Starting phenix.real_space_refine on Thu Aug 6 12:34:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpf_61698/08_2026/9jpf_61698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpf_61698/08_2026/9jpf_61698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jpf_61698/08_2026/9jpf_61698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpf_61698/08_2026/9jpf_61698.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jpf_61698/08_2026/9jpf_61698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpf_61698/08_2026/9jpf_61698.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 11 5.16 5 C 9267 2.51 5 N 2719 2.21 5 O 2883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14906 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2096 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 20, 'TRANS': 245} Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2543 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 300} Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2606 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "D" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1895 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain breaks: 2 Chain: "E" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2606 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "F" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2606 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "G" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 554 Classifications: {'RNA': 26} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 11, 'rna3p': 14} Time building chain proxies: 3.39, per 1000 atoms: 0.23 Number of scatterers: 14906 At special positions: 0 Unit cell: (114.724, 117.236, 133.147, 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 11 16.00 P 26 15.00 O 2883 8.00 N 2719 7.00 C 9267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 702.4 milliseconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 35.4% alpha, 9.6% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.698A pdb=" N LEU A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 removed outlier: 4.148A pdb=" N ARG A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.529A pdb=" N ALA A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.698A pdb=" N GLU A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.725A pdb=" N ALA A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'B' and resid 34 through 53 removed outlier: 5.047A pdb=" N ALA B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 179 Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.709A pdb=" N ALA B 232 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 233 " --> pdb=" O GLU B 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.504A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 302 " --> pdb=" O GLN B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.525A pdb=" N ARG C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.734A pdb=" N TRP C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 303 through 314 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.611A pdb=" N ASN D 144 " --> pdb=" O HIS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 152 removed outlier: 3.768A pdb=" N LEU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 152 " --> pdb=" O TRP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.745A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.565A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 303 through 314 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 29 through 33 removed outlier: 3.995A pdb=" N ARG E 33 " --> pdb=" O TRP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 39 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 145 through 153 removed outlier: 6.440A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 266 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 58 through 62 removed outlier: 3.559A pdb=" N ARG F 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 303 through 314 removed outlier: 3.600A pdb=" N ARG F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 removed outlier: 3.551A pdb=" N GLN A 103 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 228 through 232 current: chain 'B' and resid 102 through 114 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 102 through 114 current: chain 'B' and resid 142 through 144 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 142 through 144 current: chain 'B' and resid 277 through 290 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 277 through 290 current: chain 'B' and resid 313 through 317 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 279 removed outlier: 7.651A pdb=" N TRP B 29 " --> pdb=" O TRP A 302 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 304 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA6, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.539A pdb=" N ALA C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 