Starting phenix.real_space_refine on Fri Feb 6 02:40:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yfo_72903/02_2026/9yfo_72903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yfo_72903/02_2026/9yfo_72903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yfo_72903/02_2026/9yfo_72903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yfo_72903/02_2026/9yfo_72903.map" model { file = "/net/cci-nas-00/data/ceres_data/9yfo_72903/02_2026/9yfo_72903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yfo_72903/02_2026/9yfo_72903.cif" } resolution = 3.23 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= 0.029 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 97 5.49 5 S 52 5.16 5 C 6867 2.51 5 N 1997 2.21 5 O 2338 1.98 5 H 10581 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21932 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5485 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 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: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2150 Classifications: {'peptide': 133} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 125} Chain: "D" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5526 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain breaks: 1 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: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2080 Classifications: {'peptide': 128} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1063 Classifications: {'peptide': 64} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 57} Chain: "I" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 3123 Classifications: {'RNA': 97} Modifications used: {'3*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 40, 'rna3p_pyr': 42} Link IDs: {'rna2p': 15, 'rna3p': 81} Chain breaks: 6 Time building chain proxies: 3.78, per 1000 atoms: 0.17 Number of scatterers: 21932 At special positions: 0 Unit cell: (95.22, 114.264, 134.964, 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 52 16.00 P 97 15.00 O 2338 8.00 N 1997 7.00 C 6867 6.00 H 10581 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 598.6 milliseconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 12 sheets defined 37.1% alpha, 13.9% beta 37 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.342A pdb=" N TYR A 53 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.120A pdb=" N ARG A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 103 through 116 Processing helix 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: 3.732A pdb=" N VAL A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.850A pdb=" N VAL A 296 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.979A pdb=" N PHE B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 32 removed outlier: 3.527A pdb=" N ASP C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 removed outlier: 4.173A pdb=" N SER C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.775A pdb=" N ILE C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 113 through 122 removed outlier: 3.745A pdb=" N ILE C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.623A pdb=" N GLY C 153 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.723A pdb=" N TRP D 54 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.881A pdb=" N ARG D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 103 through 116 Processing helix chain 'D' and resid 141 through 149 removed outlier: 4.481A pdb=" N LYS D 146 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 178 removed outlier: 3.710A 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 264 through 279 Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 292 through 296 removed outlier: 4.041A pdb=" N VAL D 296 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.560A pdb=" N CYS D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.511A pdb=" N PHE F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'G' and resid 26 through 33 Processing helix chain 'G' and resid 42 through 58 removed outlier: 4.195A pdb=" N SER G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 77 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: 3.818A 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 53 Processing helix chain 'H' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.557A pdb=" N ARG A 324 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS A 299 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL A 338 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A 301 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 347 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 98 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 92 through 98 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 215 through 222 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 215 through 222 current: chain 'A' and resid 256 through 257 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 72 removed outlier: 6.199A pdb=" N ILE B 141 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE B 97 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 108 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS B 123 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU B 110 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 81 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 65 removed outlier: 6.739A pdb=" N VAL C 82 " --> pdb=" O CYS C 109 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR