Starting phenix.real_space_refine on Sat Jul 4 20:36:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yfm_72898/07_2026/9yfm_72898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yfm_72898/07_2026/9yfm_72898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yfm_72898/07_2026/9yfm_72898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yfm_72898/07_2026/9yfm_72898.map" model { file = "/net/cci-nas-00/data/ceres_data/9yfm_72898/07_2026/9yfm_72898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yfm_72898/07_2026/9yfm_72898.cif" } resolution = 2.95 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= 0.002 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 96 5.49 5 S 54 5.16 5 C 7184 2.51 5 N 2089 2.21 5 O 2404 1.98 5 H 11093 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22920 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1475 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "C" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1992 Classifications: {'peptide': 123} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 115} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1544 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1030 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 55} Chain: "G" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2057 Classifications: {'peptide': 126} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1001 Classifications: {'peptide': 59} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "A" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5421 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 1 Chain: "D" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5305 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 13, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 3095 Classifications: {'RNA': 96} Modifications used: {'3*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 40, 'rna3p_pyr': 41} Link IDs: {'rna2p': 15, 'rna3p': 80} Chain breaks: 6 Time building chain proxies: 4.19, per 1000 atoms: 0.18 Number of scatterers: 22920 At special positions: 0 Unit cell: (94.392, 115.92, 158.148, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 96 15.00 O 2404 8.00 N 2089 7.00 C 7184 6.00 H 11093 1.00 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: 2.45 Conformation dependent library (CDL) restraints added in 648.9 milliseconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 34.9% alpha, 17.4% beta 31 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.680A pdb=" N ILE C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 138 through 153 Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.532A pdb=" N PHE E 133 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.614A pdb=" N CYS G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 58 removed outlier: 3.989A pdb=" N SER G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 66 through 76 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 113 through 121 removed outlier: 3.788A pdb=" N ILE G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 41 through 52 Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.680A pdb=" N LEU A 64 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.771A pdb=" N ARG A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 140 through 143 removed outlier: 3.753A pdb=" N ARG A 143 " --> pdb=" O ARG A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.875A pdb=" N VAL A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 304 through 313 removed outlier: 4.568A pdb=" N ASN A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.360A pdb=" N SER A 389 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.909A pdb=" N ARG D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 141 through 149 removed outlier: 4.602A pdb=" N LYS D 146 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 removed outlier: 3.756A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 281 through 287 Processing helix chain 'D' and resid 292 through 296 removed outlier: 3.649A pdb=" N VAL D 296 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 313 removed outlier: 4.469A pdb=" N ASN D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 98 removed outlier: 6.793A pdb=" N PHE B 139 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR B 118 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 110 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.714A pdb=" N PHE E 139 " --> pdb=" O LEU E 70 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE E 82 " --> pdb=" O GLY E 74 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR E 76 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR E 118 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE E 119 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE E 111 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER E 121 " --> pdb=" O ASP E 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 16 Processing sheet with id=AA7, first strand: chain 'G' and resid 63 through 65 Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 16 Processing sheet with id=AA9, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.907A pdb=" N PHE A 302 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR A 325 