20 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 20 current: chain 'C' and resid 90 through 99 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 90 through 99 current: chain 'C' and resid 169 through 175 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 175 current: chain 'C' and resid 252 through 255 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 50 removed outlier: 4.641A pdb=" N ALA C 82 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.601A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 20 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 20 current: chain 'D' and resid 91 through 99 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 99 current: chain 'D' and resid 169 through 177 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 13 removed outlier: 3.642A pdb=" N ALA E 108 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 20 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 20 current: chain 'E' and resid 90 through 99 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 90 through 99 current: chain 'E' and resid 169 through 177 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 50 removed outlier: 3.586A pdb=" N VAL E 79 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL E 49 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN E 77 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 229 through 230 removed outlier: 4.548A pdb=" N THR E 245 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.508A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 14 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY F 334 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 18 through 19 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 19 current: chain 'F' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 90 through 92 current: chain 'F' and resid 169 through 173 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 44 through 51 removed outlier: 3.724A pdb=" N ASN F 75 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN F 241 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ASP F 80 " --> pdb=" O SER F 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 248 through 249 Processing sheet with id=AC1, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC2, first strand: chain 'F' and resid 287 through 288 446 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4338 1.33 - 1.45: 2454 1.45 - 1.57: 8404 1.57 - 1.69: 51 1.69 - 1.81: 15 Bond restraints: 15262 Sorted by residual: bond pdb=" CB GLN F 38 " pdb=" CG GLN F 38 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB GLU A 247 " pdb=" CG GLU A 247 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB GLN B 168 " pdb=" CG GLN B 168 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" CB LYS C 66 " pdb=" CG LYS C 66 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CB LYS C 301 " pdb=" CG LYS C 301 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 ... (remaining 15257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 20620 2.48 - 4.97: 206 4.97 - 7.45: 18 7.45 - 9.94: 4 9.94 - 12.42: 1 Bond angle restraints: 20849 Sorted by residual: angle pdb=" N ILE B 97 " pdb=" CA ILE B 97 " pdb=" C ILE B 97 " ideal model delta sigma weight residual 112.29 106.92 5.37 9.40e-01 1.13e+00 3.26e+01 angle pdb=" O5' C G 14 " pdb=" C5' C G 14 " pdb=" C4' C G 14 " ideal model delta sigma weight residual 109.40 113.24 -3.84 8.00e-01 1.56e+00 2.30e+01 angle pdb=" CA GLN B 168 " pdb=" CB GLN B 168 " pdb=" CG GLN B 168 " ideal model delta sigma weight residual 114.10 122.44 -8.34 2.00e+00 2.50e-01 1.74e+01 angle pdb=" N ILE C 53 " pdb=" CA ILE C 53 " pdb=" C ILE C 53 " ideal model delta sigma weight residual 106.21 110.65 -4.44 1.07e+00 8.73e-01 1.72e+01 angle pdb=" CB ILE C 53 " pdb=" CG1 ILE C 53 " pdb=" CD1 ILE C 53 " ideal model delta sigma weight residual 113.80 121.90 -8.10 2.10e+00 2.27e-01 1.49e+01 ... (remaining 20844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7841 17.97 - 35.93: 976 35.93 - 53.89: 288 53.89 - 71.86: 78 71.86 - 89.82: 25 Dihedral angle restraints: 9208 sinusoidal: 3892 harmonic: 5316 Sorted by residual: dihedral pdb=" O4' U G 24 " pdb=" C1' U G 24 " pdb=" N1 U G 24 " pdb=" C2 U G 24 " ideal model delta sinusoidal sigma weight residual -160.00 -86.08 -73.92 1 1.50e+01 4.44e-03 3.08e+01 dihedral pdb=" O4' U G 22 " pdb=" C1' U G 22 " pdb=" N1 U G 22 " pdb=" C2 U G 22 " ideal model delta sinusoidal sigma weight residual -160.00 -98.22 -61.78 1 1.50e+01 4.44e-03 2.25e+01 dihedral pdb=" CA ASN B 82 " pdb=" C ASN B 82 " pdb=" N LEU B 83 " pdb=" CA LEU B 83 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 9205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2087 0.071 - 0.142: 238 0.142 - 0.213: 5 0.213 - 0.284: 0 0.284 - 0.355: 1 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CG LEU F 330 " pdb=" CB LEU F 330 " pdb=" CD1 LEU F 330 " pdb=" CD2 LEU F 330 