C 111 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 84 " --> pdb=" O THR C 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.611A pdb=" N ARG D 324 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS D 299 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL D 338 " --> pdb=" O LYS D 299 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D 301 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN D 333 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 346 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL D 345 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL D 371 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU D 347 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL D 317 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 120 through 122 removed outlier: 4.264A pdb=" N GLY D 92 " --> pdb=" O ILE D 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 131 through 132 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 131 through 132 current: chain 'D' and resid 215 through 222 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 215 through 222 current: chain 'D' and resid 256 through 257 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 180 through 184 Processing sheet with id=AB1, first strand: chain 'F' and resid 13 through 16 Processing sheet with id=AB2, first strand: chain 'G' and resid 63 through 65 Processing sheet with id=AB3, first strand: chain 'H' and resid 13 through 16 304 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 10558 1.01 - 1.21: 31 1.21 - 1.42: 4838 1.42 - 1.62: 6853 1.62 - 1.82: 81 Bond restraints: 22361 Sorted by residual: bond pdb=" N ILE C 81 " pdb=" CA ILE C 81 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.29e-02 6.01e+03 1.43e+01 bond pdb=" C LYS D 367 " pdb=" O LYS D 367 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.32e-02 5.74e+03 1.20e+01 bond pdb=" CA SER B 121 " pdb=" CB SER B 121 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.66e-02 3.63e+03 1.18e+01 bond pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" CA SER A 282 " pdb=" CB SER A 282 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.56e-02 4.11e+03 1.07e+01 ... (remaining 22356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 40028 2.63 - 5.26: 448 5.26 - 7.89: 30 7.89 - 10.52: 4 10.52 - 13.15: 4 Bond angle restraints: 40514 Sorted by residual: angle pdb=" C LYS G 48 " pdb=" CA LYS G 48 " pdb=" CB LYS G 48 " ideal model delta sigma weight residual 110.85 97.70 13.15 1.70e+00 3.46e-01 5.99e+01 angle pdb=" N LYS D 259 " pdb=" CA LYS D 259 " pdb=" CB LYS D 259 " ideal model delta sigma weight residual 110.61 99.72 10.89 1.51e+00 4.39e-01 5.20e+01 angle pdb=" N VAL C 100 " pdb=" CA VAL C 100 " pdb=" CB VAL C 100 " ideal model delta sigma weight residual 110.56 121.81 -11.25 1.67e+00 3.59e-01 4.54e+01 angle pdb=" C PHE B 128 " pdb=" CA PHE B 128 " pdb=" CB PHE B 128 " ideal model delta sigma weight residual 109.62 121.10 -11.48 1.79e+00 3.12e-01 4.11e+01 angle pdb=" N GLY F 11 " pdb=" CA GLY F 11 " pdb=" C GLY F 11 " ideal model delta sigma weight residual 115.32 106.80 8.52 1.38e+00 5.25e-01 3.81e+01 ... (remaining 40509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 9985 35.69 - 71.38: 532 71.38 - 107.06: 51 107.06 - 142.75: 2 142.75 - 178.44: 4 Dihedral angle restraints: 10574 sinusoidal: 6651 harmonic: 3923 Sorted by residual: dihedral pdb=" CD ARG C 64 " pdb=" NE ARG C 64 " pdb=" CZ ARG C 64 " pdb=" NH1 ARG C 64 " ideal model delta sinusoidal sigma weight residual 0.00 -79.71 79.71 1 1.00e+01 1.00e-02 7.89e+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 50.44 -178.44 1 1.70e+01 3.46e-03 6.64e+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 232.00 62.53 169.47 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 10571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1290 0.040 - 0.080: 454 0.080 - 0.120: 121 0.120 - 0.160: 31 0.160 - 0.199: 12 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CA ILE B 82 " pdb=" N ILE B 82 " pdb=" C ILE B 82 " pdb=" CB ILE B 82 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA LYS G 48 " pdb=" N LYS G 48 " pdb=" C LYS G 48 " pdb=" CB LYS G 48 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 1905 not shown) Planarity restraints: 2893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 64 " 1.100 9.50e-02 1.11e+02 3.67e-01 1.46e+02 pdb=" NE ARG C 64 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 64 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 64 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 64 " 0.020 2.00e-02 2.50e+03 pdb="HH11 ARG C 64 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C 64 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 64 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 64 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 146 " -0.756 9.50e-02 1.11e+02 2.53e-01 6.99e+01 pdb=" NE ARG C 146 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG C 146 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 146 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 146 " -0.023 2.00e-02 2.50e+03 pdb="HH11 ARG C 146 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C 146 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 146 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 146 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 105 " 0.006 2.00e-02 2.50e+03 1.70e-02 1.01e+01 pdb=" N9 G I 105 " -0.004 2.00e-02 