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 300 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS A 299 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 333 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE A 349 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU A 368 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 317 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 92 through 97 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 92 through 97 current: chain 'A' and resid 131 through 138 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 131 through 138 current: chain 'A' and resid 197 through 210 removed outlier: 5.781A pdb=" N SER A 204 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER A 221 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU A 206 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP A 219 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.510A pdb=" N ARG D 324 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS D 299 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 338 " --> pdb=" O LYS D 299 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE D 301 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN D 333 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D 349 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU D 368 " --> pdb=" O ILE D 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 91 through 98 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 98 current: chain 'D' and resid 131 through 139 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 131 through 139 current: chain 'D' and resid 197 through 210 removed outlier: 5.647A pdb=" N SER D 204 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N SER D 221 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 206 " --> pdb=" O TRP D 219 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP D 219 " --> pdb=" O LEU D 206 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11069 1.03 - 1.22: 46 1.22 - 1.42: 5071 1.42 - 1.61: 7089 1.61 - 1.81: 84 Bond restraints: 23359 Sorted by residual: bond pdb=" CA PHE D 159 " pdb=" C PHE D 159 " ideal model delta sigma weight residual 1.522 1.477 0.046 1.23e-02 6.61e+03 1.38e+01 bond pdb=" N ILE E 105 " pdb=" CA ILE E 105 " ideal model delta sigma weight residual 1.459 1.491 -0.033 9.10e-03 1.21e+04 1.30e+01 bond pdb=" C VAL C 82 " pdb=" O VAL C 82 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.07e-02 8.73e+03 1.28e+01 bond pdb=" C ARG G 64 " pdb=" O ARG G 64 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.14e-02 7.69e+03 1.17e+01 bond pdb=" CG HIS C 59 " pdb=" CD2 HIS C 59 " ideal model delta sigma weight residual 1.354 1.318 0.036 1.10e-02 8.26e+03 1.10e+01 ... (remaining 23354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 42045 3.12 - 6.24: 266 6.24 - 9.36: 12 9.36 - 12.49: 0 12.49 - 15.61: 1 Bond angle restraints: 42324 Sorted by residual: angle pdb=" N LEU A 239 " pdb=" CA LEU A 239 " pdb=" C LEU A 239 " ideal model delta sigma weight residual 111.07 105.11 5.96 1.07e+00 8.73e-01 3.10e+01 angle pdb=" C ARG G 64 " pdb=" CA ARG G 64 " pdb=" CB ARG G 64 " ideal model delta sigma weight residual 110.74 119.11 -8.37 1.61e+00 3.86e-01 2.70e+01 angle pdb=" N GLY E 125 " pdb=" CA GLY E 125 " pdb=" C GLY E 125 " ideal model delta sigma weight residual 112.82 105.70 7.12 1.38e+00 5.25e-01 2.66e+01 angle pdb=" CA LEU B 81 " pdb=" C LEU B 81 " pdb=" O LEU B 81 " ideal model delta sigma weight residual 121.32 115.39 5.93 1.16e+00 7.43e-01 2.61e+01 angle pdb=" CA GLY C 80 " pdb=" C GLY C 80 " pdb=" O GLY C 80 " ideal model delta sigma weight residual 121.05 116.64 4.41 9.00e-01 1.23e+00 2.40e+01 ... (remaining 42319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 10419 34.86 - 69.72: 555 69.72 - 104.58: 56 104.58 - 139.44: 1 139.44 - 174.30: 4 Dihedral angle restraints: 11035 sinusoidal: 6900 harmonic: 4135 Sorted by residual: dihedral pdb=" CD ARG G 64 " pdb=" NE ARG G 64 " pdb=" CZ ARG G 64 " pdb=" NH1 ARG G 64 " ideal model delta sinusoidal sigma weight residual 0.00 86.81 -86.81 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" O4' C I 31 " pdb=" C1' C I 31 " pdb=" N1 C I 31 " pdb=" C2 C I 31 " ideal model delta sinusoidal sigma weight residual -128.00 46.30 -174.30 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C I 102 " pdb=" C1' C I 102 " pdb=" N1 C I 102 " pdb=" C2 C I 102 " ideal model delta sinusoidal sigma weight residual -128.00 41.39 -169.39 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 11032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1590 0.047 - 0.095: 239 0.095 - 0.142: 114 0.142 - 0.189: 15 0.189 - 0.237: 11 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CA ARG H 43 " pdb=" N ARG H 43 " pdb=" C ARG H 43 " pdb=" CB ARG H 43 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE C 81 " pdb=" N ILE C 81 " pdb=" C ILE C 81 " pdb=" CB ILE C 81 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL A 241 " pdb=" N VAL A 241 " pdb=" C VAL A 241 " pdb=" CB VAL A 241 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1966 not shown) Planarity restraints: 3037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 95 " -0.199 2.00e-02 2.50e+03 2.20e-01 7.28e+02 pdb=" CG ASN A 95 