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB THR C 266 " pdb=" CA THR C 266 " pdb=" OG1 THR C 266 " pdb=" CG2 THR C 266 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" C1' A G 4 " pdb=" O4' A G 4 " pdb=" C2' A G 4 " pdb=" N9 A G 4 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 2328 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A G 4 " 0.026 2.00e-02 2.50e+03 1.18e-02 3.81e+00 pdb=" N9 A G 4 " -0.027 2.00e-02 2.50e+03 pdb=" C8 A G 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A G 4 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A G 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A G 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A G 4 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A G 4 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A G 4 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A G 4 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A G 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 9 " 0.025 2.00e-02 2.50e+03 1.26e-02 3.55e+00 pdb=" N1 U G 9 " -0.025 2.00e-02 2.50e+03 pdb=" C2 U G 9 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U G 9 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U G 9 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U G 9 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U G 9 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U G 9 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U G 9 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 18 " 0.022 2.00e-02 2.50e+03 1.16e-02 3.01e+00 pdb=" N1 U G 18 " -0.024 2.00e-02 2.50e+03 pdb=" C2 U G 18 " -0.006 2.00e-02 2.50e+03 pdb=" O2 U G 18 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U G 18 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U G 18 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U G 18 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U G 18 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U G 18 " -0.003 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 183 2.59 - 3.17: 12046 3.17 - 3.75: 23768 3.75 - 4.32: 31838 4.32 - 4.90: 52946 Nonbonded interactions: 120781 Sorted by model distance: nonbonded pdb=" OE1 GLN C 258 " pdb=" O2' A G 7 " model vdw 2.014 3.040 nonbonded pdb=" OG SER B 84 " pdb=" OD1 ASN B 86 " model vdw 2.039 3.040 nonbonded pdb=" OH TYR E 305 " pdb=" O SER F 54 " model vdw 2.105 3.040 nonbonded pdb=" O SER C 54 " pdb=" OH TYR F 305 " model vdw 2.137 3.040 nonbonded pdb=" OE1 GLU B 190 " pdb=" OG SER B 285 " model vdw 2.143 3.040 ... (remaining 120776 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 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.110 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:8.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 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 : 0.003 0.043 15262 Z= 0.124 Angle : 0.588 12.421 20849 Z= 0.330 Chirality : 0.044 0.355 2331 Planarity : 0.003 0.038 2665 Dihedral : 18.003 89.825 5776 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.04 % Allowed : 29.07 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1832 helix: 0.84 (0.22), residues: 542 sheet: -0.07 (0.30), residues: 318 loop : -0.83 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 94 TYR 0.026 0.001 TYR C 247 PHE 0.025 0.001 PHE A 59 TRP 0.008 0.001 TRP F 174 HIS 0.004 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15262) covalent geometry : angle 0.58817 / 0.33 (20849) hydrogen bonds : bond 0.17347 / 11.85 ( 446) hydrogen bonds : angle 6.21573 / 4.39 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.542 Fit side-chains REVERT: A 193 GLU cc_start: 0.3935 (OUTLIER) cc_final: 0.3049 (pp20) REVERT: A 247 GLU cc_start: 0.7389 (pp20) cc_final: 0.7058 (pt0) REVERT: B 192 MET cc_start: 0.6323 (mmm) cc_final: 0.5897 (mtt) REVERT: C 59 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6882 (t) REVERT: C 172 ARG cc_start: 0.6648 (tpt-90) cc_final: 0.5448 (ptp-110) REVERT: C 183 LEU cc_start: 0.7230 (mt) cc_final: 0.6364 (pp) REVERT: C 265 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6765 (mtm110) REVERT: C 291 GLN cc_start: 0.7384 (mp10) cc_final: 0.5579 (tp40) REVERT: C 315 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5763 (t0) REVERT: D 299 LYS cc_start: 0.4340 (OUTLIER) cc_final: 0.2051 (tptt) REVERT: E 166 ARG cc_start: 0.6719 (tpp80) cc_final: 0.6487 (tpp80) REVERT: E 167 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6749 (mt0) REVERT: E 327 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6969 (mp) REVERT: E 332 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8046 (ttt90) REVERT: E 338 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: F 55 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.6963 (p0) REVERT: F 60 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.5792 (ttpt) REVERT: F 251 ASP cc_start: 0.8014 (m-30) cc_final: 0.7557 (t0) outliers start: 45 outliers final: 24 residues