2.50e+03 pdb=" C8 G I 105 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G I 105 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G I 105 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G I 105 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G I 105 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G I 105 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G I 105 " -0.051 2.00e-02 2.50e+03 pdb=" N2 G I 105 " 0.033 2.00e-02 2.50e+03 pdb=" N3 G I 105 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G I 105 " 0.004 2.00e-02 2.50e+03 pdb=" H8 G I 105 " 0.000 2.00e-02 2.50e+03 pdb=" H1 G I 105 " 0.003 2.00e-02 2.50e+03 ... (remaining 2890 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 952 2.17 - 2.78: 42238 2.78 - 3.38: 60424 3.38 - 3.99: 81335 3.99 - 4.60: 124527 Nonbonded interactions: 309476 Sorted by model distance: nonbonded pdb="HD22 ASN F 8 " pdb="HD21 ASN F 10 " model vdw 1.559 2.100 nonbonded pdb=" H LEU D 57 " pdb=" H LEU D 58 " model vdw 1.750 2.100 nonbonded pdb="HD22 ASN H 8 " pdb="HD21 ASN H 10 " model vdw 1.775 2.100 nonbonded pdb=" H LYS C 44 " pdb=" HG3 LYS C 44 " model vdw 1.797 2.270 nonbonded pdb=" H ILE G 69 " pdb="HG13 ILE G 69 " model vdw 1.832 2.270 ... (remaining 309471 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 41 through 389) selection = (chain 'D' and (resid 41 through 182 or resid 200 through 389)) } ncs_group { reference = (chain 'C' and ((resid 25 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 26 through \ 152)) selection = chain 'G' } ncs_group { reference = chain 'F' selection = (chain 'H' and resid 1 through 61) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.140 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.510 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.007 0.057 11780 Z= 0.366 Angle : 0.859 13.155 16351 Z= 0.522 Chirality : 0.047 0.199 1908 Planarity : 0.015 0.493 1710 Dihedral : 20.404 178.438 5123 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.45 % Allowed : 22.18 % Favored : 75.37 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 6.90 % 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: -1.67 (0.23), residues: 1149 helix: -0.16 (0.27), residues: 350 sheet: -2.18 (0.35), residues: 182 loop : -1.28 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 285 TYR 0.018 0.002 TYR A 71 PHE 0.032 0.002 PHE B 128 TRP 0.019 0.002 TRP A 382 HIS 0.008 0.002 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00720 (11780) covalent geometry : angle 0.85881 (16351) hydrogen bonds : bond 0.16948 ( 403) hydrogen bonds : angle 7.57254 ( 995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 349 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 324 time to evaluate : 0.581 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: A 82 LYS cc_start: 0.8503 (mptp) cc_final: 0.8197 (mptp) REVERT: A 103 SER cc_start: 0.8572 (t) cc_final: 0.8305 (p) REVERT: A 255 ILE cc_start: 0.8121 (pt) cc_final: 0.7786 (mp) REVERT: B 73 TYR cc_start: 0.6968 (t80) cc_final: 0.6350 (t80) REVERT: B 78 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7511 (mm-40) REVERT: B 103 GLU cc_start: 0.6096 (tt0) cc_final: 0.5821 (tt0) REVERT: B 110 GLU cc_start: 0.7662 (tp30) cc_final: 0.7376 (mm-30) REVERT: B 135 ASP cc_start: 0.7470 (m-30) cc_final: 0.7256 (m-30) REVERT: C 146 ARG cc_start: 0.8218 (ttt180) cc_final: 0.7741 (ttt180) REVERT: C 149 ILE cc_start: 0.8619 (mt) cc_final: 0.8371 (mt) REVERT: D 129 LYS cc_start: 0.8469 (tppt) cc_final: 0.8121 (mmmm) REVERT: D 149 GLN cc_start: 0.7892 (mm110) cc_final: 0.7310 (mm110) REVERT: D 251 VAL cc_start: 0.8578 (m) cc_final: 0.8282 (t) REVERT: D 280 ASP cc_start: 0.8023 (t0) cc_final: 0.7694 (t0) REVERT: D 281 GLU cc_start: 0.7378 (mp0) cc_final: 0.7134 (mt-10) REVERT: D 325 TYR cc_start: 0.8781 (p90) cc_final: 0.8484 (p90) REVERT: D 374 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7169 (tm-30) REVERT: F 9 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: F 43 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8333 (ttp-110) REVERT: F 50 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7737 (mtpt) REVERT: G 51 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7760 (mmtt) REVERT: G 79 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7712 (mmtt) REVERT: G 143 ASP cc_start: 0.8722 (m-30) cc_final: 0.8514 (m-30) outliers start: 25 outliers final: 20 residues processed: 336 average time/residue: 0.3038 time to fit residues: 134.9241 Evaluate side-chains 342 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 321 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 98 PRO Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 117 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN D 173 GLN G 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122701 restraints weight = 43865.068| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.05 r_work: 0.3343 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11780 Z= 0.159 Angle : 0.545 6.042 16351 Z= 0.279 Chirality : 0.039 0.170 1908 Planarity : 0.005 0.084 1710 Dihedral : 20.333 177.618 2827 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.86 % Allowed : 21.98 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.24), residues: 1149 helix: 0.50 (0.27), residues: 359 sheet: -1.89 (0.37), residues: 178 loop : -1.14 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 64 TYR 0.008 0.001 TYR G 108 PHE 0.010 0.001 PHE B 