Starting phenix.real_space_refine on Wed Feb 4 18:07:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f33_28830/02_2026/8f33_28830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f33_28830/02_2026/8f33_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_28830/02_2026/8f33_28830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f33_28830/02_2026/8f33_28830.map" model { file = "/net/cci-nas-00/data/ceres_data/8f33_28830/02_2026/8f33_28830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f33_28830/02_2026/8f33_28830.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12545 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" 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: "E" 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: D, C, B, A Time building chain proxies: 2.23, per 1000 atoms: 0.18 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: 1.10 Conformation dependent library (CDL) restraints added in 675.5 milliseconds 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: 0.46 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: 2.38 Time building geometry restraints manager: 1.50 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: 0.05 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' selection = chain 'A' } 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: 1.820 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (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 ARG 0.006 0.001 ARG B 231 TYR 0.023 0.003 TYR C 148 PHE 0.025 0.003 PHE B 247 TRP 0.034 0.003 TRP B 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00525 (12880) covalent geometry : angle 0.80137 (17545) hydrogen bonds : bond 0.11683 ( 595) hydrogen bonds : angle 6.07368 ( 1890) *********************** 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 : 0.498 Fit side-chains REVERT: D 30 GLU cc_start: 0.5858 (tp30) cc_final: 0.5526 (mm-30) REVERT: A 30 GLU cc_start: 0.5801 (tp30) cc_final: 0.5457 (mm-30) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1341 time to fit residues: 26.9334 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 : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.150297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114539 restraints weight = 15381.516| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.81 r_work: 0.3126 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 12880 Z= 0.319 Angle : 0.710 7.770 17545 Z= 0.364 Chirality : 0.053 0.170 1950 Planarity : 0.005 0.044 2235 Dihedral : 5.259 30.614 1690 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.16 % Allowed : 7.56 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.20), residues: 1525 helix: 0.00 (0.21), residues: 565 sheet: 0.74 (0.23), residues: 435 loop : -2.74 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 231 TYR 0.021 0.002 TYR C 245 PHE 0.037 0.003 PHE C 247 TRP 0.018 0.002 TRP D 206 HIS 0.004 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00752 (12880) covalent geometry : angle 0.71007 (17545) hydrogen bonds : bond 0.04525 ( 595) hydrogen bonds : angle 5.26115 ( 1890) *********************** 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 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.474 Fit side-chains REVERT: E 159 GLU cc_start: 0.7614 (pm20) cc_final: 0.6554 (tt0) REVERT: C 159 GLU cc_start: 0.7543 (pm20) cc_final: 0.6626 (tt0) REVERT: C 245 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8035 (t80) REVERT: B 247 PHE cc_start: 0.6284 (p90) cc_final: 0.5698 (p90) outliers start: 16 outliers final: 12 residues processed: 137 average time/residue: 0.1230 time to fit residues: 24.1569 Evaluate side-chains 126 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 245 TYR Chi-restraints excluded: chain C residue 277 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118078 restraints weight = 15447.893| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.75 r_work: 0.3175 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12880 Z= 0.161 Angle : 0.553 9.970 17545 Z= 0.282 Chirality : 0.047 0.140 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.615 19.400 1690 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.31 % Allowed : 9.75 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1525 helix: 0.62 (0.22), residues: 565 sheet: 0.98 (0.24), residues: 435 loop : -2.56 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 231 TYR 0.016 0.002 TYR D 245 PHE 0.031 0.002 PHE C 247 TRP 0.022 0.002 TRP E 206 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00369 (12880) covalent geometry : angle 0.55338 (17545) hydrogen bonds : bond 0.03518 ( 595) hydrogen bonds : angle 4.77948 ( 1890) *********************** 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 135 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.521 Fit side-chains REVERT: E 159 GLU cc_start: 0.7613 (pm20) cc_final: 0.6555 (tt0) REVERT: C 159 GLU cc_start: 0.7566 (pm20) cc_final: 0.6689 (tt0) REVERT: C 245 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7991 (t80) REVERT: B 247 PHE cc_start: 0.5873 (p90) cc_final: 0.5408 (p90) outliers start: 18 outliers final: 10 residues processed: 128 average time/residue: 0.1231 time to fit residues: 22.5742 Evaluate side-chains 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 MET 