Starting phenix.real_space_refine on Thu Jan 16 22:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjq_39346/01_2025/8yjq_39346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjq_39346/01_2025/8yjq_39346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjq_39346/01_2025/8yjq_39346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjq_39346/01_2025/8yjq_39346.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjq_39346/01_2025/8yjq_39346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjq_39346/01_2025/8yjq_39346.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 300 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 63 5.16 5 C 6024 2.51 5 N 1652 2.21 5 O 2059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9856 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2769 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "J" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 576 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Time building chain proxies: 6.20, per 1000 atoms: 0.63 Number of scatterers: 9856 At special positions: 0 Unit cell: (106.24, 104.58, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 58 15.00 O 2059 8.00 N 1652 7.00 C 6024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 28.3% alpha, 26.0% beta 14 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.679A pdb=" N ALA D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.630A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 removed outlier: 3.744A pdb=" N VAL D 131 " --> pdb=" O LYS D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 128 through 131' Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.564A pdb=" N GLU D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 149 removed outlier: 3.819A pdb=" N LEU D 145 " --> pdb=" O CYS D 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 147 " --> pdb=" O HIS D 143 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.595A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.950A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 219 through 230 removed outlier: 4.133A pdb=" N ASP D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.668A pdb=" N VAL D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASP D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.702A pdb=" N VAL D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 261' Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 304 through 310 removed outlier: 3.744A pdb=" N LYS D 308 " --> pdb=" O GLU D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 330 removed outlier: 3.609A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.646A pdb=" N ASP D 342 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.600A pdb=" N ALA A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.902A pdb=" N ARG A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.734A pdb=" N ALA A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.737A pdb=" N PHE A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'C' and resid 9 through 17 removed outlier: 3.657A pdb=" N LEU C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.558A pdb=" N VAL B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 216 removed outlier: 3.852A pdb=" N PHE B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.572A pdb=" N ALA D 175 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL D 31 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL D 84 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 33 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 336 through 337 removed outlier: 4.007A pdb=" N THR D 336 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 345 through 349 removed outlier: 4.409A pdb=" N LYS D 345 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN C 125 " --> pdb=" O THR D 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.601A pdb=" N THR A 59 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 4 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 100 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 99 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C 166 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 71 removed outlier: 3.793A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 26 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 251 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 235 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.518A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 180 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 111 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE B 2 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.937A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 205 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 66 through 71 removed outlier: 7.284A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.647A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2964 1.34 - 1.46: 2398 1.46 - 1.58: 4546 1.58 - 1.71: 113 1.71 - 1.83: 102 Bond restraints: 10123 Sorted by residual: bond pdb=" CA ALA D 176 " pdb=" CB ALA D 176 " ideal model delta sigma weight residual 1.524 1.486 0.037 1.30e-02 5.92e+03 8.14e+00 bond pdb=" N PHE D 85 " pdb=" CA PHE D 85 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.17e-02 7.31e+03 7.70e+00 bond pdb=" N ASP D 86 " pdb=" CA ASP D 86 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" CB ASN A 24 " pdb=" CG ASN A 24 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.39e+00 bond pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.14e+00 ... (remaining 10118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 13489 2.49 - 4.99: 332 4.99 - 7.48: 58 7.48 - 9.98: 23 9.98 - 12.47: 4 Bond angle restraints: 13906 Sorted by residual: angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 134.01 -12.47 1.91e+00 2.74e-01 4.26e+01 angle pdb=" C LYS D 314 " pdb=" N GLN D 315 " pdb=" CA GLN D 315 " ideal model delta sigma weight residual 122.36 129.01 -6.65 1.42e+00 4.96e-01 2.20e+01 angle pdb=" C ALA C 242 " pdb=" N ASP C 243 " pdb=" CA ASP C 243 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" N THR A 219 " pdb=" CA THR A 219 " pdb=" C THR A 219 " ideal model delta sigma weight