128 TRP 0.014 0.001 TRP A 382 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00355 (11780) covalent geometry : angle 0.54470 (16351) hydrogen bonds : bond 0.04567 ( 403) hydrogen bonds : angle 5.36553 ( 995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 343 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 324 time to evaluate : 0.550 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: A 103 SER cc_start: 0.8370 (t) cc_final: 0.8161 (m) REVERT: A 255 ILE cc_start: 0.8097 (pt) cc_final: 0.7771 (mp) REVERT: A 338 VAL cc_start: 0.8444 (m) cc_final: 0.8133 (t) REVERT: B 75 TRP cc_start: 0.7929 (p90) cc_final: 0.7585 (p90) REVERT: B 103 GLU cc_start: 0.6054 (tt0) cc_final: 0.5755 (tt0) REVERT: C 141 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8315 (tt) REVERT: C 146 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7889 (ttt180) REVERT: C 149 ILE cc_start: 0.8623 (mt) cc_final: 0.8357 (mt) REVERT: D 129 LYS cc_start: 0.8429 (tppt) cc_final: 0.8073 (mmmm) REVERT: D 137 CYS cc_start: 0.8532 (m) cc_final: 0.8216 (m) REVERT: D 149 GLN cc_start: 0.7848 (mm110) cc_final: 0.7239 (mm110) REVERT: D 233 VAL cc_start: 0.8220 (t) cc_final: 0.7841 (m) REVERT: D 280 ASP cc_start: 0.7953 (t0) cc_final: 0.7569 (t0) REVERT: D 281 GLU cc_start: 0.7393 (mp0) cc_final: 0.7129 (mt-10) REVERT: D 325 TYR cc_start: 0.8698 (p90) cc_final: 0.8367 (p90) REVERT: D 374 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7236 (tm-30) REVERT: F 43 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.8256 (ttp-110) REVERT: F 50 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7791 (mtpt) REVERT: G 51 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7730 (mmtt) REVERT: G 79 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7611 (mmtt) REVERT: G 143 ASP cc_start: 0.8707 (m-30) cc_final: 0.8481 (m-30) outliers start: 19 outliers final: 15 residues processed: 332 average time/residue: 0.3103 time to fit residues: 135.9140 Evaluate side-chains 335 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 319 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN C 73 GLN D 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121747 restraints weight = 43771.144| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.05 r_work: 0.3337 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11780 Z= 0.188 Angle : 0.541 6.100 16351 Z= 0.278 Chirality : 0.039 0.164 1908 Planarity : 0.004 0.038 1710 Dihedral : 20.169 177.250 2799 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.16 % Allowed : 21.59 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.05 (0.24), residues: 1149 helix: 0.69 (0.28), residues: 358 sheet: -1.80 (0.36), residues: 184 loop : -1.16 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 114 TYR 0.010 0.001 TYR D 88 PHE 0.008 0.001 PHE D 218 TRP 0.014 0.001 TRP A 382 HIS 0.005 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00422 (11780) covalent geometry : angle 0.54067 (16351) hydrogen bonds : bond 0.04549 ( 403) hydrogen bonds : angle 5.10006 ( 995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 325 time to evaluate : 0.533 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: A 82 LYS cc_start: 0.8445 (mptp) cc_final: 0.8157 (mptp) REVERT: A 103 SER cc_start: 0.8413 (t) cc_final: 0.8194 (m) REVERT: A 255 ILE cc_start: 0.8084 (pt) cc_final: 0.7752 (mp) REVERT: A 338 VAL cc_start: 0.8409 (m) cc_final: 0.8097 (t) REVERT: B 73 TYR cc_start: 0.7070 (t80) cc_final: 0.6518 (t80) REVERT: C 43 LYS cc_start: 0.7783 (tptp) cc_final: 0.7542 (tptp) REVERT: C 141 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8293 (tt) REVERT: C 146 ARG cc_start: 0.8214 (ttt180) cc_final: 0.7886 (ttt180) REVERT: C 149 ILE cc_start: 0.8631 (mt) cc_final: 0.8379 (mt) REVERT: D 129 LYS cc_start: 0.8453 (tppt) cc_final: 0.8058 (mmmm) REVERT: D 137 CYS cc_start: 0.8431 (m) cc_final: 0.8102 (m) REVERT: D 149 GLN cc_start: 0.7853 (mm110) cc_final: 0.7281 (mm110) REVERT: D 280 ASP cc_start: 0.7933 (t0) cc_final: 0.7633 (t0) REVERT: D 281 GLU cc_start: 0.7383 (mp0) cc_final: 0.7118 (mt-10) REVERT: D 325 TYR cc_start: 0.8710 (p90) cc_final: 0.8393 (p90) REVERT: D 374 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7197 (tm-30) REVERT: F 43 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8275 (ttp-110) REVERT: F 50 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7794 (mtpt) REVERT: G 51 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7755 (mmtt) REVERT: G 79 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7643 (mmtm) outliers start: 22 outliers final: 19 residues processed: 333 average time/residue: 0.2935 time to fit residues: 129.9152 Evaluate side-chains 343 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 323 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN C 73 GLN D 173 GLN F 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121653 restraints weight = 43668.543| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.04 r_work: 0.3325 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11780 Z= 0.184 Angle : 0.536 6.044 16351 Z= 0.274 Chirality : 0.039 0.166 1908 Planarity : 0.004 0.038 1710 Dihedral : 20.127 177.125 2797 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.85 % Allowed : 20.71 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.24), residues: 1149 helix: 0.84 (0.28), residues: 357 sheet: -1.81 (0.36), residues: 174 loop : -1.12 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 