processed: 160 average time/residue: 0.4522 time to fit residues: 81.3141 Evaluate side-chains 149 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.232340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.189059 restraints weight = 21344.449| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.66 r_work: 0.4146 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15262 Z= 0.207 Angle : 0.634 11.066 20849 Z= 0.325 Chirality : 0.045 0.295 2331 Planarity : 0.005 0.046 2665 Dihedral : 12.599 87.345 2482 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 7.03 % Allowed : 25.22 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.19), residues: 1832 helix: 0.50 (0.22), residues: 543 sheet: -0.35 (0.30), residues: 299 loop : -0.93 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 85 TYR 0.015 0.002 TYR D 114 PHE 0.014 0.002 PHE C 95 TRP 0.016 0.002 TRP C 30 HIS 0.005 0.001 HIS E 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (15262) covalent geometry : angle 0.63427 / 0.32 (20849) hydrogen bonds : bond 0.04733 / 3.22 ( 446) hydrogen bonds : angle 5.36357 / 3.66 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 125 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7089 (pp20) cc_final: 0.6838 (pt0) REVERT: B 65 ARG cc_start: 0.7912 (ptp-110) cc_final: 0.7693 (ptp-110) REVERT: B 321 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5340 (t80) REVERT: C 57 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7213 (mp) REVERT: C 291 GLN cc_start: 0.7635 (mp10) cc_final: 0.5889 (tp40) REVERT: D 305 TYR cc_start: 0.2397 (OUTLIER) cc_final: 0.1187 (m-80) REVERT: E 137 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7230 (mtp180) REVERT: E 338 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: F 15 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: F 55 ASN cc_start: 0.7767 (p0) cc_final: 0.6980 (p0) REVERT: F 174 TRP cc_start: 0.5491 (OUTLIER) cc_final: 0.4176 (m-10) outliers start: 104 outliers final: 45 residues processed: 212 average time/residue: 0.3759 time to fit residues: 90.9882 Evaluate side-chains 163 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 232 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 178 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN B 19 ASN D 141 ASN E 164 HIS ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.233089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.190007 restraints weight = 21646.680| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 2.69 r_work: 0.4158 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15262 Z= 0.158 Angle : 0.587 10.822 20849 Z= 0.300 Chirality : 0.045 0.328 2331 Planarity : 0.004 0.036 2665 Dihedral : 12.089 88.061 2440 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 7.10 % Allowed : 24.48 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1832 helix: 0.53 (0.22), residues: 543 sheet: -0.54 (0.30), residues: 313 loop : -0.95 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 166 TYR 0.013 0.002 TYR E 271 PHE 0.017 0.001 PHE A 59 TRP 0.011 0.001 TRP C 30 HIS 0.004 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15262) covalent geometry : angle 0.58682 / 0.30 (20849) hydrogen bonds : bond 0.04106 / 2.79 ( 446) hydrogen bonds : angle 5.14048 / 3.49 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 125 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7048 (pp20) cc_final: 0.6743 (pt0) REVERT: B 161 MET cc_start: 0.6749 (mmm) cc_final: 0.5495 (pmm) REVERT: B 321 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5421 (t80) REVERT: C 291 GLN cc_start: 0.7548 (mp10) cc_final: 0.5826 (tp40) REVERT: D 305 TYR cc_start: 0.2397 (OUTLIER) cc_final: 0.1295 (m-80) REVERT: E 338 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: F 15 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: F 55 ASN cc_start: 0.7693 (p0) cc_final: 0.6894 (p0) REVERT: F 174 TRP cc_start: 0.5489 (OUTLIER) cc_final: 0.4307 (m-10) REVERT: F 230 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: F 232 ILE cc_start: 0.5603 (OUTLIER) cc_final: 0.5392 (pp) REVERT: F 299 LYS cc_start: 0.7241 (tptp) cc_final: 0.6653 (tmmm) outliers start: 105 outliers final: 44 residues processed: 212 average time/residue: 0.3767 time to fit residues: 90.9557 Evaluate side-chains 160 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 15 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.229990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.187087 restraints weight = 21385.972| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.60 r_work: 0.4130 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 15262 Z= 0.255 Angle : 0.712 13.800 20849 Z= 0.361 Chirality : 0.049 0.378 2331 Planarity : 0.005 0.058 2665 Dihedral : 12.310 89.848 2437 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 7.71 % Allowed : 24.00 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1832 helix: 0.11 (0.21), residues: 542 sheet: -0.72 (0.29), residues: 311 loop : -1.19 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.020 0.002 TYR F 247 PHE 0.018 0.002 PHE C 95 TRP 0.021 0.002 TRP C 30 HIS 0.007 0.002 HIS E 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 (15262) covalent geometry : angle 0.71197 / 0.36 (20849) hydrogen bonds : bond 0.04587 / 3.12 ( 446) hydrogen bonds : angle 5.38923 / 3.68 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 123 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 192 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.6865 (ptm-80) REVERT: A 193 GLU cc_start: 0.3640 (OUTLIER) cc_final: 0.2413 (pp20) REVERT: A 201 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5559 (tp) REVERT: B 65 ARG cc_start: 0.7935 (ptp-110) cc_final: 0.7663 (ptp-110) REVERT: B 161 MET cc_start: 0.6770 (mmm) cc_final: 0.5686 (pmm) REVERT: B 321 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5519 (t80) REVERT: C 98 ARG cc_start: 0.5486 (OUTLIER) cc_final: 0.3296 (mtt90) REVERT: C 291 GLN cc_start: 0.7650 (mp10) cc_final: 0.5950 (tp40) REVERT: D 305 TYR cc_start: 0.2442 (OUTLIER) cc_final: 0.1209 (m-80) REVERT: E 167 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7004 (mt0) REVERT: E 297 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7425 (tm-30) REVERT: E 338 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: F 15 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: F 55 ASN cc_start: 0.7706 (p0) cc_final: 0.6916 (p0) REVERT: F 174 TRP cc_start: 0.5930 (OUTLIER) cc_final: 0.4917 (m-10) REVERT: F 230 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: F 232 ILE cc_start: 0.5907 (OUTLIER) cc_final: 0.5676 (pp) REVERT: F 260 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7145 (mt) outliers start: 114 outliers final: 58 residues processed: 221 average time/residue: 0.3537 time to fit residues: 89.3123 Evaluate side-chains 187 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 117 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 175 optimal weight: 0.0470 chunk 102 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 ASN C 129 GLN D 141 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.233826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.195367 restraints weight = 21366.007| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.92 r_work: 0.4192 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15262 Z= 0.126 Angle : 0.575 10.911 20849 Z= 0.293 Chirality : 0.044 0.316 2331 Planarity : 0.004 0.034 2665 Dihedral : 12.026 88.457 2435 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.15 % Allowed : 25.83 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1832 helix: 0.54 (0.22), residues: 543 sheet: -0.76 (0.29), residues: 313 loop : -0.98 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.011 0.001 TYR C 325 PHE 0.019 0.001 PHE A 59 TRP 0.008 0.001 TRP F 270 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15262) covalent geometry : angle 0.57471 / 0.29 (20849) hydrogen bonds : bond 0.03651 / 2.50 ( 446) hydrogen bonds : angle 4.93798 / 3.35 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 129 time to evaluate : 0.417 Fit side-chains REVERT: A 193 GLU cc_start: 0.3671 (OUTLIER) cc_final: 0.2708 (pp20) REVERT: A 201 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5732 (tp) REVERT: B 161 MET cc_start: 0.6710 (mmm) cc_final: 0.5531 (pmm) REVERT: B 321 PHE cc_start: 0.6102 (OUTLIER) cc_final: 0.5352 (t80) REVERT: C 98 ARG cc_start: 0.5301 (OUTLIER) cc_final: 0.3073 (mtt90) REVERT: C 172 ARG cc_start: 0.6560 (tpt-90) cc_final: 0.5431 (ptp-110) REVERT: C 291 GLN cc_start: 0.7562 (mp10) cc_final: 0.5970 (tp40) REVERT: C 335 VAL cc_start: 0.5933 (t) cc_final: 0.5342 (t) REVERT: D 305 TYR cc_start: 0.2632 (OUTLIER) cc_final: 0.1546 (m-80) REVERT: E 327 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.7050 (mp) REVERT: E 338 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: F 15 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: F 29 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6219 (m-30) REVERT: F 55 ASN cc_start: 0.7626 (p0) cc_final: 0.6870 (p0) REVERT: F 230 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: F 232 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5574 (pp) REVERT: F 299 LYS cc_start: 0.7193 (tptp) cc_final: 0.6630 (tmmm) outliers start: 91 outliers final: 43 residues processed: 203 average time/residue: 0.3637 time to fit residues: 84.0627 Evaluate side-chains 168 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 114 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 56 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 98 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 overall best weight: 2.