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 277 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 277 ILE Chi-restraints excluded: chain A residue 239 MET 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 71 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 HIS D 284 HIS C 284 HIS B 284 HIS A 284 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.152927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119363 restraints weight = 15322.724| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.67 r_work: 0.3141 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 12880 Z= 0.338 Angle : 0.707 9.500 17545 Z= 0.361 Chirality : 0.053 0.179 1950 Planarity : 0.005 0.041 2235 Dihedral : 5.203 20.392 1690 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.27 % Allowed : 9.82 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1525 helix: 0.53 (0.22), residues: 565 sheet: 0.65 (0.24), residues: 435 loop : -2.59 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 231 TYR 0.026 0.003 TYR C 245 PHE 0.035 0.003 PHE B 247 TRP 0.022 0.002 TRP E 206 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00801 (12880) covalent geometry : angle 0.70682 (17545) hydrogen bonds : bond 0.04397 ( 595) hydrogen bonds : angle 5.09911 ( 1890) *********************** 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 180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.359 Fit side-chains REVERT: D 245 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7856 (t80) REVERT: C 245 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8110 (t80) REVERT: B 245 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 245 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.7899 (t80) outliers start: 45 outliers final: 18 residues processed: 170 average time/residue: 0.1043 time to fit residues: 26.0294 Evaluate side-chains 146 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 181 VAL 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 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 89 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.153131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119125 restraints weight = 15360.616| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.74 r_work: 0.3192 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12880 Z= 0.115 Angle : 0.523 8.177 17545 Z= 0.270 Chirality : 0.045 0.131 1950 Planarity : 0.004 0.046 2235 Dihedral : 4.387 16.399 1690 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.96 % Allowed : 12.00 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1525 helix: 0.84 (0.22), residues: 565 sheet: 0.97 (0.25), residues: 435 loop : -2.38 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 231 TYR 0.013 0.001 TYR C 245 PHE 0.030 0.001 PHE A 247 TRP 0.024 0.002 TRP E 206 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00253 (12880) covalent geometry : angle 0.52306 (17545) hydrogen bonds : bond 0.03146 ( 595) hydrogen bonds : angle 4.60092 ( 1890) *********************** 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 163 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.428 Fit side-chains REVERT: E 245 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7890 (t80) REVERT: D 223 PHE cc_start: 0.6749 (m-80) cc_final: 0.6531 (m-80) REVERT: D 245 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7889 (t80) REVERT: C 245 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 245 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7911 (t80) REVERT: A 223 PHE cc_start: 0.6883 (m-80) cc_final: 0.6679 (m-80) REVERT: A 245 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7873 (t80) outliers start: 27 outliers final: 13 residues processed: 151 average time/residue: 0.1078 time to fit residues: 23.3629 Evaluate side-chains 140 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 D residue 118 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 54 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.148574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113913 restraints weight = 15457.705| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.76 r_work: 0.3116 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 12880 Z= 0.244 Angle : 0.615 8.413 17545 Z= 0.315 Chirality : 0.049 0.158 1950 Planarity : 0.005 0.044 2235 Dihedral : 4.776 17.340 1690 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.62 % Allowed : 12.58 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1525 helix: 0.74 (0.22), residues: 565 sheet: 0.82 (0.24), residues: 435 loop : -2.42 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.021 0.002 TYR C 245 PHE 0.036 0.002 PHE B 247 TRP 0.023 0.002 TRP E 206 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00573 (12880) covalent geometry : angle 0.61501 (17545) hydrogen bonds : bond 0.03787 ( 595) hydrogen bonds : angle 4.81411 ( 1890) *********************** 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 162 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.346 Fit side-chains REVERT: E 159 GLU cc_start: 0.7620 (pm20) cc_final: 0.7369 (pm20) REVERT: E 245 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7986 (t80) REVERT: D 245 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7900 (t80) REVERT: C 159 GLU cc_start: 0.7565 (pm20) cc_final: 0.7281 (pm20) REVERT: C 245 