114 TYR 0.012 0.001 TYR A 71 PHE 0.009 0.001 PHE B 98 TRP 0.014 0.001 TRP A 382 HIS 0.007 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00414 (11780) covalent geometry : angle 0.53614 (16351) hydrogen bonds : bond 0.04312 ( 403) hydrogen bonds : angle 4.88944 ( 995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 322 time to evaluate : 0.552 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: A 82 LYS cc_start: 0.8457 (mptp) cc_final: 0.8192 (mptp) REVERT: A 97 ASP cc_start: 0.7931 (t0) cc_final: 0.7520 (m-30) REVERT: A 103 SER cc_start: 0.8423 (t) cc_final: 0.8220 (m) REVERT: A 255 ILE cc_start: 0.8074 (pt) cc_final: 0.7752 (mp) REVERT: A 276 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 338 VAL cc_start: 0.8425 (m) cc_final: 0.8102 (t) REVERT: C 43 LYS cc_start: 0.7808 (tptp) cc_final: 0.7539 (tptp) REVERT: C 48 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8147 (mmtm) REVERT: C 141 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (tt) REVERT: C 146 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7900 (ttt180) REVERT: C 149 ILE cc_start: 0.8634 (mt) cc_final: 0.8383 (mt) REVERT: D 90 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7513 (mmtm) REVERT: D 101 ASN cc_start: 0.8138 (m110) cc_final: 0.7936 (m110) REVERT: D 129 LYS cc_start: 0.8467 (tppt) cc_final: 0.8110 (mmmm) REVERT: D 137 CYS cc_start: 0.8414 (m) cc_final: 0.8086 (m) REVERT: D 149 GLN cc_start: 0.7848 (mm110) cc_final: 0.7292 (mm110) REVERT: D 251 VAL cc_start: 0.8565 (m) cc_final: 0.8256 (t) REVERT: D 280 ASP cc_start: 0.7919 (t0) cc_final: 0.7650 (t0) REVERT: D 281 GLU cc_start: 0.7404 (mp0) cc_final: 0.7113 (mt-10) REVERT: D 325 TYR cc_start: 0.8713 (p90) cc_final: 0.8374 (p90) REVERT: D 374 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7218 (tm-30) REVERT: F 43 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8251 (ttp-110) REVERT: G 51 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7763 (mmtt) REVERT: G 61 ASN cc_start: 0.7504 (t0) cc_final: 0.7224 (t0) outliers start: 29 outliers final: 21 residues processed: 335 average time/residue: 0.3101 time to fit residues: 138.5160 Evaluate side-chains 341 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 319 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121128 restraints weight = 43464.092| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.03 r_work: 0.3343 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11780 Z= 0.207 Angle : 0.546 6.122 16351 Z= 0.279 Chirality : 0.039 0.168 1908 Planarity : 0.004 0.039 1710 Dihedral : 20.117 176.924 2786 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.45 % Allowed : 21.98 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1149 helix: 0.81 (0.28), residues: 358 sheet: -1.85 (0.36), residues: 174 loop : -1.13 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 114 TYR 0.012 0.001 TYR D 88 PHE 0.009 0.001 PHE D 218 TRP 0.016 0.001 TRP A 382 HIS 0.008 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00465 (11780) covalent geometry : angle 0.54591 (16351) hydrogen bonds : bond 0.04444 ( 403) hydrogen bonds : angle 4.88006 ( 995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 0.559 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: A 82 LYS cc_start: 0.8499 (mptp) cc_final: 0.8259 (mptp) REVERT: A 103 SER cc_start: 0.8402 (t) cc_final: 0.8115 (p) REVERT: A 255 ILE cc_start: 0.8067 (pt) cc_final: 0.7762 (mp) REVERT: A 276 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 331 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7879 (tp) REVERT: A 338 VAL cc_start: 0.8469 (m) cc_final: 0.8141 (t) REVERT: B 73 TYR cc_start: 0.7150 (t80) cc_final: 0.6639 (t80) REVERT: B 77 VAL cc_start: 0.8029 (t) cc_final: 0.7741 (m) REVERT: C 43 LYS cc_start: 0.7810 (tptp) cc_final: 0.7500 (tptp) REVERT: C 48 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8161 (mmtm) REVERT: C 141 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8274 (tt) REVERT: C 146 ARG cc_start: 0.8188 (ttt180) cc_final: 0.7893 (ttt180) REVERT: C 149 ILE cc_start: 0.8633 (mt) cc_final: 0.8393 (mt) REVERT: D 90 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7553 (mmtm) REVERT: D 101 ASN cc_start: 0.8140 (m110) cc_final: 0.7938 (m110) REVERT: D 129 LYS cc_start: 0.8446 (tppt) cc_final: 0.8081 (mmmm) REVERT: D 137 CYS cc_start: 0.8421 (m) cc_final: 0.8086 (m) REVERT: D 149 GLN cc_start: 0.7901 (mm110) cc_final: 0.7340 (mm110) REVERT: D 251 VAL cc_start: 0.8584 (m) cc_final: 0.8268 (t) REVERT: D 280 ASP cc_start: 0.7885 (t0) cc_final: 0.7619 (t0) REVERT: D 281 GLU cc_start: 0.7359 (mp0) cc_final: 0.7074 (mt-10) REVERT: D 325 TYR cc_start: 0.8712 (p90) cc_final: 0.8368 (p90) REVERT: D 374 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7154 (tm-30) REVERT: F 43 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8237 (ttp-110) REVERT: G 51 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7723 (mmtt) REVERT: G 61 ASN cc_start: 0.7615 (t0) cc_final: 0.7319 (t0) outliers start: 25 outliers final: 22 residues processed: 334 average time/residue: 0.3037 time to fit residues: 135.2771 Evaluate side-chains 346 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 322 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN D 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122482 restraints weight = 43670.961| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.03 r_work: 0.3356 