 restraints weight = 15261.844| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.74 r_work: 0.3157 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 12880 Z= 0.195 Angle : 0.565 9.876 17545 Z= 0.290 Chirality : 0.048 0.147 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.602 17.551 1690 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.76 % Allowed : 9.53 % Favored : 87.71 % 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: -0.27 (0.21), residues: 1525 helix: 0.86 (0.22), residues: 565 sheet: 0.96 (0.24), residues: 435 loop : -2.42 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 206 HIS 0.002 0.001 HIS D 177 PHE 0.032 0.002 PHE B 247 TYR 0.018 0.002 TYR C 245 ARG 0.003 0.000 ARG E 231 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 595) hydrogen bonds : angle 4.73082 ( 1890) covalent geometry : bond 0.00453 (12880) covalent geometry : angle 0.56533 (17545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.410 Fit side-chains REVERT: E 245 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8007 (t80) REVERT: D 245 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 245 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8096 (t80) REVERT: B 245 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.7982 (t80) REVERT: A 245 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7973 (t80) outliers start: 38 outliers final: 17 residues processed: 160 average time/residue: 0.2785 time to fit residues: 63.9619 Evaluate side-chains 138 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 64 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116603 restraints weight = 15278.648| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.73 r_work: 0.3149 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12880 Z= 0.211 Angle : 0.589 9.063 17545 Z= 0.302 Chirality : 0.048 0.152 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.687 17.583 1690 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.40 % Allowed : 10.40 % Favored : 87.20 % 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: -0.32 (0.21), residues: 1525 helix: 0.90 (0.22), residues: 565 sheet: 0.93 (0.25), residues: 405 loop : -2.35 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 206 HIS 0.003 0.001 HIS D 177 PHE 0.032 0.002 PHE A 247 TYR 0.020 0.002 TYR C 245 ARG 0.003 0.000 ARG E 231 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 595) hydrogen bonds : angle 4.73747 ( 1890) covalent geometry : bond 0.00494 (12880) covalent geometry : angle 0.58881 (17545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.516 Fit side-chains REVERT: E 159 GLU cc_start: 0.7595 (pm20) cc_final: 0.7326 (pm20) REVERT: E 245 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7904 (t80) REVERT: D 245 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 159 GLU cc_start: 0.7693 (pm20) cc_final: 0.6702 (tt0) REVERT: C 245 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8134 (t80) REVERT: B 245 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 247 PHE cc_start: 0.6393 (p90) cc_final: 0.5700 (p90) REVERT: A 245 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 247 PHE cc_start: 0.6433 (p90) cc_final: 0.5771 (p90) outliers start: 33 outliers final: 17 residues processed: 150 average time/residue: 0.2704 time to fit residues: 58.2804 Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 132 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.155081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120611 restraints weight = 15351.518| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.79 r_work: 0.3208 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12880 Z= 0.112 Angle : 0.503 8.749 17545 Z= 0.258 Chirality : 0.045 0.131 1950 Planarity : 0.004 0.046 2235 Dihedral : 4.192 16.245 1690 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.96 % Allowed : 11.20 % Favored : 86.84 % 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 (0.22), residues: 1525 helix: 1.43 (0.22), residues: 535 sheet: 0.97 (0.26), residues: 435 loop : -2.23 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 206 HIS 0.001 0.000 HIS E 177 PHE 0.030 0.001 PHE E 247 TYR 0.013 0.001 TYR C 245 ARG 0.002 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 595) hydrogen bonds : angle 4.43015 ( 1890) covalent geometry : bond 0.00247 (12880) covalent geometry : angle 0.50295 (17545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.358 Fit side-chains REVERT: E 245 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7866 (t80) REVERT: D 245 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8003 (t80) REVERT: C 159 GLU cc_start: 0.7653 (pm20) cc_final: 0.6622 (tt0) REVERT: C 223 PHE