Starting phenix.real_space_refine on Fri Aug 7 18:34:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yfm_72898/08_2026/9yfm_72898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yfm_72898/08_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_72898/08_2026/9yfm_72898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yfm_72898/08_2026/9yfm_72898.map" model { file = "/net/cci-nas-00/data/ceres_data/9yfm_72898/08_2026/9yfm_72898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yfm_72898/08_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-2.2rc3-6140/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: 3.27, per 1000 atoms: 0.14 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: 1.63 Conformation dependent library (CDL) restraints added in 433.7 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: 2.88 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: 3.58 Time building geometry restraints manager: 2.24 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: 42044 3.12 - 6.24: 267 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: 1484 0.047 - 0.095: 272 0.095 - 0.142: 187 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- 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= 0.298 Angle : 0.820 8.989 16997 Z= 0.561 Chirality : 0.051 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 0.00458 / 0.30 (12266) covalent geometry : angle 0.82041 / 0.56 (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 : 0.345 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: 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: 0.7494 (mm-30) REVERT: A 101 ASN cc_start: 0.7600 (m-40) cc_final: 0.7345 (t0) 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: 0.9256 time to fit residues: 264.7333 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 : 0.403 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.172163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.149872 restraints weight = 52088.522| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.58 r_work: 0.4015 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 12266 Z= 0.243 Angle : 0.600 7.866 16997 Z= 0.322 Chirality : 0.041 0.162 1969 Planarity : 0.010 0.365 1800 Dihedral : 19.707 175.086 2851 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.80 % Allowed : 29.41 % Favored : 67.79 % 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: -0.25 (0.27), residues: 342 sheet: -1.72 (0.34), residues: 203 loop : -0.96 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 13 TYR 0.016 0.002 TYR A 155 PHE 0.020 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 0.00546 / 0.24 (12266) covalent geometry : angle 0.59958 / 0.32 (16997) hydrogen bonds : bond 0.05394 / 3.62 ( 414) hydrogen bonds : angle 5.87404 / 4.04 ( 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 285 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.548 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: 0.7528 (OUTLIER) cc_final: 0.6431 (tpt) REVERT: C 121 MET cc_start: 0.6294 (mmm) cc_final: 0.5889 (mmm) REVERT: E 110 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7534 (mm-30) REVERT: G 143 ASP cc_start: 0.8218 (m-30) cc_final: 0.7961 (m-30) REVERT: G 145 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.6972 (p) REVERT: A 101 ASN cc_start: 0.7619 (m-40) cc_final: 0.7361 (t0) REVERT: A 352 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7640 (tmm) REVERT: D 110 TRP cc_start: 0.7133 (m-10) cc_final: 0.6874 (m-10) outliers start: 30 outliers final: 20 residues processed: 268 average time/residue: 0.9591 time to fit residues: 282.2649 Evaluate side-chains 271 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 E residue 122 VAL 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 352 MET 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 359 SER 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: 4.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.172136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.149679 restraints weight = 51886.981| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.57 r_work: 0.4010 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 12266 Z= 0.210 Angle : 0.572 6.985 16997 Z= 0.306 Chirality : 0.040 0.163 1969 Planarity : 0.006 0.151 1800 Dihedral : 19.668 175.529 2841 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % 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: -1.40 (0.23), residues: 1203 helix: -0.20 (0.27), residues: 342 sheet: -1.81 (0.33), residues: 209 loop : -0.95 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 250 TYR 0.014 0.002 TYR A 155 PHE 0.021 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 0.00474 / 0.21 (12266) covalent geometry : angle 0.57173 / 0.31 (16997) hydrogen bonds : bond 0.04909 / 3.29 ( 414) hydrogen bonds : angle 5.61468 / 3.86 ( 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 289 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.361 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: B 124 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6347 (tpt) REVERT: C 102 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7099 (mm-30) REVERT: C 121 MET cc_start: 0.6287 (mmm) cc_final: 0.5858 (mmm) REVERT: E 110 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7498 (mm-30) REVERT: G 143 ASP cc_start: 0.8270 (m-30) cc_final: 0.7933 (m-30) REVERT: G 144 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7699 (tm-30) REVERT: G 145 VAL cc_start: 0.7272 (OUTLIER) cc_final: 0.6889 (p) REVERT: D 110 TRP cc_start: 0.7139 (m-10) cc_final: 0.6878 (m-10) outliers start: 37 outliers final: 22 residues processed: 268 average time/residue: 0.9420 time to fit residues: 277.1766 Evaluate side-chains 274 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 89 ASP 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 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 360 CYS Chi-restraints excluded: chain D residue 373 MET 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: 2.