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11780 Z= 0.131 Angle : 0.509 5.624 16351 Z= 0.257 Chirality : 0.038 0.160 1908 Planarity : 0.004 0.038 1710 Dihedral : 20.042 176.351 2786 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.06 % Allowed : 22.57 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.25), residues: 1149 helix: 1.08 (0.28), residues: 360 sheet: -1.82 (0.36), residues: 174 loop : -1.04 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 114 TYR 0.008 0.001 TYR D 88 PHE 0.007 0.001 PHE D 218 TRP 0.011 0.001 TRP A 382 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00295 (11780) covalent geometry : angle 0.50886 (16351) hydrogen bonds : bond 0.04011 ( 403) hydrogen bonds : angle 4.66455 ( 995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 327 time to evaluate : 0.541 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: A 69 ASN cc_start: 0.7630 (m-40) cc_final: 0.7421 (m-40) REVERT: A 82 LYS cc_start: 0.8468 (mptp) cc_final: 0.8210 (mptp) REVERT: A 97 ASP cc_start: 0.7985 (t0) cc_final: 0.7573 (m-30) REVERT: A 255 ILE cc_start: 0.8008 (pt) cc_final: 0.7706 (mp) REVERT: A 276 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 338 VAL cc_start: 0.8428 (m) cc_final: 0.8056 (t) REVERT: B 77 VAL cc_start: 0.8009 (t) cc_final: 0.7743 (m) REVERT: C 43 LYS cc_start: 0.7765 (tptp) cc_final: 0.7419 (tptp) REVERT: C 48 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8142 (mmtm) REVERT: C 76 LEU cc_start: 0.8590 (mt) cc_final: 0.8386 (mm) REVERT: C 141 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8284 (tt) REVERT: C 146 ARG cc_start: 0.8167 (ttt180) cc_final: 0.7869 (ttt180) REVERT: C 149 ILE cc_start: 0.8614 (mt) cc_final: 0.8374 (mt) REVERT: D 90 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7536 (mmtm) REVERT: D 129 LYS cc_start: 0.8446 (tppt) cc_final: 0.8072 (mmmm) REVERT: D 137 CYS cc_start: 0.8403 (m) cc_final: 0.8037 (m) REVERT: D 149 GLN cc_start: 0.7852 (mm110) cc_final: 0.7286 (mm110) REVERT: D 251 VAL cc_start: 0.8552 (m) cc_final: 0.8228 (t) REVERT: D 280 ASP cc_start: 0.7881 (t0) cc_final: 0.7643 (t0) REVERT: D 281 GLU cc_start: 0.7384 (mp0) cc_final: 0.7099 (mt-10) REVERT: D 325 TYR cc_start: 0.8694 (p90) cc_final: 0.8316 (p90) REVERT: D 374 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7162 (tm-30) REVERT: F 50 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7862 (mtpt) REVERT: G 51 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7668 (mmtt) REVERT: G 61 ASN cc_start: 0.7607 (t0) cc_final: 0.7278 (t0) outliers start: 21 outliers final: 18 residues processed: 336 average time/residue: 0.2928 time to fit residues: 131.4980 Evaluate side-chains 343 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 324 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.150952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119909 restraints weight = 43675.021| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.04 r_work: 0.3328 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 11780 Z= 0.304 Angle : 0.600 6.620 16351 Z= 0.308 Chirality : 0.042 0.180 1908 Planarity : 0.005 0.044 1710 Dihedral : 20.162 176.137 2783 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.65 % Allowed : 22.18 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -1.11 (0.24), residues: 1149 helix: 0.61 (0.27), residues: 358 sheet: -1.81 (0.36), residues: 184 loop : -1.18 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 114 TYR 0.017 0.002 TYR D 88 PHE 0.013 0.002 PHE A 218 TRP 0.021 0.002 TRP A 382 HIS 0.009 0.002 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00683 (11780) covalent geometry : angle 0.60021 (16351) hydrogen bonds : bond 0.04958 ( 403) hydrogen bonds : angle 4.98025 ( 995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 0.410 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: A 82 LYS cc_start: 0.8491 (mptp) cc_final: 0.8277 (mptp) REVERT: A 255 ILE cc_start: 0.8058 (pt) cc_final: 0.7758 (mp) REVERT: B 73 TYR cc_start: 0.7078 (t80) cc_final: 0.6810 (t80) REVERT: B 77 VAL cc_start: 0.8054 (t) cc_final: 0.7765 (m) REVERT: C 48 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8177 (mmtm) REVERT: C 76 LEU cc_start: 0.8623 (mt) cc_final: 0.8417 (mm) REVERT: C 141 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8317 (tt) REVERT: C 146 ARG cc_start: 0.8214 (ttt180) cc_final: 0.7917 (ttt180) REVERT: C 149 ILE cc_start: 0.8640 (mt) cc_final: 0.8388 (mt) REVERT: D 90 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7556 (mmtm) REVERT: D 101 ASN cc_start: 0.8145 (m110) cc_final: 0.7925 (m110) REVERT: D 129 LYS cc_start: 0.8469 (tppt) cc_final: 0.8108 (mmmm) REVERT: D 137 CYS cc_start: 0.8489 (m) cc_final: 0.8155 (m) REVERT: D 149 GLN cc_start: 0.7921 (mm110) cc_final: 0.7376 (mm110) REVERT: D 233 VAL cc_start: 0.8273 (t) cc_final: 0.7923 (m) REVERT: D 251 VAL cc_start: 0.8581 (m) cc_final: 0.8280 (t) REVERT: D 325 TYR cc_start: 0.8757 (p90) cc_final: 0.8436 (p90) REVERT: D 374 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7155 (tm-30) REVERT: F 43 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.8281 (ttp-110) REVERT: G 47 LYS cc_start: 0.8213 (tttm) cc_final: 0.7844 (tttm) REVERT: G 51 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7588 (mmtt) REVERT: G 61 ASN cc_start: 0.7702 (t0) cc_final: 0.7406 (t0) outliers start: 27 outliers final: 24 residues processed: 337 average time/residue: 0.2889 time to fit residues: 129.5333 Evaluate