Starting phenix.real_space_refine on Mon Dec 30 05:30:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f33_28830/12_2024/8f33_28830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f33_28830/12_2024/8f33_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_28830/12_2024/8f33_28830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f33_28830/12_2024/8f33_28830.map" model { file = "/net/cci-nas-00/data/ceres_data/8f33_28830/12_2024/8f33_28830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f33_28830/12_2024/8f33_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-5532/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: 5.31, per 1000 atoms: 0.42 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: 3.05 Conformation dependent library (CDL) restraints added in 1.7 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: 1.35 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: 4.00 Time building geometry restraints manager: 3.52 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.130 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 27.130 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- 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= 0.340 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 *********************** 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 : 1.351 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: 0.2987 time to fit residues: 60.2148 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 : 1.487 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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= 0.271 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 *********************** 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 : 1.504 Fit side-chains REVERT: E 159 GLU cc_start: 0.7225 (pm20) cc_final: 0.6361 (tt0) REVERT: C 159 GLU cc_start: 0.7247 (pm20) cc_final: 0.6455 (tt0) REVERT: C 245 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7672 (t80) REVERT: B 247 PHE cc_start: 0.5641 (p90) cc_final: 0.4974 (p90) REVERT: A 30 GLU cc_start: 0.5798 (tp30) cc_final: 0.5426 (mm-30) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.3068 time to fit residues: 47.4262 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 : 1.588 ------------------------------------------------------------------------------- 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 75 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1647 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= 0.313 Angle : 0.586 8.926 17545 Z= 0.301 Chirality : 0.048 0.151 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.785 24.456 1690 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.31 % Allowed : 8.65 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.42 (0.21), residues: 1525 helix: 0.71 (0.22), residues: 565 sheet: 0.96 (0.24), residues: 435 loop : -2.56 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 206 HIS 0.003 0.001 HIS C 177 PHE 0.033 0.002 PHE B 247 TYR 0.019 0.002 TYR C 245 ARG 0.003 0.000 ARG E 231 *********************** 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 139 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.460 Fit side-chains REVERT: E 159 GLU cc_start: 0.7234 (pm20) cc_final: 0.6424 (tt0) REVERT: E 245 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7737 (t80) REVERT: E 247 PHE cc_start: 0.6086 (p90) cc_final: 0.5511 (p90) REVERT: D 245 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7851 (t80) REVERT: C 159 GLU cc_start: 0.7266 (pm20) cc_final: 0.6535 (tt0) REVERT: C 245 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7870 (t80) REVERT: B 245 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 247 PHE cc_start: 0.5902 (p90) cc_final: 0.5403 (p90) REVERT: A 245 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7788 (t80) REVERT: A 247 PHE cc_start: 0.6038 (p90) cc_final: 0.5519 (p90) outliers start: 18 outliers final: 12 residues processed: 133 average time/residue: 0.2839 time to fit residues: 53.5967 Evaluate side-chains 133 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 134 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 0.0470 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12880 Z= 0.349 Angle : 0.600 10.566 17545 Z= 0.307 Chirality : 0.049 0.154 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.752 17.861 1690 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.84 % Allowed : 9.38 % Favored : 87.78 % 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: -0.34 (0.21), residues: 1525 helix: 0.81 (0.22), residues: 565 sheet: 0.89 (0.24), residues: 435 loop : -2.44 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 206 HIS 0.003 0.001 HIS D 177 PHE 0.032 0.002 PHE C 247 TYR 0.021 0.002 TYR C 245 ARG 0.004 0.000 ARG E 231 *********************** 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 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 1.440 Fit side-chains REVERT: E 245 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7854 (t80) REVERT: D 245 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7769 (t80) REVERT: C 245 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7990 (t80) REVERT: B 245 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7738 (t80) REVERT: A 245 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7795 (t80) outliers start: 39 outliers final: 17 residues processed: 158 average time/residue: 0.2644 time to fit residues: 59.9832 Evaluate side-chains 139 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 120 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2010 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= 0.236 Angle : 0.544 8.487 17545 Z= 0.280 Chirality : 0.047 0.143 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.511 17.223 1690 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.25 % Allowed : 10.40 % Favored : 87.35 % 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: 1.00 (0.22), residues: 565 sheet: 1.01 (0.26), residues: 405 loop : -2.32 (0.24), residues: 555 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 0.031 0.002 PHE A 247 TYR 0.017 0.002 TYR C 245 ARG 0.002 0.000 ARG E 231 *********************** 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 159 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.422 Fit side-chains REVERT: E 245 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7762 (t80) REVERT: D 245 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7700 (t80) REVERT: C 245 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7932 (t80) REVERT: B 245 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7705 (t80) REVERT: B 247 PHE cc_start: 0.5998 (p90) cc_final: 0.5352 (p90) REVERT: A 245 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7678 (t80) REVERT: A 247 PHE cc_start: 0.6016 (p90) cc_final: 0.5127 (p90) outliers start: 31 outliers final: 22 residues processed: 151 average time/residue: 0.2640 time to fit residues: 57.8452 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 : 1.372 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2063 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= 0.206 Angle : 0.526 10.675 17545 Z= 0.270 Chirality : 0.046 0.138 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.342 16.817 1690 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.47 % Allowed : 10.76 % Favored : 86.76 % 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: -0.10 (0.22), residues: 1525 helix: 1.10 (0.22), residues: 565 sheet: 1.09 (0.26), residues: 405 loop : -2.28 (0.24), residues: 555 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 0.030 0.001 PHE E 247 TYR 0.016 0.001 TYR C 245 ARG 0.002 0.000 ARG E 231 *********************** 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 156 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.553 Fit side-chains REVERT: E 59 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7538 (mm-30) REVERT: E 245 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7772 (t80) REVERT: D 245 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7790 (t80) REVERT: C 159 GLU cc_start: 0.7451 (pm20) cc_final: 0.6605 (tt0) REVERT: C 223 PHE cc_start: 0.6590 (m-80) cc_final: 0.6380 (m-80) REVERT: C 245 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7818 (t80) REVERT: B 245 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7679 (t80) REVERT: B 247 PHE cc_start: 0.5963 (p90) cc_final: 0.5279 (p90) REVERT: A 59 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 233 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6746 (mp10) REVERT: A 245 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 247 PHE cc_start: 0.5909 (p90) cc_final: 0.4967 (p90) outliers start: 34 outliers final: 20 residues processed: 149 average time/residue: 0.2678 time to fit residues: 57.2999 Evaluate side-chains 144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 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 118 LEU 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 233 GLN 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 16 optimal weight: 0.0030 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 0.0770 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.7550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2122 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= 0.143 Angle : 0.484 8.334 17545 Z= 0.250 Chirality : 0.045 0.134 1950 Planarity : 0.004 0.047 2235 Dihedral : 4.017 15.756 1690 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.89 % Allowed : 11.27 % 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: 0.09 (0.22), residues: 1525 helix: 1.62 (0.22), residues: 530 sheet: 0.93 (0.26), residues: 400 loop : -2.13 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 206 HIS 0.001 0.000 HIS E 177 PHE 0.028 0.001 PHE B 247 TYR 0.011 0.001 TYR C 245 ARG 0.003 0.000 ARG E 231 *********************** 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 152 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: E 159 GLU cc_start: 0.7249 (pm20) cc_final: 0.6968 (pm20) REVERT: E 245 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7757 (t80) REVERT: E 247 PHE cc_start: 0.5735 (p90) cc_final: 0.4908 (p90) REVERT: D 245 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7708 (t80) REVERT: D 270 TYR cc_start: 0.7938 (m-80) cc_final: 0.7646 (m-80) REVERT: C 159 GLU cc_start: 0.7410 (pm20) cc_final: 0.6508 (tt0) REVERT: C 223 PHE cc_start: 0.6585 (m-80) cc_final: 0.6353 (m-80) REVERT: C 245 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 245 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7696 (t80) REVERT: A 233 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: A 245 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7697 (t80) outliers start: 26 outliers final: 11 residues processed: 142 average time/residue: 0.2599 time to fit residues: 53.1890 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 : 1.323 ------------------------------------------------------------------------------- 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 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 233 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12880 Z= 0.176 Angle : 0.501 8.424 17545 Z= 0.259 Chirality : 0.045 0.143 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.078 15.978 1690 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.45 % Allowed : 12.36 % Favored : 86.18 % 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: 0.15 (0.22), residues: 1525 helix: 1.67 (0.23), residues: 530 sheet: 0.96 (0.26), residues: 400 loop : -2.08 (0.23), residues: 595 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 0.029 