residual 109.81 118.92 -9.11 2.21e+00 2.05e-01 1.70e+01 angle pdb=" CB MET A 119 " pdb=" CG MET A 119 " pdb=" SD MET A 119 " ideal model delta sigma weight residual 112.70 124.81 -12.11 3.00e+00 1.11e-01 1.63e+01 ... (remaining 13901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5046 17.91 - 35.82: 722 35.82 - 53.73: 285 53.73 - 71.64: 64 71.64 - 89.55: 12 Dihedral angle restraints: 6129 sinusoidal: 2883 harmonic: 3246 Sorted by residual: dihedral pdb=" CA MET C 139 " pdb=" C MET C 139 " pdb=" N PRO C 140 " pdb=" CA PRO C 140 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PRO D 81 " pdb=" C PRO D 81 " pdb=" N VAL D 82 " pdb=" CA VAL D 82 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ILE D 33 " pdb=" C ILE D 33 " pdb=" N ASP D 34 " pdb=" CA ASP D 34 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1310 0.061 - 0.121: 236 0.121 - 0.182: 41 0.182 - 0.243: 9 0.243 - 0.303: 4 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CB ILE B 128 " pdb=" CA ILE B 128 " pdb=" CG1 ILE B 128 " pdb=" CG2 ILE B 128 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB ILE A 128 " pdb=" CA ILE A 128 " pdb=" CG1 ILE A 128 " pdb=" CG2 ILE A 128 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASP A 243 " pdb=" N ASP A 243 " pdb=" C ASP A 243 " pdb=" CB ASP A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1597 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 207 " -0.015 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE B 207 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 207 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 207 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE B 207 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 207 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 207 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 128 " -0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO B 129 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 220 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.045 5.00e-02 4.00e+02 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 3210 2.87 - 3.38: 8198 3.38 - 3.89: 17220 3.89 - 4.39: 19050 4.39 - 4.90: 32017 Nonbonded interactions: 79695 Sorted by model distance: nonbonded pdb=" OD2 ASP A 41 " pdb=" OG SER A 43 " model vdw 2.366 3.040 nonbonded pdb=" OE1 GLU D 158 " pdb=" OH TYR D 234 " model vdw 2.378 3.040 nonbonded pdb=" OG SER A 222 " pdb=" O THR A 224 " model vdw 2.379 3.040 nonbonded pdb=" OG SER A 141 " pdb=" O SER A 222 " model vdw 2.392 3.040 nonbonded pdb=" ND2 ASN D 302 " pdb=" OE1 GLU D 305 " model vdw 2.433 3.120 ... (remaining 79690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 1 through 254) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.320 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.010 Set scattering table: 0.090 Process input model: 28.510 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10123 Z= 0.326 Angle : 0.971 12.473 13906 Z= 0.492 Chirality : 0.054 0.303 1600 Planarity : 0.007 0.081 1590 Dihedral : 19.575 89.548 4014 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.20), residues: 1107 helix: -4.24 (0.13), residues: 289 sheet: -1.66 (0.27), residues: 327 loop : -1.82 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 28 HIS 0.002 0.001 HIS D 280 PHE 0.052 0.003 PHE B 207 TYR 0.054 0.003 TYR A 249 ARG 0.010 0.001 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.115 Fit side-chains REVERT: D 21 ASN cc_start: 0.7921 (m110) cc_final: 0.7675 (m-40) REVERT: D 189 VAL cc_start: 0.9002 (t) cc_final: 0.8627 (p) REVERT: A 125 GLN cc_start: 0.7939 (pp30) cc_final: 0.7665 (pp30) REVERT: B 59 THR cc_start: 0.8043 (m) cc_final: 0.7586 (p) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2040 time to fit residues: 42.7214 Evaluate side-chains 107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN A 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.161264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.127953 restraints weight = 13974.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.133858 restraints weight = 7814.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.134690 restraints weight = 4715.126| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10123 Z= 0.237 Angle : 0.586 6.551 13906 Z= 0.323 Chirality : 0.043 0.146 1600 Planarity : 0.005 0.055 1590 Dihedral : 20.727 79.009 1871 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.24 % Allowed : 8.26 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.22), residues: 1107 helix: -2.21 (0.23), residues: 309 sheet: -1.59 (0.27), residues: 322 loop : -1.41 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.003 0.001 HIS C 44 PHE 0.020 0.001 PHE D 207 TYR 0.014 0.002 TYR D 26 ARG 0.002 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.061 Fit side-chains REVERT: B 75 MET cc_start: 0.8819 (tpp) cc_final: 0.7952 (ttt) REVERT: B 143 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7109 (mm-30) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.2206 time to fit residues: 40.8353 Evaluate side-chains 104 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 HIS ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 71 ASN C 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.155923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121111 restraints weight = 13941.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.125432 restraints weight = 7600.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.128139 restraints weight = 5114.218| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10123 Z= 0.296 Angle : 0.594 6.505 13906 Z= 0.322 Chirality : 0.044 0.145 1600 Planarity : 0.004 0.046 1590 Dihedral : 20.609 81.093 1871 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.86 % Allowed : 11.25 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1107 helix: -1.02 (0.27), residues: 312 sheet: -1.98 (0.25), residues: 330 loop : -1.07 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 28 HIS 0.003 0.001 HIS C 44 PHE 0.020 0.002 PHE D 207 TYR 0.019 0.002 TYR D 26 ARG 0.002 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.068 Fit side-chains REVERT: D 86 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: A 124 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: A 146 ARG cc_start: 0.7872 (ptp90) cc_final: 0.7584 (ptp-170) REVERT: B 75 MET cc_start: 0.8858 (tpp) cc_final: 0.8182 (ttt) outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 0.2532 time to fit residues: 42.2313 Evaluate side-chains 107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN C 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.155319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.120980 restraints weight = 13706.