side-chains 348 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 283 TYR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121830 restraints weight = 43329.674| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.03 r_work: 0.3337 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11780 Z= 0.145 Angle : 0.528 7.105 16351 Z= 0.266 Chirality : 0.038 0.167 1908 Planarity : 0.004 0.040 1710 Dihedral : 20.059 175.365 2783 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.45 % Allowed : 23.36 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1149 helix: 0.95 (0.28), residues: 359 sheet: -1.78 (0.36), residues: 169 loop : -1.04 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 114 TYR 0.009 0.001 TYR D 88 PHE 0.008 0.001 PHE D 218 TRP 0.012 0.001 TRP A 382 HIS 0.003 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00324 (11780) covalent geometry : angle 0.52791 (16351) hydrogen bonds : bond 0.04134 ( 403) hydrogen bonds : angle 4.70143 ( 995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 326 time to evaluate : 0.484 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: A 69 ASN cc_start: 0.7649 (m-40) cc_final: 0.7444 (m-40) REVERT: A 82 LYS cc_start: 0.8468 (mptp) cc_final: 0.8236 (mptp) REVERT: A 97 ASP cc_start: 0.8000 (t0) cc_final: 0.7667 (m-30) REVERT: A 104 SER cc_start: 0.8222 (m) cc_final: 0.7891 (p) REVERT: A 255 ILE cc_start: 0.8033 (pt) cc_final: 0.7738 (mp) REVERT: A 329 ILE cc_start: 0.8345 (mm) cc_final: 0.7940 (mt) REVERT: A 338 VAL cc_start: 0.8447 (m) cc_final: 0.8113 (t) REVERT: B 73 TYR cc_start: 0.7160 (t80) cc_final: 0.6765 (t80) REVERT: B 77 VAL cc_start: 0.8042 (t) cc_final: 0.7786 (m) REVERT: B 110 GLU cc_start: 0.7615 (tp30) cc_final: 0.7142 (mm-30) REVERT: C 48 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8134 (mmtm) REVERT: C 76 LEU cc_start: 0.8599 (mt) cc_final: 0.8392 (mm) REVERT: C 141 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8302 (tt) REVERT: C 146 ARG cc_start: 0.8194 (ttt180) cc_final: 0.7897 (ttt180) REVERT: C 149 ILE cc_start: 0.8612 (mt) cc_final: 0.8354 (mt) REVERT: D 90 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7591 (mmtm) REVERT: D 129 LYS cc_start: 0.8453 (tppt) cc_final: 0.8091 (mmmm) REVERT: D 137 CYS cc_start: 0.8449 (m) cc_final: 0.8130 (m) REVERT: D 149 GLN cc_start: 0.7852 (mm110) cc_final: 0.7295 (mm110) REVERT: D 233 VAL cc_start: 0.8253 (t) cc_final: 0.7858 (m) REVERT: D 251 VAL cc_start: 0.8555 (m) cc_final: 0.8245 (t) REVERT: D 280 ASP cc_start: 0.7985 (t0) cc_final: 0.7748 (t0) REVERT: D 281 GLU cc_start: 0.7374 (mp0) cc_final: 0.7112 (mt-10) REVERT: D 283 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7483 (t80) REVERT: D 325 TYR cc_start: 0.8710 (p90) cc_final: 0.8355 (p90) REVERT: D 374 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7198 (tm-30) REVERT: G 51 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7562 (mmtt) REVERT: G 61 ASN cc_start: 0.7653 (t0) cc_final: 0.7362 (t0) outliers start: 25 outliers final: 22 residues processed: 337 average time/residue: 0.2773 time to fit residues: 125.3446 Evaluate side-chains 350 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 326 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 283 TYR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN D 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.151686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120651 restraints weight = 43483.644| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.03 r_work: 0.3324 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 11780 Z= 0.222 Angle : 0.564 8.268 16351 Z= 0.286 Chirality : 0.040 0.169 1908 Planarity : 0.004 0.042 1710 Dihedral : 20.097 174.883 2783 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.26 % Allowed : 23.95 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1149 helix: 0.80 (0.28), residues: 359 sheet: -1.79 (0.36), residues: 169 loop : -1.09 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 51 TYR 0.013 0.002 TYR D 88 PHE 0.009 0.001 PHE A 218 TRP 0.016 0.002 TRP A 382 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00499 (11780) covalent geometry : angle 0.56372 (16351) hydrogen bonds : bond 0.04551 ( 403) hydrogen bonds : angle 4.81360 ( 995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 346 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 323 time to evaluate : 0.587 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: A 82 LYS cc_start: 0.8497 (mptp) cc_final: 0.8281 (mptp) REVERT: A 104 SER cc_start: 0.8275 (m) cc_final: 0.7943 (p) REVERT: A 255 ILE cc_start: 0.8041 (pt) cc_final: 0.7755 (mp) REVERT: A 338 VAL cc_start: 0.8473 (m) cc_final: 0.8133 (t) REVERT: B 73 TYR cc_start: 0.7116 (t80) cc_final: 0.6806 (t80) REVERT: B 77 VAL cc_start: 0.8073 (t) cc_final: 0.7811 (m) REVERT: C 48 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8150 (mmtm) REVERT: C 141 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8299 (tt) REVERT: C 146 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7896 (ttt180) REVERT: C 149 ILE cc_start: 0.8614 (mt) cc_final: 0.8353 (mt) REVERT: D 90 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7619 (mmtm) REVERT: D 129 LYS cc_start: 0.8460 (tppt) cc_final: 0.8075 (mmmm) REVERT: D 137 CYS cc_start: 0.8494 (m) cc_final: 0.8164 (m) REVERT: D 149 GLN cc_start: 0.7884 (mm110) cc_final: 0.7354 (mm110) REVERT: D 233 VAL cc_start: 0.8279 (t) cc_final: 0.7915 (m) REVERT: D 280 ASP