0.001 PHE D 247 TYR 0.014 0.001 TYR C 245 ARG 0.002 0.000 ARG C 231 *********************** 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 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: E 159 GLU cc_start: 0.7289 (pm20) cc_final: 0.6977 (pm20) REVERT: E 245 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7736 (t80) REVERT: E 247 PHE cc_start: 0.5882 (p90) cc_final: 0.5057 (p90) REVERT: D 245 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7761 (t80) REVERT: D 270 TYR cc_start: 0.7959 (m-80) cc_final: 0.7593 (m-80) REVERT: C 159 GLU cc_start: 0.7410 (pm20) cc_final: 0.6523 (tt0) REVERT: C 245 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7917 (t80) REVERT: B 245 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7688 (t80) REVERT: A 233 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: A 245 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7713 (t80) outliers start: 20 outliers final: 11 residues processed: 128 average time/residue: 0.2674 time to fit residues: 49.6943 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 : 1.501 ------------------------------------------------------------------------------- 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 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 233 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 88 optimal weight: 30.0000 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 182 GLN C 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12880 Z= 0.218 Angle : 0.527 8.690 17545 Z= 0.273 Chirality : 0.046 0.152 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.228 16.457 1690 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.38 % Allowed : 12.65 % 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: 0.07 (0.22), residues: 1525 helix: 1.18 (0.22), residues: 565 sheet: 1.24 (0.26), residues: 405 loop : -2.17 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 206 HIS 0.002 0.001 HIS D 177 PHE 0.031 0.001 PHE D 247 TYR 0.016 0.002 TYR C 245 ARG 0.002 0.000 ARG D 231 *********************** 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 141 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: E 245 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7779 (t80) REVERT: E 247 PHE cc_start: 0.5935 (p90) cc_final: 0.4953 (p90) REVERT: D 245 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7676 (t80) REVERT: D 247 PHE cc_start: 0.5778 (p90) cc_final: 0.4869 (p90) REVERT: C 159 GLU cc_start: 0.7439 (pm20) cc_final: 0.6539 (tt0) REVERT: C 223 PHE cc_start: 0.6713 (m-80) cc_final: 0.6441 (m-80) REVERT: C 245 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7927 (t80) REVERT: B 245 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7674 (t80) REVERT: B 247 PHE cc_start: 0.5863 (p90) cc_final: 0.5078 (p90) REVERT: A 233 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: A 245 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 247 PHE cc_start: 0.5845 (p90) cc_final: 0.4863 (p90) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.2770 time to fit residues: 52.6502 Evaluate side-chains 133 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 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 233 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 0.0770 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2272 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= 0.160 Angle : 0.494 7.708 17545 Z= 0.257 Chirality : 0.045 0.148 1950 Planarity : 0.004 0.044 2235 Dihedral : 4.044 15.707 1690 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.38 % Allowed : 12.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1525 helix: 1.71 (0.23), residues: 530 sheet: 1.04 (0.27), residues: 400 loop : -2.00 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.029 0.001 PHE A 247 TYR 0.013 0.001 TYR C 245 ARG 0.002 0.000 ARG B 91 ********************** 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 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: E 159 GLU cc_start: 0.7323 (pm20) cc_final: 0.7105 (pm20) REVERT: E 245 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7773 (t80) REVERT: D 245 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7756 (t80) REVERT: D 270 TYR cc_start: 0.7943 (m-80) cc_final: 0.7628 (m-80) REVERT: C 159 GLU cc_start: 0.7448 (pm20) cc_final: 0.7153 (pm20) REVERT: C 245 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7930 (t80) REVERT: B 245 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7700 (t80) REVERT: A 233 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6684 (mp10) REVERT: A 245 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7703 (t80) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 0.2722 time to fit residues: 51.4626 Evaluate side-chains 138 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 233 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.151481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116874 restraints weight = 15197.312| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.77 r_work: 0.3170 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2295 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= 0.238 Angle : 0.540 8.657 17545 Z= 0.280 Chirality : 0.047 0.156 1950 Planarity : 0.004 0.043 2235 Dihedral : 4.277 16.298 1690 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.38 % Allowed : 12.80 % Favored : 85.82 % 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: 0.13 (0.22), residues: 1525 helix: 1.19 (0.22), residues: 565 sheet: 1.15 (0.26), residues: 410 loop : -2.01 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 206 HIS 0.002 0.001 HIS D 177 PHE 0.031 0.002 PHE B 247 TYR 0.017 0.002 TYR C 245 ARG 0.002 0.000 ARG B 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.45 seconds wall clock time: 43 minutes 11.55 seconds (2591.55 seconds total)