cc_start: 0.6686 (m-80) cc_final: 0.6470 (m-80) REVERT: C 245 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7968 (t80) REVERT: B 223 PHE cc_start: 0.6802 (m-80) cc_final: 0.6594 (m-80) REVERT: B 245 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7949 (t80) REVERT: A 233 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: A 245 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7928 (t80) outliers start: 27 outliers final: 12 residues processed: 136 average time/residue: 0.2666 time to fit residues: 52.4786 Evaluate side-chains 135 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 84 optimal weight: 0.0170 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116520 restraints weight = 15356.259| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.75 r_work: 0.3151 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12880 Z= 0.188 Angle : 0.562 7.855 17545 Z= 0.289 Chirality : 0.047 0.148 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.473 16.895 1690 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.25 % Allowed : 11.42 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1525 helix: 0.99 (0.22), residues: 565 sheet: 1.06 (0.26), residues: 405 loop : -2.27 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.032 0.002 PHE B 247 TYR 0.018 0.002 TYR C 245 ARG 0.004 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 595) hydrogen bonds : angle 4.59368 ( 1890) covalent geometry : bond 0.00438 (12880) covalent geometry : angle 0.56174 (17545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.367 Fit side-chains REVERT: E 159 GLU cc_start: 0.7631 (pm20) cc_final: 0.7400 (pm20) REVERT: E 245 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7938 (t80) REVERT: D 245 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7941 (t80) REVERT: C 159 GLU cc_start: 0.7660 (pm20) cc_final: 0.6644 (tt0) REVERT: C 223 PHE cc_start: 0.6734 (m-80) cc_final: 0.6471 (m-80) REVERT: C 245 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8119 (t80) REVERT: B 245 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7913 (t80) REVERT: B 247 PHE cc_start: 0.6326 (p90) cc_final: 0.5551 (p90) REVERT: A 233 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6892 (mp10) REVERT: A 245 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7880 (t80) REVERT: A 247 PHE cc_start: 0.6280 (p90) cc_final: 0.5546 (p90) outliers start: 31 outliers final: 17 residues processed: 148 average time/residue: 0.2667 time to fit residues: 55.8488 Evaluate side-chains 141 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 7 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 118 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 113 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121955 restraints weight = 15254.038| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.78 r_work: 0.3225 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12880 Z= 0.101 Angle : 0.491 9.202 17545 Z= 0.253 Chirality : 0.045 0.132 1950 Planarity : 0.004 0.045 2235 Dihedral : 4.027 15.378 1690 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.82 % Allowed : 11.93 % Favored : 86.25 % 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: 0.21 (0.22), residues: 1525 helix: 1.58 (0.22), residues: 530 sheet: 1.10 (0.26), residues: 435 loop : -2.18 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 206 HIS 0.001 0.000 HIS E 177 PHE 0.028 0.001 PHE E 247 TYR 0.012 0.001 TYR C 248 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.02927 ( 595) hydrogen bonds : angle 4.35086 ( 1890) covalent geometry : bond 0.00218 (12880) covalent geometry : angle 0.49147 (17545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.375 Fit side-chains REVERT: E 159 GLU cc_start: 0.7618 (pm20) cc_final: 0.7347 (pm20) REVERT: E 245 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7857 (t80) REVERT: D 245 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7966 (t80) REVERT: D 270 TYR cc_start: 0.8090 (m-80) cc_final: 0.7823 (m-80) REVERT: C 159 GLU cc_start: 0.7618 (pm20) cc_final: 0.6618 (tt0) REVERT: C 233 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: C 245 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.8026 (t80) REVERT: B 245 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 245 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7985 (t80) outliers start: 25 outliers final: 9 residues processed: 137 average time/residue: 0.2550 time to fit residues: 50.1541 Evaluate side-chains 138 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116883 restraints weight = 15361.214| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.77 r_work: 0.3204 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12880 