cc_start: 0.8006 (t0) cc_final: 0.7789 (t0) REVERT: D 281 GLU cc_start: 0.7340 (mp0) cc_final: 0.7078 (mt-10) REVERT: D 283 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7527 (t80) REVERT: D 325 TYR cc_start: 0.8723 (p90) cc_final: 0.8387 (p90) REVERT: D 374 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7167 (tm-30) REVERT: F 43 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.8246 (ttp-110) REVERT: G 51 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7568 (mmtt) REVERT: G 61 ASN cc_start: 0.7692 (t0) cc_final: 0.7403 (t0) outliers start: 23 outliers final: 21 residues processed: 333 average time/residue: 0.2995 time to fit residues: 133.0588 Evaluate side-chains 345 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 322 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 283 TYR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121257 restraints weight = 43873.981| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.04 r_work: 0.3329 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11780 Z= 0.168 Angle : 0.538 8.415 16351 Z= 0.272 Chirality : 0.039 0.166 1908 Planarity : 0.004 0.041 1710 Dihedral : 20.035 173.970 2783 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.36 % Allowed : 23.75 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1149 helix: 1.00 (0.28), residues: 359 sheet: -1.80 (0.36), residues: 169 loop : -1.03 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 114 TYR 0.011 0.001 TYR D 88 PHE 0.011 0.001 PHE B 152 TRP 0.012 0.001 TRP A 382 HIS 0.005 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00375 (11780) covalent geometry : angle 0.53815 (16351) hydrogen bonds : bond 0.04218 ( 403) hydrogen bonds : angle 4.68139 ( 995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 63 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 323 time to evaluate : 0.554 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: A 82 LYS cc_start: 0.8499 (mptp) cc_final: 0.8287 (mptp) REVERT: A 97 ASP cc_start: 0.8015 (t0) cc_final: 0.7658 (m-30) REVERT: A 104 SER cc_start: 0.8194 (m) cc_final: 0.7866 (p) REVERT: A 255 ILE cc_start: 0.8011 (pt) cc_final: 0.7726 (mp) REVERT: A 270 ASP cc_start: 0.7777 (m-30) cc_final: 0.7461 (m-30) REVERT: A 329 ILE cc_start: 0.8403 (mm) cc_final: 0.8000 (mt) REVERT: A 338 VAL cc_start: 0.8452 (m) cc_final: 0.8098 (t) REVERT: A 357 MET cc_start: 0.7896 (mtm) cc_final: 0.7680 (mtp) REVERT: B 73 TYR cc_start: 0.7164 (t80) cc_final: 0.6815 (t80) REVERT: B 77 VAL cc_start: 0.8072 (t) cc_final: 0.7810 (m) REVERT: B 110 GLU cc_start: 0.7618 (tp30) cc_final: 0.7144 (mm-30) REVERT: C 48 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8124 (mmtm) REVERT: C 141 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8298 (tt) REVERT: C 146 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7886 (ttt180) REVERT: C 149 ILE cc_start: 0.8599 (mt) cc_final: 0.8337 (mt) REVERT: D 90 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7622 (mmtm) REVERT: D 129 LYS cc_start: 0.8444 (tppt) cc_final: 0.8086 (mmmm) REVERT: D 137 CYS cc_start: 0.8461 (m) cc_final: 0.8135 (m) REVERT: D 149 GLN cc_start: 0.7863 (mm110) cc_final: 0.7322 (mm110) REVERT: D 233 VAL cc_start: 0.8261 (t) cc_final: 0.7861 (m) REVERT: D 251 VAL cc_start: 0.8583 (m) cc_final: 0.8279 (t) REVERT: D 280 ASP cc_start: 0.8006 (t0) cc_final: 0.7778 (t0) REVERT: D 281 GLU cc_start: 0.7370 (mp0) cc_final: 0.7105 (mt-10) REVERT: D 283 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7543 (t80) REVERT: D 325 TYR cc_start: 0.8710 (p90) cc_final: 0.8357 (p90) REVERT: D 343 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7532 (mt-10) REVERT: D 374 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7214 (tm-30) REVERT: G 51 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7556 (mmtt) REVERT: G 61 ASN cc_start: 0.7672 (t0) cc_final: 0.7402 (t0) outliers start: 24 outliers final: 21 residues processed: 334 average time/residue: 0.3084 time to fit residues: 137.0943 Evaluate side-chains 343 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 177 LYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 283 TYR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 13 ARG Chi-restraints excluded: chain H residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 20 optimal weight: 0.0270 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN D 69 ASN D 101 ASN G 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.153988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123069 restraints weight = 43503.212| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.03 r_work: 0.3369 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11780 Z= 0.103 Angle : 0.510 8.430 16351 Z= 0.254 Chirality : 0.037 0.149 1908 Planarity : 0.004 0.042 1710 Dihedral : 19.900 176.871 2783 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.67 % Allowed : 24.34 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1149 helix: 1.31 (0.29), residues: 360 sheet: -1.85 (0.37), residues: 162 loop : -0.93 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 114 TYR 0.007 0.001 TYR D 88 PHE 0.007 0.001 PHE B 152 TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.00234 (11780) covalent geometry : angle 0.50982 (16351) hydrogen bonds : bond 0.03859 ( 403) hydrogen bonds : angle 4.46053 ( 995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6658.76 seconds wall clock time: 113 minutes 33.52 seconds (6813.52 seconds total)