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.0020 chunk 94 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 HIS A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.173462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.151078 restraints weight = 52025.731| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.59 r_work: 0.4032 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12266 Z= 0.130 Angle : 0.537 6.900 16997 Z= 0.283 Chirality : 0.039 0.164 1969 Planarity : 0.005 0.065 1800 Dihedral : 19.622 176.235 2838 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.52 % Allowed : 29.51 % 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: -1.19 (0.23), residues: 1203 helix: 0.11 (0.28), residues: 342 sheet: -1.79 (0.33), residues: 208 loop : -0.86 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 285 TYR 0.012 0.001 TYR E 73 PHE 0.023 0.001 PHE E 93 TRP 0.014 0.001 TRP D 219 HIS 0.005 0.001 HIS H 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12266) covalent geometry : angle 0.53656 / 0.28 (16997) hydrogen bonds : bond 0.04399 / 2.98 ( 414) hydrogen bonds : angle 5.33430 / 3.67 ( 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 281 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.660 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: 0.7583 (OUTLIER) cc_final: 0.6364 (tpt) REVERT: C 121 MET cc_start: 0.6292 (mmm) cc_final: 0.5857 (mmm) REVERT: E 110 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7511 (mm-30) REVERT: G 144 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7694 (tm-30) REVERT: G 145 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.6962 (p) REVERT: A 100 SER cc_start: 0.7649 (m) cc_final: 0.7359 (t) REVERT: D 110 TRP cc_start: 0.7110 (m-10) cc_final: 0.6851 (m-10) outliers start: 27 outliers final: 17 residues processed: 266 average time/residue: 0.9601 time to fit residues: 280.0903 Evaluate side-chains 271 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 98 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 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 360 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.172454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.150150 restraints weight = 51636.740| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.56 r_work: 0.4019 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1378 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= 0.187 Angle : 0.555 6.886 16997 Z= 0.294 Chirality : 0.040 0.164 1969 Planarity : 0.005 0.068 1800 Dihedral : 19.597 176.126 2833 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.99 % Allowed : 29.32 % Favored : 67.69 % 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: -1.28 (0.23), residues: 1203 helix: 0.08 (0.27), residues: 342 sheet: -1.95 (0.32), residues: 208 loop : -0.90 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 285 TYR 0.014 0.001 TYR A 155 PHE 0.029 0.002 PHE E 133 TRP 0.014 0.002 TRP D 219 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (12266) covalent geometry : angle 0.55542 / 0.29 (16997) hydrogen bonds : bond 0.04385 / 2.96 ( 414) hydrogen bonds : angle 5.30256 / 3.64 ( 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 288 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 256 time to evaluate : 0.356 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: 0.7626 (OUTLIER) cc_final: 0.6499 (tpt) REVERT: C 121 MET cc_start: 0.6120 (mmm) cc_final: 0.5710 (mmm) REVERT: E 110 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 101 ASN cc_start: 0.7628 (m-40) cc_final: 0.7420 (m-40) REVERT: D 110 TRP cc_start: 0.7134 (m-10) cc_final: 0.6871 (m-10) outliers start: 32 outliers final: 21 residues processed: 268 average time/residue: 0.8901 time to fit residues: 262.5702 Evaluate side-chains 277 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 81 LEU 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 100 SER 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 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 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: 0.9980 chunk 119 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.171551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.149258 restraints weight = 52052.387| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.56 r_work: 0.4008 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 12266 Z= 0.223 Angle : 0.580 7.352 16997 Z= 0.308 Chirality : 0.041 0.168 1969 Planarity : 0.005 0.036 1800 Dihedral : 19.593 175.966 2830 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.89 % Allowed : 28.85 % Favored : 68.25 % 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: -0.03 (0.27), residues: 344 sheet: -1.93 (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 0.026 0.002 PHE E 133 TRP 0.016 0.002 TRP D 219 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (12266) covalent geometry : angle 0.57956 / 0.31 (16997) hydrogen bonds : bond 0.04421 / 2.96 ( 414) hydrogen bonds : angle 5.31198 / 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 291 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 