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 95 " 0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN A 95 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 95 " -0.331 2.00e-02 2.50e+03 pdb="HD22 ASN A 95 " 0.325 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 64 " -1.120 9.50e-02 1.11e+02 3.74e-01 1.52e+02 pdb=" NE ARG G 64 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 64 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G 64 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 64 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG G 64 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG G 64 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG G 64 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG G 64 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 13 " -0.959 9.50e-02 1.11e+02 3.20e-01 1.12e+02 pdb=" NE ARG H 13 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG H 13 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG H 13 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 13 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG H 13 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG H 13 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 13 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 13 " 0.000 2.00e-02 2.50e+03 ... (remaining 3034 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 6430 2.31 - 2.89: 51412 2.89 - 3.46: 59642 3.46 - 4.03: 84642 4.03 - 4.60: 124822 Nonbonded interactions: 326948 Sorted by model distance: nonbonded pdb=" H THR H 27 " pdb=" HG1 THR H 27 " model vdw 1.742 2.100 nonbonded pdb="HO2' G I 16 " pdb=" H6 U I 17 " model vdw 1.825 2.100 nonbonded pdb=" HD1 PHE A 61 " pdb=" HE2 PHE A 302 " model vdw 1.829 2.100 nonbonded pdb=" HE1 PHE A 218 " pdb=" HG CYS A 232 " model vdw 1.841 2.270 nonbonded pdb=" H SER C 58 " pdb=" HG SER C 58 " model vdw 1.842 2.100 ... (remaining 326943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 389) selection = (chain 'D' and (resid 55 through 188 or (resid 194 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name \ HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 195 through 389)) } ncs_group { reference = chain 'B' selection = (chain 'E' and resid 63 through 153) } ncs_group { reference = (chain 'C' and (resid 33 through 76 or (resid 79 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE \ 2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 80 through 152)) selection = (chain 'G' and ((resid 33 and (name N or name CA or name C or name O or name CB \ or name SG or name HA or name HB2 or name HB3 or name HG )) or resid 34 through \ 152)) } ncs_group { reference = (chain 'F' and resid 1 through 59) selection = chain 'H' } 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 28.290 Find NCS groups from input model: 0.230 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 0.056 12266 Z= 0.293 Angle : 0.780 8.989 16997 Z= 0.512 Chirality : 0.046 0.237 1969 Planarity : 0.019 0.502 1800 Dihedral : 20.060 174.296 5310 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.49 % Favored : 95.34 % Rotamer: Outliers : 1.96 % Allowed : 26.52 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.20 (0.23), residues: 1203 helix: -0.07 (0.28), residues: 339 sheet: -1.64 (0.35), residues: 194 loop : -0.85 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 13 TYR 0.015 0.001 TYR G 26 PHE 0.018 0.001 PHE D 218 TRP 0.012 0.001 TRP D 219 HIS 0.008 0.001 HIS H 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.29 (12266) covalent geometry : angle 0.78015 / 0.51 (16997) hydrogen bonds : bond 0.14165 / 9.29 ( 414) hydrogen bonds : angle 7.00395 / 4.80 ( 1022) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 MET cc_start: 0.6962 (ppp) cc_final: 0.6652 (ppp) REVERT: C 121 MET cc_start: 0.6305 (mmm) cc_final: 0.5898 (mmm) REVERT: E 110 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7495 (mm-30) REVERT: D 110 TRP cc_start: 0.7071 (m-10) cc_final: 0.6811 (m-10) outliers start: 21 outliers final: 9 residues processed: 261 average time/residue: 1.0580 time to fit residues: 302.4813 Evaluate side-chains 250 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 241 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 31 HIS A 333 GLN D 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.172223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.149896 restraints weight = 52156.504| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.58 r_work: 0.4015 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 12266 Z= 0.241 Angle : 0.590 7.737 16997 Z= 0.319 Chirality : 0.041 0.172 1969 Planarity : 0.011 0.373 1800 Dihedral : 19.766 173.904 2851 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.71 % Allowed : 29.32 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.23), residues: 1203 helix: -0.23 (0.27), residues: 342 sheet: -1.73 (0.34), residues: 203 loop : -0.97 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 13 TYR 0.015 0.002 TYR A 155 PHE 0.021 0.002 PHE D 218 TRP 0.015 0.002 TRP D 219 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (12266) covalent geometry : angle 0.58964 / 0.32 (16997) hydrogen bonds : bond 0.05402 / 3.62 ( 414) hydrogen bonds : angle 5.90191 / 4.06 ( 