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 228 PHE cc_start: 0.5693 (m-10) cc_final: 0.5464 (t80) REVERT: B 245 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 245 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7877 (t80) outliers start: 36 outliers final: 22 residues processed: 154 average time/residue: 0.1121 time to fit residues: 24.8038 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 : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR 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 118 LEU 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 93 MET Chi-restraints excluded: chain C residue 118 LEU 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 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 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 239 MET Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 277 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.151200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116829 restraints weight = 15252.818| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.75 r_work: 0.3169 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12880 Z= 0.149 Angle : 0.551 9.725 17545 Z= 0.282 Chirality : 0.046 0.139 1950 Planarity : 0.004 0.045 2235 Dihedral : 4.436 16.264 1690 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.75 % Allowed : 13.24 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1525 helix: 0.78 (0.22), residues: 565 sheet: 0.97 (0.25), residues: 435 loop : -2.31 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.016 0.002 TYR C 245 PHE 0.030 0.001 PHE A 247 TRP 0.025 0.002 TRP E 220 HIS 0.002 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00340 (12880) covalent geometry : angle 0.55092 (17545) hydrogen bonds : bond 0.03329 ( 595) hydrogen bonds : angle 4.65214 ( 1890) *********************** 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 149 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.310 Fit side-chains REVERT: E 159 GLU cc_start: 0.7632 (pm20) cc_final: 0.7336 (pm20) REVERT: E 245 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7946 (t80) REVERT: D 228 PHE cc_start: 0.5817 (m-10) cc_final: 0.5578 (t80) REVERT: D 245 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7901 (t80) REVERT: C 228 PHE cc_start: 0.5975 (m-10) cc_final: 0.5572 (t80) REVERT: C 245 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8032 (t80) REVERT: B 245 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7952 (t80) REVERT: A 245 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7919 (t80) outliers start: 24 outliers final: 17 residues processed: 141 average time/residue: 0.1194 time to fit residues: 23.8347 Evaluate side-chains 141 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 LEU 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 D residue 118 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 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 = 0.153642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119783 restraints weight = 15312.368| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.73 r_work: 0.3108 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12880 Z= 0.274 Angle : 0.656 10.676 17545 Z= 0.334 Chirality : 0.050 0.170 1950 Planarity : 0.005 0.042 2235 Dihedral : 4.890 18.618 1690 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.55 % Allowed : 12.44 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1525 helix: 0.60 (0.22), residues: 565 sheet: 0.76 (0.24), residues: 435 loop : -2.39 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 231 TYR 0.023 0.002 TYR C 245 PHE 0.047 0.002 PHE A 247 TRP 0.032 0.002 TRP E 220 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00646 (12880) covalent geometry : angle 0.65566 (17545) hydrogen bonds : bond 0.04006 ( 595) hydrogen bonds : angle 4.91226 ( 1890) *********************** 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 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.484 Fit side-chains REVERT: E 245 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7958 (t80) REVERT: D 228 PHE cc_start: 0.5780 (m-10) cc_final: 0.5505 (t80) REVERT: D 245 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7934 (t80) REVERT: C 159 GLU cc_start: 0.7592 (pm20) cc_final: 0.7326 (pm20) REVERT: C 228 PHE cc_start: 0.6065 (m-10) cc_final: 0.5541 (t80) REVERT: C 245 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 245 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7941 (t80) REVERT: A 245 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7999 (t80) outliers start: 35 outliers final: 22 residues processed: 153 average time/residue: 0.1135 time to fit residues: 24.7571 Evaluate side-chains 148 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR 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 12 VAL 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 12 VAL Chi-restraints excluded: chain C residue 93 MET 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 191 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 12 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118054 restraints weight = 15314.393| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.76 r_work: 0.3179 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12880 Z= 0.122 Angle : 0.543 