260 time to evaluate : 0.519 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: 0.7697 (OUTLIER) cc_final: 0.6742 (tpt) REVERT: C 71 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6381 (tt0) REVERT: C 121 MET cc_start: 0.6127 (mmm) cc_final: 0.5708 (mmm) REVERT: E 110 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7510 (mm-30) REVERT: G 143 ASP cc_start: 0.8229 (m-30) cc_final: 0.7817 (m-30) REVERT: A 101 ASN cc_start: 0.7654 (m-40) cc_final: 0.7429 (m-40) REVERT: D 110 TRP cc_start: 0.7130 (m-10) cc_final: 0.6876 (m-10) REVERT: D 334 GLU cc_start: 0.6953 (tp30) cc_final: 0.6691 (tp30) outliers start: 31 outliers final: 24 residues processed: 272 average time/residue: 0.8664 time to fit residues: 259.1456 Evaluate side-chains 284 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 131 LEU 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 14 GLN 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 98 LYS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 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: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4430 r_free = 0.4430 target = 0.173117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.150826 restraints weight = 51621.296| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.57 r_work: 0.4028 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.1560 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= 0.131 Angle : 0.548 7.600 16997 Z= 0.288 Chirality : 0.039 0.167 1969 Planarity : 0.004 0.038 1800 Dihedral : 19.571 176.604 2830 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.45 % Allowed : 28.66 % Favored : 67.88 % 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: 0.30 (0.28), residues: 338 sheet: -1.91 (0.32), residues: 206 loop : -0.86 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.012 0.001 TYR E 73 PHE 0.025 0.002 PHE E 133 TRP 0.015 0.001 TRP D 219 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (12266) covalent geometry : angle 0.54799 / 0.29 (16997) hydrogen bonds : bond 0.04109 / 2.78 ( 414) hydrogen bonds : angle 5.11901 / 3.52 ( 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 293 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.394 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: 0.7669 (OUTLIER) cc_final: 0.6725 (tpt) REVERT: C 121 MET cc_start: 0.6096 (mmm) cc_final: 0.5668 (mmm) REVERT: E 110 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7504 (mm-30) REVERT: G 143 ASP cc_start: 0.8153 (m-30) cc_final: 0.7734 (m-30) REVERT: A 101 ASN cc_start: 0.7606 (m-40) cc_final: 0.7386 (m-40) REVERT: D 110 TRP cc_start: 0.7116 (m-10) cc_final: 0.6852 (m-10) REVERT: D 334 GLU cc_start: 0.6945 (tp30) cc_final: 0.6690 (tp30) outliers start: 37 outliers final: 24 residues processed: 271 average time/residue: 0.9900 time to fit residues: 294.8475 Evaluate side-chains 279 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 14 GLN 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 98 LYS 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 177 LYS Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 360 CYS 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: 1.9990 chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.172016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.149711 restraints weight = 51522.383| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.55 r_work: 0.4013 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 12266 Z= 0.193 Angle : 0.579 8.458 16997 Z= 0.304 Chirality : 0.040 0.169 1969 Planarity : 0.005 0.063 1800 Dihedral : 19.575 176.406 2830 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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: -1.25 (0.23), residues: 1203 helix: 0.22 (0.28), residues: 338 sheet: -1.85 (0.32), residues: 217 loop : -0.96 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.020 0.002 TYR D 88 PHE 0.025 0.002 PHE E 133 TRP 0.015 0.002 TRP D 219 HIS 0.004 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (12266) covalent geometry : angle 0.57915 / 0.30 (16997) hydrogen bonds : bond 0.04203 / 2.82 ( 414) hydrogen bonds : angle 5.16148 / 3.55 ( 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 286 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 0.371 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: 0.7759 (OUTLIER) cc_final: 0.6917 (tpt) REVERT: C 121 MET cc_start: 0.6091 (mmm) cc_final: 0.5668 (mmm) REVERT: E 110 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7519 (mm-30) REVERT: E 134 LYS cc_start: 0.8273 (mttt) cc_final: 0.8015 (mtmm) REVERT: G 143 ASP cc_start: 0.8220 (m-30) cc_final: 0.7792 (m-30) REVERT: A 101 ASN cc_start: 0.7634 (m-40) cc_final: 0.7403 (m-40) REVERT: A 305 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7212 (t0) REVERT: D 110 TRP cc_start: 0.7117 (m-10) cc_final: 0.6866 (m-10) REVERT: D 334 GLU cc_start: 0.6953 (tp30) cc_final: 0.6695 (tp30) outliers start: 29 outliers final: 21 residues processed: 265 average time/residue: 0.9689 time to fit residues: 281.7297 Evaluate side-chains 278 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 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 98 LYS Chi-restraints excluded: chain A residue 100 SER 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 177 LYS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 360 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 120 optimal weight: 10.0000 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.172535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.150162 