1022) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6441 (tpt) REVERT: C 121 MET cc_start: 0.6280 (mmm) cc_final: 0.5878 (mmm) REVERT: E 110 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7528 (mm-30) REVERT: G 145 VAL cc_start: 0.7316 (OUTLIER) cc_final: 0.6978 (p) REVERT: D 110 TRP cc_start: 0.7137 (m-10) cc_final: 0.6876 (m-10) outliers start: 29 outliers final: 18 residues processed: 266 average time/residue: 1.0243 time to fit residues: 298.6827 Evaluate side-chains 270 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 78 GLN Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.172287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.149938 restraints weight = 51907.630| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.57 r_work: 0.4021 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 12266 Z= 0.201 Angle : 0.564 6.713 16997 Z= 0.303 Chirality : 0.041 0.168 1969 Planarity : 0.006 0.136 1800 Dihedral : 19.729 174.034 2841 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.17 % Allowed : 28.48 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.23), residues: 1203 helix: -0.20 (0.27), residues: 342 sheet: -1.81 (0.34), residues: 204 loop : -0.96 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 285 TYR 0.014 0.001 TYR A 155 PHE 0.020 0.002 PHE D 218 TRP 0.015 0.002 TRP D 219 HIS 0.005 0.001 HIS H 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (12266) covalent geometry : angle 0.56430 / 0.30 (16997) hydrogen bonds : bond 0.04757 / 3.19 ( 414) hydrogen bonds : angle 5.58669 / 3.84 ( 1022) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.6356 (tpt) REVERT: C 121 MET cc_start: 0.6303 (mmm) cc_final: 0.5880 (mmm) REVERT: E 110 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7495 (mm-30) REVERT: G 143 ASP cc_start: 0.8252 (m-30) cc_final: 0.7963 (m-30) REVERT: G 144 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7710 (tm-30) REVERT: G 145 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.6885 (p) REVERT: D 110 TRP cc_start: 0.7112 (m-10) cc_final: 0.6847 (m-10) outliers start: 34 outliers final: 22 residues processed: 269 average time/residue: 1.1070 time to fit residues: 326.3153 Evaluate side-chains 273 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 325 TYR Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 360 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.0030 chunk 94 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.173849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.151387 restraints weight = 52020.234| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.59 r_work: 0.4043 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12266 Z= 0.121 Angle : 0.538 7.060 16997 Z= 0.284 Chirality : 0.039 0.160 1969 Planarity : 0.005 0.065 1800 Dihedral : 19.663 174.720 2835 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.99 % Allowed : 29.41 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.13 (0.23), residues: 1203 helix: 0.13 (0.28), residues: 343 sheet: -1.76 (0.33), residues: 208 loop : -0.80 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 285 TYR 0.012 0.001 TYR E 73 PHE 0.023 0.001 PHE E 93 TRP 0.013 0.001 TRP D 219 HIS 0.005 0.001 HIS H 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12266) covalent geometry : angle 0.53760 / 0.28 (16997) hydrogen bonds : bond 0.04274 / 2.89 ( 414) hydrogen bonds : angle 5.30694 / 3.65 ( 1022) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6368 (tpt) REVERT: C 71 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: C 121 MET cc_start: 0.6310 (mmm) cc_final: 0.5875 (mmm) REVERT: E 110 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7452 (mm-30) REVERT: G 144 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7597 (tm-30) REVERT: G 145 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.6892 (p) REVERT: D 110 TRP cc_start: 0.7074 (m-10) cc_final: 0.6817 (m-10) outliers start: 32 outliers final: 18 residues processed: 264 average time/residue: 1.1281 time to fit residues: 326.3020 Evaluate side-chains 270 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 123 LYS Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 360 CYS Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.172507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.150144 restraints weight = 51632.923| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.56 r_work: 0.4021 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12266 Z= 0.183 Angle : 0.550 7.015 16997 Z= 0.293 Chirality : 0.040 0.160 1969 Planarity : 0.004 0.057 1800 Dihedral : 19.636 174.497 2833 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.99 % Allowed : 28.38 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.22 (0.23), residues: 1203 helix: 0.11 (0.27), residues: 342 sheet: -1.80 (0.33), residues: 207 loop : -0.90 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 250 TYR 0.013 0.001 TYR A 155 PHE 0.025 0.002 PHE E 133 TRP 0.014 0.002 TRP D 219 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (12266) covalent geometry : angle 0.55048 / 0.29 (16997) hydrogen bonds : bond 0.04307 / 2.89 ( 414) hydrogen bonds : angle 5.27495 / 3.63 ( 1022) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6462 (tpt) REVERT: C 71 