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.125201 restraints weight = 7475.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127831 restraints weight = 5024.536| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10123 Z= 0.266 Angle : 0.564 5.986 13906 Z= 0.306 Chirality : 0.043 0.144 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.555 77.713 1871 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.06 % Allowed : 14.45 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.24), residues: 1107 helix: -0.60 (0.28), residues: 317 sheet: -1.97 (0.25), residues: 328 loop : -0.97 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 274 HIS 0.006 0.001 HIS D 276 PHE 0.018 0.001 PHE D 207 TYR 0.016 0.001 TYR D 26 ARG 0.004 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.039 Fit side-chains REVERT: D 148 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.5821 (mmt) REVERT: C 115 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: B 75 MET cc_start: 0.8845 (tpp) cc_final: 0.8139 (ttt) outliers start: 20 outliers final: 11 residues processed: 111 average time/residue: 0.2389 time to fit residues: 37.0977 Evaluate side-chains 107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.155985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121632 restraints weight = 13768.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.125921 restraints weight = 7460.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.128615 restraints weight = 4991.546| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10123 Z= 0.230 Angle : 0.544 6.626 13906 Z= 0.296 Chirality : 0.043 0.145 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.380 76.295 1871 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.37 % Allowed : 15.38 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.24), residues: 1107 helix: -0.11 (0.30), residues: 311 sheet: -1.97 (0.25), residues: 331 loop : -0.81 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.006 0.001 HIS D 276 PHE 0.016 0.001 PHE D 207 TYR 0.015 0.001 TYR D 26 ARG 0.004 0.000 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.072 Fit side-chains REVERT: D 40 TYR cc_start: 0.8748 (m-80) cc_final: 0.8482 (m-80) REVERT: D 148 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6065 (mmt) REVERT: C 115 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: B 198 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7432 (mp0) outliers start: 23 outliers final: 12 residues processed: 113 average time/residue: 0.2468 time to fit residues: 39.6726 Evaluate side-chains 108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 105 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 GLN C 38 GLN C 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.157178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.123089 restraints weight = 13862.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.127355 restraints weight = 7453.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.130060 restraints weight = 4982.775| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10123 Z= 0.193 Angle : 0.536 10.771 13906 Z= 0.289 Chirality : 0.042 0.144 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.306 74.813 1871 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.17 % Allowed : 16.00 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1107 helix: 0.13 (0.30), residues: 310 sheet: -1.81 (0.25), residues: 338 loop : -0.70 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 28 HIS 0.006 0.001 HIS D 276 PHE 0.014 0.001 PHE D 207 TYR 0.013 0.001 TYR D 26 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.067 Fit side-chains REVERT: D 40 TYR cc_start: 0.8737 (m-80) cc_final: 0.8453 (m-80) REVERT: D 148 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.5855 (mmt) REVERT: A 59 THR cc_start: 0.7925 (p) cc_final: 0.7695 (p) REVERT: A 196 THR cc_start: 0.7871 (m) cc_final: 0.7618 (p) REVERT: A 239 TYR cc_start: 0.8960 (m-80) cc_final: 0.8590 (m-80) REVERT: C 115 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: B 198 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7436 (mp0) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 0.2564 time to fit residues: 39.4798 Evaluate side-chains 106 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.141354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106506 restraints weight = 14937.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109721 restraints weight = 11792.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111375 restraints weight = 6879.893| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10123 Z= 0.236 Angle : 0.553 8.199 13906 Z= 0.296 Chirality : 0.043 0.143 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.250 76.285 1871 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.48 % Allowed : 16.31 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.25), residues: 1107 helix: 0.23 (0.30), residues: 310 sheet: -1.77 (0.25), residues: 334 loop : -0.63 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.005 0.001 HIS D 276 PHE 0.016 0.001 PHE D 207 TYR 0.015 0.001 TYR D 26 ARG 0.008 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 1.041 Fit side-chains REVERT: D 40 TYR cc_start: 0.8749 (m-80) cc_final: 0.8499 (m-80) REVERT: D 148 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.6210 (mmt) REVERT: A 59 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7788 (p) REVERT: A 239 TYR cc_start: 0.9013 (m-80) cc_final: 0.8646 (m-80) REVERT: C 115 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: B 198 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7460 (mp0) outliers start: 24 outliers final: 14 residues processed: 106 average time/residue: 0.2425 time to fit residues: 36.1107 Evaluate side-chains 108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.139871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105133 restraints weight = 14838.