restraints weight = 51764.499| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.57 r_work: 0.4021 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12266 Z= 0.167 Angle : 0.574 8.272 16997 Z= 0.301 Chirality : 0.040 0.169 1969 Planarity : 0.005 0.069 1800 Dihedral : 19.575 176.490 2830 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.33 % Allowed : 29.97 % Favored : 67.69 % 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: -1.21 (0.23), residues: 1203 helix: 0.29 (0.28), residues: 338 sheet: -1.83 (0.32), residues: 217 loop : -0.96 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 185 TYR 0.015 0.001 TYR D 88 PHE 0.022 0.002 PHE D 218 TRP 0.014 0.001 TRP D 219 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (12266) covalent geometry : angle 0.57380 / 0.30 (16997) hydrogen bonds : bond 0.04140 / 2.79 ( 414) hydrogen bonds : angle 5.11590 / 3.52 ( 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 280 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.433 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: B 124 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6924 (tpt) REVERT: C 121 MET cc_start: 0.6084 (mmm) cc_final: 0.5672 (mmm) REVERT: E 110 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7513 (mm-30) REVERT: E 134 LYS cc_start: 0.8258 (mttt) cc_final: 0.8005 (mtmm) REVERT: G 143 ASP cc_start: 0.8200 (m-30) cc_final: 0.7787 (m-30) REVERT: A 101 ASN cc_start: 0.7631 (m-40) cc_final: 0.7404 (m-40) REVERT: A 305 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7217 (t0) REVERT: D 110 TRP cc_start: 0.7124 (m-10) cc_final: 0.6864 (m-10) REVERT: D 334 GLU cc_start: 0.6938 (tp30) cc_final: 0.6685 (tp30) outliers start: 25 outliers final: 23 residues processed: 264 average time/residue: 0.9297 time to fit residues: 269.4229 Evaluate side-chains 279 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 14 GLN Chi-restraints excluded: chain F residue 20 ILE 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 H residue 17 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 100 SER 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 177 LYS Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain D residue 360 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.0270 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 99 optimal weight: 0.0470 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.173451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.151235 restraints weight = 51637.128| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.56 r_work: 0.4035 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12266 Z= 0.121 Angle : 0.564 8.502 16997 Z= 0.295 Chirality : 0.039 0.168 1969 Planarity : 0.005 0.071 1800 Dihedral : 19.558 176.744 2830 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.43 % Allowed : 29.69 % Favored : 67.88 % 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: -1.07 (0.23), residues: 1203 helix: 0.47 (0.29), residues: 338 sheet: -1.82 (0.33), residues: 217 loop : -0.89 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.016 0.001 TYR D 88 PHE 0.022 0.002 PHE E 133 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 0.00281 / 0.12 (12266) covalent geometry : angle 0.56441 / 0.29 (16997) hydrogen bonds : bond 0.03987 / 2.70 ( 414) hydrogen bonds : angle 5.06173 / 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: 26 poor density : 257 time to evaluate : 0.398 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: 0.7697 (OUTLIER) cc_final: 0.6834 (tpt) REVERT: C 102 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7101 (mm-30) REVERT: C 121 MET cc_start: 0.6079 (mmm) cc_final: 0.5663 (mmm) REVERT: E 110 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7486 (mm-30) REVERT: E 134 LYS cc_start: 0.8266 (mttt) cc_final: 0.8012 (mtmm) REVERT: G 143 ASP cc_start: 0.8183 (m-30) cc_final: 0.7759 (m-30) REVERT: A 101 ASN cc_start: 0.7601 (m-40) cc_final: 0.7380 (m-40) REVERT: D 110 TRP cc_start: 0.7103 (m-10) cc_final: 0.6838 (m-10) outliers start: 26 outliers final: 20 residues processed: 267 average time/residue: 0.9530 time to fit residues: 280.2624 Evaluate side-chains 275 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 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 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 360 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.172526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.150327 restraints weight = 51652.332| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.55 r_work: 0.4024 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 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 : 0.004 0.075 12266 Z= 0.175 Angle : 0.583 8.633 16997 Z= 0.303 Chirality : 0.040 0.169 1969 Planarity : 0.004 0.053 1800 Dihedral : 19.559 176.549 2830 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.24 % Allowed : 30.07 % Favored : 67.69 % 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: -1.15 (0.23), residues: 1203 helix: 0.42 (0.28), residues: 338 sheet: -1.81 (0.33), residues: 217 loop : -0.96 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 185 TYR 0.015 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 E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12266) covalent geometry : angle 0.58279 / 0.30 (16997) hydrogen bonds : bond 0.04055 / 2.73 ( 414) hydrogen bonds : angle 5.07018 / 3.50 ( 1022) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7612.71 seconds wall clock time: 129 minutes 16.55 seconds (7756.55 seconds total)