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: C 121 MET cc_start: 0.6126 (mmm) cc_final: 0.5686 (mmm) REVERT: E 110 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7513 (mm-30) REVERT: D 110 TRP cc_start: 0.7106 (m-10) cc_final: 0.6856 (m-10) outliers start: 32 outliers final: 20 residues processed: 271 average time/residue: 1.0155 time to fit residues: 302.3166 Evaluate side-chains 276 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 360 CYS Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.171418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.149026 restraints weight = 51979.036| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.55 r_work: 0.4006 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 12266 Z= 0.228 Angle : 0.577 7.453 16997 Z= 0.310 Chirality : 0.041 0.175 1969 Planarity : 0.005 0.039 1800 Dihedral : 19.645 174.280 2830 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.27 % Allowed : 28.29 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.43 (0.23), residues: 1203 helix: -0.04 (0.27), residues: 344 sheet: -1.92 (0.32), residues: 219 loop : -1.03 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 250 TYR 0.015 0.002 TYR A 155 PHE 0.025 0.002 PHE D 218 TRP 0.015 0.002 TRP D 219 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (12266) covalent geometry : angle 0.57749 / 0.31 (16997) hydrogen bonds : bond 0.04387 / 2.93 ( 414) hydrogen bonds : angle 5.30887 / 3.65 ( 1022) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6744 (tpt) REVERT: C 71 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6352 (tt0) REVERT: C 121 MET cc_start: 0.6134 (mmm) cc_final: 0.5716 (mmm) REVERT: E 110 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7530 (mm-30) REVERT: G 143 ASP cc_start: 0.8231 (m-30) cc_final: 0.7835 (m-30) REVERT: D 110 TRP cc_start: 0.7154 (m-10) cc_final: 0.6893 (m-10) REVERT: D 334 GLU cc_start: 0.6927 (tp30) cc_final: 0.6674 (tp30) outliers start: 35 outliers final: 25 residues processed: 272 average time/residue: 0.9975 time to fit residues: 298.7206 Evaluate side-chains 283 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 360 CYS Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 14 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.172107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.149762 restraints weight = 51721.320| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.56 r_work: 0.4016 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12266 Z= 0.181 Angle : 0.572 7.718 16997 Z= 0.303 Chirality : 0.040 0.166 1969 Planarity : 0.004 0.042 1800 Dihedral : 19.639 174.518 2830 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.45 % Allowed : 28.57 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.30 (0.23), residues: 1203 helix: 0.15 (0.28), residues: 337 sheet: -1.87 (0.32), residues: 217 loop : -0.98 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 285 TYR 0.015 0.001 TYR D 88 PHE 0.026 0.002 PHE E 133 TRP 0.015 0.002 TRP D 219 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (12266) covalent geometry : angle 0.57180 / 0.30 (16997) hydrogen bonds : bond 0.04205 / 2.82 ( 414) hydrogen bonds : angle 5.20479 / 3.58 ( 1022) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6881 (tpt) REVERT: C 71 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6371 (tt0) REVERT: C 121 MET cc_start: 0.6113 (mmm) cc_final: 0.5693 (mmm) REVERT: E 110 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7521 (mm-30) REVERT: G 143 ASP cc_start: 0.8174 (m-30) cc_final: 0.7758 (m-30) REVERT: D 110 TRP cc_start: 0.7134 (m-10) cc_final: 0.6871 (m-10) outliers start: 37 outliers final: 25 residues processed: 271 average time/residue: 1.0530 time to fit residues: 313.6531 Evaluate side-chains 284 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 360 CYS Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 14 GLN F 31 HIS A 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.171855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.149473 restraints weight = 51541.814| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.56 r_work: 0.4012 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12266 Z= 0.191 Angle : 0.583 8.246 16997 Z= 0.309 Chirality : 0.041 0.168 1969 Planarity : 0.005 0.061 1800 Dihedral : 19.639 174.560 2830 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.17 % Allowed : 29.23 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.29 (0.23), residues: 1203 helix: 0.15 (0.28), residues: 338 sheet: -1.83 (0.32), residues: 217 loop : -1.00 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.029 0.002 TYR D 88 PHE 0.025 0.002 PHE D 218 TRP 0.015 0.002 TRP D 219 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (12266) covalent geometry : angle 0.58325 / 0.31 (16997) hydrogen bonds : bond 0.04195 / 2.81 ( 414) hydrogen bonds : angle 5.18675 / 3.57 ( 1022) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6977 (tpt) REVERT: C 71 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.6378 (tt0) REVERT: C 121 MET cc_start: 0.6111 (mmm) cc_final: 0.5686 (mmm) REVERT: E 110 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7526 (mm-30) REVERT: E 134 LYS cc_start: 0.8260 (mttt) cc_final: 0.8024 (mtmm) REVERT: G 143 ASP cc_start: 0.8208 (m-30) cc_final: 0.7803 (m-30) REVERT: D 110 TRP cc_start: 0.7138 (m-10) cc_final: 0.6873 (m-10) REVERT: D 334 GLU cc_start: 0.6921 (tp30) cc_final: 0.6669 (tp30) outliers start: 34 outliers final: 23 residues processed: 269 average time/residue: 1.0256 time to fit residues: 303.4410 Evaluate side-chains 280 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 360 CYS Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 31 HIS A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.171253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.149002 restraints weight = 52029.666| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 2.56 r_work: 0.4003 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 12266 Z= 0.240 Angle : 0.609 8.448 16997 Z= 0.325 Chirality : 0.042 0.180 1969 Planarity : 0.005 0.066 1800 Dihedral : 19.652 174.287 2830 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.99 % Allowed : 29.41 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.42 (0.23), residues: 1203 helix: 0.03 (0.28), residues: 338 sheet: -1.88 (0.32), residues: 217 loop : -1.07 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.020 0.002 TYR D 88 PHE 0.029 0.002 PHE D 218 TRP 0.015 0.002 TRP D 219 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.24 (12266) covalent geometry : angle 0.60908 / 0.33 (16997) hydrogen bonds : bond 0.04347 / 2.91 ( 414) hydrogen bonds : angle 5.28140 / 3.64 ( 1022) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7125 (tpt) REVERT: C 71 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: C 102 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7144 (mt-10) REVERT: C 121 MET cc_start: 0.6108 (mmm) cc_final: 0.5680 (mmm) REVERT: E 110 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7551 (mm-30) REVERT: E 134 LYS cc_start: 0.8254 (mttt) cc_final: 0.8003 (mtmm) REVERT: G 143 ASP cc_start: 0.8221 (m-30) cc_final: 0.7828 (m-30) REVERT: A 305 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7237 (t0) REVERT: D 110 TRP cc_start: 0.7167 (m-10) cc_final: 0.6902 (m-10) REVERT: D 334 GLU cc_start: 0.6936 (tp30) cc_final: 0.6690 (tp30) outliers start: 32 outliers final: 23 residues processed: 266 average time/residue: 1.0214 time to fit residues: 298.8403 Evaluate side-chains 278 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 360 CYS Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 71 GLN F 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.172862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.150628 restraints weight = 51660.695| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.56 r_work: 0.4030 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12266 Z= 0.139 Angle : 0.572 9.134 16997 Z= 0.301 Chirality : 0.040 0.165 1969 Planarity : 0.004 0.052 1800 Dihedral : 19.627 174.969 2830 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.33 % Allowed : 30.07 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.14 (0.23), residues: 1203 helix: 0.37 (0.28), residues: 338 sheet: -1.83 (0.33), residues: 217 loop : -0.91 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.018 0.001 TYR D 88 PHE 0.022 0.002 PHE E 133 TRP 0.014 0.001 TRP D 219 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12266) covalent geometry : angle 0.57245 / 0.30 (16997) hydrogen bonds : bond 0.03989 / 2.69 ( 414) hydrogen bonds : angle 5.07480 / 3.50 ( 1022) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7031 (tpt) REVERT: C 102 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7082 (mm-30) REVERT: C 121 MET cc_start: 0.6112 (mmm) cc_final: 0.5677 (mmm) REVERT: E 110 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7548 (mm-30) REVERT: E 134 LYS cc_start: 0.8249 (mttt) cc_final: 0.8001 (mtmm) REVERT: G 143 ASP cc_start: 0.8199 (m-30) cc_final: 0.7806 (m-30) REVERT: A 318 LEU cc_start: 0.8365 (mt) cc_final: 0.8160 (mm) REVERT: D 110 TRP cc_start: 0.7126 (m-10) cc_final: 0.6873 (m-10) outliers start: 25 outliers final: 19 residues processed: 265 average time/residue: 1.0240 time to fit residues: 298.4295 Evaluate side-chains 275 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 373 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.172435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.150150 restraints weight = 51806.715| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.56 r_work: 0.4023 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12266 Z= 0.168 Angle : 0.584 8.556 16997 Z= 0.307 Chirality : 0.040 0.159 1969 Planarity : 0.004 0.053 1800 Dihedral : 19.616 175.238 2830 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.33 % Allowed : 30.44 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.18 (0.23), residues: 1203 helix: 0.33 (0.28), residues: 338 sheet: -1.84 (0.32), residues: 217 loop : -0.95 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 185 TYR 0.017 0.001 TYR D 88 PHE 0.024 0.002 PHE D 218 TRP 0.013 0.001 TRP D 219 HIS 0.004 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (12266) covalent geometry : angle 0.58441 / 0.31 (16997) hydrogen bonds : bond 0.04033 / 2.72 ( 414) hydrogen bonds : angle 5.08219 / 3.50 ( 1022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8426.84 seconds wall clock time: 143 minutes 13.94 seconds (8593.94 seconds total)