12.060 17545 Z= 0.275 Chirality : 0.046 0.141 1950 Planarity : 0.004 0.046 2235 Dihedral : 4.305 15.423 1690 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.82 % Allowed : 13.09 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1525 helix: 1.13 (0.22), residues: 535 sheet: 0.84 (0.25), residues: 465 loop : -2.20 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 91 TYR 0.013 0.001 TYR C 245 PHE 0.036 0.001 PHE A 247 TRP 0.030 0.002 TRP E 220 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00273 (12880) covalent geometry : angle 0.54296 (17545) hydrogen bonds : bond 0.03168 ( 595) hydrogen bonds : angle 4.58556 ( 1890) *********************** 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 144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.460 Fit side-chains REVERT: E 159 GLU cc_start: 0.7677 (pm20) cc_final: 0.7469 (pm20) REVERT: E 245 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7860 (t80) REVERT: D 245 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7946 (t80) REVERT: C 159 GLU cc_start: 0.7588 (pm20) cc_final: 0.7330 (pm20) REVERT: C 228 PHE cc_start: 0.5963 (m-10) cc_final: 0.5544 (t80) REVERT: C 245 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 245 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 245 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7991 (t80) outliers start: 25 outliers final: 20 residues processed: 136 average time/residue: 0.1160 time to fit residues: 22.3186 Evaluate side-chains 144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 118 LEU 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 12 VAL 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 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 12 VAL 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 12 VAL 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 15 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 119 optimal weight: 0.0010 chunk 9 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115458 restraints weight = 15398.922| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.76 r_work: 0.3146 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12880 Z= 0.180 Angle : 0.585 11.944 17545 Z= 0.297 Chirality : 0.047 0.156 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.524 17.294 1690 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.04 % Allowed : 12.95 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1525 helix: 0.82 (0.22), residues: 565 sheet: 1.06 (0.25), residues: 425 loop : -2.22 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 231 TYR 0.018 0.002 TYR C 245 PHE 0.038 0.002 PHE A 247 TRP 0.039 0.002 TRP E 220 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00418 (12880) covalent geometry : angle 0.58515 (17545) hydrogen bonds : bond 0.03504 ( 595) hydrogen bonds : angle 4.65747 ( 1890) ********************** 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 146 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.431 Fit side-chains REVERT: E 159 GLU cc_start: 0.7639 (pm20) cc_final: 0.7413 (pm20) REVERT: E 245 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7928 (t80) REVERT: D 245 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7965 (t80) REVERT: C 159 GLU cc_start: 0.7593 (pm20) cc_final: 0.7317 (pm20) REVERT: C 228 PHE cc_start: 0.6009 (m-10) cc_final: 0.5539 (t80) REVERT: C 245 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8076 (t80) REVERT: B 245 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7951 (t80) REVERT: A 245 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8005 (t80) outliers start: 28 outliers final: 23 residues processed: 140 average time/residue: 0.1189 time to fit residues: 23.7996 Evaluate side-chains 144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain D residue 118 LEU 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 12 VAL 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 239 MET Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain B residue 12 VAL 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 B residue 277 ILE Chi-restraints excluded: chain A residue 12 VAL 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 87 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.150992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116187 restraints weight = 15343.227| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.78 r_work: 0.3169 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2471 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= 0.159 Angle : 0.568 12.159 17545 Z= 0.288 Chirality : 0.047 0.152 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.427 16.783 1690 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.11 % Allowed : 13.02 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1525 helix: 0.86 (0.22), residues: 565 sheet: 1.12 (0.25), residues: 425 loop : -2.18 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 141 TYR 0.016 0.002 TYR C 245 PHE 0.037 0.002 PHE A 247 TRP 0.040 0.002 TRP E 220 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00365 (12880) covalent geometry : angle 0.56782 (17545) hydrogen bonds : bond 0.03374 ( 595) hydrogen bonds : angle 4.61058 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.64 seconds wall clock time: 49 minutes 45.81 seconds (2985.81 seconds total)