Z= 0.163 Angle : 0.545 10.777 17545 Z= 0.279 Chirality : 0.047 0.149 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.306 16.158 1690 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.24 % Allowed : 12.87 % Favored : 85.89 % 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: 0.04 (0.22), residues: 1525 helix: 1.14 (0.22), residues: 565 sheet: 1.19 (0.26), residues: 405 loop : -2.14 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 206 HIS 0.002 0.001 HIS D 177 PHE 0.032 0.002 PHE D 247 TYR 0.017 0.002 TYR C 245 ARG 0.002 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 595) hydrogen bonds : angle 4.50253 ( 1890) covalent geometry : bond 0.00374 (12880) covalent geometry : angle 0.54488 (17545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: E 159 GLU cc_start: 0.7605 (pm20) cc_final: 0.7335 (pm20) REVERT: E 245 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7920 (t80) REVERT: E 247 PHE cc_start: 0.6160 (p90) cc_final: 0.5282 (p90) REVERT: D 245 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7922 (t80) REVERT: C 159 GLU cc_start: 0.7702 (pm20) cc_final: 0.6690 (tt0) REVERT: C 245 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8088 (t80) REVERT: B 245 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7913 (t80) REVERT: B 247 PHE cc_start: 0.6219 (p90) cc_final: 0.5484 (p90) REVERT: A 245 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 247 PHE cc_start: 0.6150 (p90) cc_final: 0.5150 (p90) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.3432 time to fit residues: 63.3667 Evaluate side-chains 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN D 284 HIS B 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117115 restraints weight = 15288.164| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.76 r_work: 0.3171 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12880 Z= 0.157 Angle : 0.541 10.778 17545 Z= 0.278 Chirality : 0.046 0.152 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.294 15.874 1690 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.45 % Allowed : 12.58 % Favored : 85.96 % 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: 0.11 (0.22), residues: 1525 helix: 1.10 (0.22), residues: 565 sheet: 1.20 (0.25), residues: 435 loop : -2.14 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 220 HIS 0.002 0.001 HIS D 177 PHE 0.030 0.001 PHE E 247 TYR 0.017 0.002 TYR C 245 ARG 0.002 0.000 ARG E 231 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 595) hydrogen bonds : angle 4.52658 ( 1890) covalent geometry : bond 0.00361 (12880) covalent geometry : angle 0.54111 (17545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: E 159 GLU cc_start: 0.7610 (pm20) cc_final: 0.7338 (pm20) REVERT: E 245 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7915 (t80) REVERT: E 247 PHE cc_start: 0.6192 (p90) cc_final: 0.5417 (p90) REVERT: D 245 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7877 (t80) REVERT: C 159 GLU cc_start: 0.7707 (pm20) cc_final: 0.7386 (pm20) REVERT: C 245 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8057 (t80) REVERT: B 245 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7921 (t80) REVERT: B 247 PHE cc_start: 0.6219 (p90) cc_final: 0.5463 (p90) REVERT: A 228 PHE cc_start: 0.5851 (m-10) cc_final: 0.5527 (t80) REVERT: A 245 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7903 (t80) outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.2623 time to fit residues: 50.6174 Evaluate side-chains 137 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.154018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119895 restraints weight = 15284.552| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.75 r_work: 0.3279 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12880 Z= 0.111 Angle : 0.498 9.145 17545 Z= 0.258 Chirality : 0.045 0.145 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.032 15.088 1690 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.38 % Allowed : 12.51 % Favored : 86.11 % 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: 0.35 (0.22), residues: 1525 helix: 1.66 (0.22), residues: 530 sheet: 1.16 (0.26), residues: 435 loop : -2.05 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 220 HIS 0.002 0.000 HIS E 177 PHE 0.028 0.001 PHE A 247 TYR 0.012 0.001 TYR C 245 ARG 0.002 0.000 ARG E 91 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 595) hydrogen bonds : angle 4.34633 ( 1890) covalent geometry : bond 0.00245 (12880) covalent geometry : angle 0.49835 (17545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.25 seconds wall clock time: 110 minutes 17.60 seconds (6617.60 seconds total)