Starting phenix.real_space_refine on Sun Dec 29 06:51:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjq_39346/12_2024/8yjq_39346.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjq_39346/12_2024/8yjq_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_39346/12_2024/8yjq_39346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjq_39346/12_2024/8yjq_39346.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjq_39346/12_2024/8yjq_39346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjq_39346/12_2024/8yjq_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-5532/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: 6.92, per 1000 atoms: 0.70 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 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: 3.44 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: 3.39 Time building geometry restraints manager: 2.90 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- 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 : 1.070 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: 0.2065 time to fit residues: 43.1824 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 : 1.056 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.970 Fit side-chains REVERT: A 146 ARG cc_start: 0.7657 (ptp90) cc_final: 0.7448 (ptp90) REVERT: B 75 MET cc_start: 0.8848 (tpp) cc_final: 0.7999 (ttt) REVERT: B 143 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7143 (mm-30) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.2202 time to fit residues: 40.6259 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 : 1.132 ------------------------------------------------------------------------------- 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 57 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 HIS C 38 GLN C 71 ASN C 108 GLN C 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10123 Z= 0.341 Angle : 0.623 6.765 13906 Z= 0.336 Chirality : 0.044 0.147 1600 Planarity : 0.004 0.046 1590 Dihedral : 20.653 81.310 1871 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.37 % Allowed : 11.87 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.23), residues: 1107 helix: -1.08 (0.27), residues: 312 sheet: -2.02 (0.25), residues: 331 loop : -1.10 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 28 HIS 0.004 0.001 HIS C 44 PHE 0.020 0.002 PHE D 207 TYR 0.020 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 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.031 Fit side-chains REVERT: D 86 ASP cc_start: 0.5733 (OUTLIER) cc_final: 0.5061 (m-30) REVERT: A 38 GLN cc_start: 0.7561 (mp10) cc_final: 0.7161 (mp10) REVERT: A 124 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: C 115 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: B 75 MET cc_start: 0.8904 (tpp) cc_final: 0.8269 (ttt) outliers start: 23 outliers final: 12 residues processed: 126 average time/residue: 0.2369 time to fit residues: 41.1522 Evaluate side-chains 114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 7 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 11 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3280 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= 0.285 Angle : 0.576 6.242 13906 Z= 0.312 Chirality : 0.043 0.149 1600 Planarity : 0.003 0.045 1590 Dihedral : 20.610 78.189 1871 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.06 % Allowed : 14.96 % Favored : 82.97 % 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: -2.00 (0.24), residues: 1107 helix: -0.63 (0.28), residues: 318 sheet: -2.08 (0.26), residues: 316 loop : -1.05 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.007 0.001 HIS D 276 PHE 0.018 0.001 PHE D 207 TYR 0.017 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 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.050 Fit side-chains REVERT: D 148 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.5970 (mmt) REVERT: A 59 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7619 (p) REVERT: B 75 MET cc_start: 0.8900 (tpp) cc_final: 0.8206 (ttt) outliers start: 20 outliers final: 10 residues processed: 112 average time/residue: 0.2459 time to fit residues: 38.1708 Evaluate side-chains 111 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain B residue 159 VAL 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 91 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 1 optimal weight: 0.0270 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 56 optimal weight: 0.0170 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3348 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= 0.170 Angle : 0.521 6.630 13906 Z= 0.285 Chirality : 0.042 0.144 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.385 76.050 1871 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.86 % Allowed : 16.00 % Favored : 82.15 % 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: -1.57 (0.24), residues: 1107 helix: -0.07 (0.30), residues: 310 sheet: -1.89 (0.25), residues: 338 loop : -0.82 (0.28), residues: 459 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 0.014 0.001 PHE D 207 TYR 0.012 0.001 TYR D 26 ARG 0.003 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 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.054 Fit side-chains REVERT: D 40 TYR cc_start: 0.8681 (m-80) cc_final: 0.8436 (m-80) REVERT: D 148 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.5761 (mmt) REVERT: A 59 THR cc_start: 0.7886 (p) cc_final: 0.7629 (p) REVERT: A 196 THR cc_start: 0.7829 (m) cc_final: 0.7500 (p) REVERT: C 115 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: B 198 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7389 (mp0) outliers start: 18 outliers final: 8 residues processed: 122 average time/residue: 0.2407 time to fit residues: 40.7657 Evaluate side-chains 108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 148 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 139 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 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 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.0040 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10123 Z= 0.198 Angle : 0.541 10.425 13906 Z= 0.290 Chirality : 0.042 0.142 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.291 74.993 1871 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.27 % Allowed : 16.72 % Favored : 81.01 % 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: -1.37 (0.24), residues: 1107 helix: 0.15 (0.30), residues: 310 sheet: -1.84 (0.25), residues: 333 loop : -0.68 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.006 0.001 HIS D 276 PHE 0.015 0.001 PHE D 207 TYR 0.013 0.001 TYR D 26 ARG 0.008 0.000 ARG B 64 *********************** 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 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.057 Fit side-chains REVERT: D 40 TYR cc_start: 0.8711 (m-80) cc_final: 0.8434 (m-80) REVERT: D 148 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.5926 (mmt) REVERT: A 59 THR cc_start: 0.7966 (p) cc_final: 0.7713 (p) REVERT: A 196 THR cc_start: 0.7763 (m) cc_final: 0.7511 (p) REVERT: A 239 TYR cc_start: 0.9008 (m-80) cc_final: 0.8632 (m-80) REVERT: C 115 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: B 198 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7427 (mp0) outliers start: 22 outliers final: 10 residues processed: 112 average time/residue: 0.2347 time to fit residues: 36.9384 Evaluate side-chains 