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108970 restraints weight = 8240.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111490 restraints weight = 5664.238| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10123 Z= 0.218 Angle : 0.547 8.371 13906 Z= 0.293 Chirality : 0.042 0.147 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.239 76.599 1871 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.17 % Allowed : 17.03 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1107 helix: 0.35 (0.30), residues: 308 sheet: -1.71 (0.25), residues: 333 loop : -0.61 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.005 0.001 HIS D 276 PHE 0.015 0.001 PHE D 207 TYR 0.014 0.001 TYR D 26 ARG 0.007 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 1.131 Fit side-chains REVERT: D 40 TYR cc_start: 0.8713 (m-80) cc_final: 0.8358 (m-80) REVERT: D 148 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6110 (mmt) REVERT: A 59 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7783 (p) REVERT: A 146 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7585 (ttm110) REVERT: A 196 THR cc_start: 0.7867 (m) cc_final: 0.7548 (p) REVERT: A 239 TYR cc_start: 0.9024 (m-80) cc_final: 0.8660 (m-80) REVERT: C 115 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: B 198 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7436 (mp0) outliers start: 21 outliers final: 16 residues processed: 106 average time/residue: 0.2468 time to fit residues: 36.5327 Evaluate side-chains 112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.139566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.104842 restraints weight = 14877.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108712 restraints weight = 8275.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111241 restraints weight = 5648.834| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10123 Z= 0.228 Angle : 0.557 7.915 13906 Z= 0.297 Chirality : 0.043 0.144 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.250 77.158 1871 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.37 % Allowed : 17.13 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.25), residues: 1107 helix: 0.35 (0.30), residues: 308 sheet: -1.69 (0.25), residues: 327 loop : -0.67 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.005 0.001 HIS D 276 PHE 0.015 0.001 PHE D 207 TYR 0.014 0.001 TYR D 26 ARG 0.007 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.032 Fit side-chains REVERT: D 40 TYR cc_start: 0.8733 (m-80) cc_final: 0.8352 (m-80) REVERT: D 148 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6080 (mmt) REVERT: A 59 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7791 (p) REVERT: A 196 THR cc_start: 0.7864 (m) cc_final: 0.7544 (p) REVERT: A 239 TYR cc_start: 0.9030 (m-80) cc_final: 0.8668 (m-80) REVERT: C 115 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7242 (mt-10) REVERT: B 8 GLN cc_start: 0.7090 (pm20) cc_final: 0.6879 (pm20) REVERT: B 198 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7441 (mp0) outliers start: 23 outliers final: 17 residues processed: 105 average time/residue: 0.2417 time to fit residues: 35.7087 Evaluate side-chains 111 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.0010 chunk 59 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 64 optimal weight: 0.0270 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.141091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106365 restraints weight = 14742.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.110162 restraints weight = 8150.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.112764 restraints weight = 5604.363| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10123 Z= 0.189 Angle : 0.541 7.832 13906 Z= 0.289 Chirality : 0.042 0.162 1600 Planarity : 0.003 0.045 1590 Dihedral : 20.235 77.977 1871 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.06 % Allowed : 18.06 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1107 helix: 0.47 (0.31), residues: 305 sheet: -1.57 (0.25), residues: 341 loop : -0.62 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.004 0.001 HIS D 276 PHE 0.014 0.001 PHE D 207 TYR 0.012 0.001 TYR D 26 ARG 0.006 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.044 Fit side-chains REVERT: D 40 TYR cc_start: 0.8715 (m-80) cc_final: 0.8358 (m-80) REVERT: D 148 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.5993 (mmt) REVERT: A 59 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7829 (p) REVERT: A 196 THR cc_start: 0.7821 (m) cc_final: 0.7512 (p) REVERT: A 239 TYR cc_start: 0.9020 (m-80) cc_final: 0.8654 (m-80) REVERT: C 115 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: B 198 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7383 (mp0) outliers start: 20 outliers final: 14 residues processed: 111 average time/residue: 0.2281 time to fit residues: 36.2283 Evaluate side-chains 112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 311 CYS Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108032 restraints weight = 14748.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111768 restraints weight = 8080.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112753 restraints weight = 5717.736| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10123 Z= 0.183 Angle : 0.541 7.677 13906 Z= 0.288 Chirality : 0.042 0.174 1600 Planarity : 0.003 0.045 1590 Dihedral : 20.217 77.396 1871 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.96 % Allowed : 18.58 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1107 helix: 0.48 (0.31), residues: 305 sheet: -1.55 (0.25), residues: 346 loop : -0.61 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 28 HIS 0.004 0.000 HIS D 276 PHE 0.030 0.001 PHE A 207 TYR 0.012 0.001 TYR D 26 ARG 0.006 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2983.24 seconds wall clock time: 54 minutes 46.87 seconds (3286.87 seconds total)