108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.4980 chunk 12 optimal weight: 0.0570 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10123 Z= 0.189 Angle : 0.536 8.941 13906 Z= 0.287 Chirality : 0.042 0.142 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.212 73.972 1871 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.17 % Allowed : 16.82 % Favored : 81.01 % 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: -1.10 (0.25), residues: 1107 helix: 0.32 (0.30), residues: 307 sheet: -1.39 (0.24), residues: 376 loop : -0.63 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 28 HIS 0.005 0.001 HIS D 276 PHE 0.014 0.001 PHE D 207 TYR 0.013 0.001 TYR D 26 ARG 0.005 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 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.320 Fit side-chains REVERT: D 148 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.5726 (mmt) REVERT: A 59 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7740 (p) REVERT: A 196 THR cc_start: 0.7740 (m) cc_final: 0.7502 (p) REVERT: A 239 TYR cc_start: 0.8990 (m-80) cc_final: 0.8610 (m-80) REVERT: C 115 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: B 198 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7423 (mp0) outliers start: 21 outliers final: 12 residues processed: 110 average time/residue: 0.2602 time to fit residues: 41.0427 Evaluate side-chains 110 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 69 optimal weight: 0.1980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.0060 chunk 105 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10123 Z= 0.176 Angle : 0.529 8.325 13906 Z= 0.284 Chirality : 0.041 0.139 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.181 75.520 1871 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.96 % Allowed : 17.75 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1107 helix: 0.42 (0.31), residues: 305 sheet: -1.25 (0.25), residues: 374 loop : -0.62 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 28 HIS 0.006 0.001 HIS D 276 PHE 0.014 0.001 PHE D 207 TYR 0.012 0.001 TYR D 26 ARG 0.005 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 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.993 Fit side-chains REVERT: D 40 TYR cc_start: 0.8677 (m-80) cc_final: 0.8408 (m-80) REVERT: D 148 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.5676 (mmt) REVERT: A 59 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 239 TYR cc_start: 0.8990 (m-80) cc_final: 0.8627 (m-80) REVERT: C 115 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: C 229 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7863 (mtp) REVERT: B 198 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7378 (mp0) outliers start: 19 outliers final: 11 residues processed: 118 average time/residue: 0.2155 time to fit residues: 36.2285 Evaluate side-chains 113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 255 SER 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 C residue 229 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 VAL 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 96 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10123 Z= 0.310 Angle : 0.608 8.170 13906 Z= 0.321 Chirality : 0.044 0.187 1600 Planarity : 0.003 0.043 1590 Dihedral : 20.288 76.207 1871 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.06 % Allowed : 18.27 % Favored : 79.67 % 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: -1.15 (0.25), residues: 1107 helix: 0.42 (0.31), residues: 300 sheet: -1.53 (0.24), residues: 366 loop : -0.67 (0.29), residues: 441 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 0.018 0.002 PHE D 207 TYR 0.017 0.002 TYR D 26 ARG 0.005 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 118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.039 Fit side-chains REVERT: D 40 TYR cc_start: 0.8753 (m-80) cc_final: 0.8426 (m-80) REVERT: D 86 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.5237 (m-30) REVERT: D 148 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6151 (mmt) REVERT: A 59 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7779 (p) REVERT: A 239 TYR cc_start: 0.9022 (m-80) cc_final: 0.8640 (m-80) REVERT: C 115 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: C 229 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7855 (mtp) REVERT: B 198 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7496 (mp0) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 0.2521 time to fit residues: 38.5967 Evaluate side-chains 115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 86 ASP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 255 SER 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 C residue 229 MET 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 Chi-restraints excluded: chain B residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4070 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= 0.265 Angle : 0.585 7.593 13906 Z= 0.310 Chirality : 0.043 0.175 1600 Planarity : 0.003 0.044 1590 Dihedral : 20.327 77.039 1871 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.27 % Allowed : 18.27 % 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: -1.18 (0.25), residues: 1107 helix: 0.34 (0.30), residues: 305 sheet: -1.52 (0.25), residues: 362 loop : -0.71 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.001 HIS A 246 PHE 0.017 0.001 PHE D 207 TYR 0.015 0.001 TYR D 26 ARG 0.005 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 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.973 Fit side-chains REVERT: D 40 TYR cc_start: 0.8712 (m-80) cc_final: 0.8405 (m-80) REVERT: D 86 ASP cc_start: 0.5906 (OUTLIER) cc_final: 0.5187 (m-30) REVERT: D 148 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.6261 (mmt) REVERT: A 59 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7822 (p) REVERT: A 239 TYR cc_start: 0.8993 (m-80) cc_final: 0.8631 (m-80) REVERT: C 115 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: B 198 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7439 (mp0) outliers start: 22 outliers final: 16 residues processed: 111 average time/residue: 0.2285 time to fit residues: 35.5601 Evaluate side-chains 118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 86 ASP Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 311 CYS 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 139 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 Chi-restraints excluded: chain B residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.141518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107738 restraints weight = 14556.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111353 restraints weight = 10700.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.112559 restraints weight = 6089.753| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10123 Z= 0.187 Angle : 0.557 7.401 13906 Z= 0.297 Chirality : 0.042 0.176 1600 Planarity : 0.003 0.045 1590 Dihedral : 20.266 77.995 1871 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.06 % Allowed : 18.58 % Favored : 79.36 % 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: -1.05 (0.25), residues: 1107 helix: 0.45 (0.31), residues: 307 sheet: -1.39 (0.25), residues: 376 loop : -0.65 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.002 0.000 HIS D 276 PHE 0.016 0.001 PHE A 207 TYR 0.012 0.001 TYR D 26 ARG 0.003 0.000 ARG D 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.53 seconds wall clock time: 38 minutes 0.38 seconds (2280.38 seconds total)