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.230747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.187860 restraints weight = 21212.087| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.60 r_work: 0.4155 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15262 Z= 0.220 Angle : 0.671 13.976 20849 Z= 0.340 Chirality : 0.047 0.391 2331 Planarity : 0.005 0.043 2665 Dihedral : 12.081 89.829 2430 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.76 % Allowed : 25.63 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1832 helix: 0.30 (0.21), residues: 542 sheet: -0.88 (0.29), residues: 310 loop : -1.12 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 192 TYR 0.015 0.002 TYR F 247 PHE 0.015 0.002 PHE C 95 TRP 0.018 0.002 TRP C 30 HIS 0.005 0.001 HIS E 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (15262) covalent geometry : angle 0.67073 / 0.34 (20849) hydrogen bonds : bond 0.04159 / 2.82 ( 446) hydrogen bonds : angle 5.16366 / 3.53 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 125 time to evaluate : 0.420 Fit side-chains REVERT: A 193 GLU cc_start: 0.3649 (OUTLIER) cc_final: 0.2561 (pp20) REVERT: A 201 ILE cc_start: 0.6205 (OUTLIER) cc_final: 0.5761 (tp) REVERT: B 161 MET cc_start: 0.6778 (mmm) cc_final: 0.5702 (pmm) REVERT: B 206 GLU cc_start: 0.4198 (OUTLIER) cc_final: 0.3792 (tp30) REVERT: B 321 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5547 (t80) REVERT: C 98 ARG cc_start: 0.5463 (OUTLIER) cc_final: 0.3236 (mtt90) REVERT: C 172 ARG cc_start: 0.6565 (tpt-90) cc_final: 0.5526 (ptp-110) REVERT: C 192 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5770 (mm) REVERT: C 193 ASP cc_start: 0.6690 (m-30) cc_final: 0.6357 (m-30) REVERT: C 291 GLN cc_start: 0.7602 (mp10) cc_final: 0.6017 (tp40) REVERT: D 305 TYR cc_start: 0.2640 (OUTLIER) cc_final: 0.1390 (m-80) REVERT: E 167 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6970 (mt0) REVERT: E 332 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8182 (ttt90) REVERT: E 338 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: F 15 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: F 55 ASN cc_start: 0.7660 (p0) cc_final: 0.6897 (p0) REVERT: F 174 TRP cc_start: 0.5733 (OUTLIER) cc_final: 0.4487 (m-10) REVERT: F 230 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: F 232 ILE cc_start: 0.5954 (OUTLIER) cc_final: 0.5729 (pp) REVERT: F 258 GLN cc_start: 0.5697 (mt0) cc_final: 0.5128 (mt0) outliers start: 100 outliers final: 51 residues processed: 207 average time/residue: 0.3479 time to fit residues: 83.0502 Evaluate side-chains 178 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 113 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 129 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 0.0470 chunk 109 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 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 = 0.4724 r_free = 0.4724 target = 0.233264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.190743 restraints weight = 21040.383| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 2.63 r_work: 0.4193 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15262 Z= 0.137 Angle : 0.598 12.647 20849 Z= 0.303 Chirality : 0.044 0.342 2331 Planarity : 0.004 0.054 2665 Dihedral : 11.958 88.860 2430 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.02 % Allowed : 26.50 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.19), residues: 1832 helix: 0.52 (0.22), residues: 543 sheet: -0.89 (0.29), residues: 316 loop : -0.98 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 192 TYR 0.012 0.001 TYR C 325 PHE 0.022 0.001 PHE A 59 TRP 0.017 0.001 TRP B 239 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15262) covalent geometry : angle 0.59788 / 0.30 (20849) hydrogen bonds : bond 0.03645 / 2.49 ( 446) hydrogen bonds : angle 4.92207 / 3.35 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 129 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 193 GLU cc_start: 0.3558 (OUTLIER) cc_final: 0.2498 (pp20) REVERT: A 201 ILE cc_start: 0.6217 (OUTLIER) cc_final: 0.5801 (tp) REVERT: B 161 MET cc_start: 0.6738 (mmm) cc_final: 0.5675 (pmm) REVERT: B 206 GLU cc_start: 0.4258 (OUTLIER) cc_final: 0.3971 (tp30) REVERT: B 274 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6760 (pp20) REVERT: B 321 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5485 (t80) REVERT: C 37 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: C 98 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.3086 (mtt90) REVERT: C 172 ARG cc_start: 0.6545 (tpt-90) cc_final: 0.5642 (ptp-110) REVERT: C 193 ASP cc_start: 0.6587 (m-30) cc_final: 0.6251 (m-30) REVERT: C 291 GLN cc_start: 0.7602 (mp10) cc_final: 0.5953 (tp40) REVERT: C 335 VAL cc_start: 0.5920 (t) cc_final: 0.5657 (m) REVERT: D 305 TYR cc_start: 0.2663 (OUTLIER) cc_final: 0.1559 (m-80) REVERT: E 167 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: E 327 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7174 (mp) REVERT: E 338 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: F 29 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6261 (m-30) REVERT: F 55 ASN cc_start: 0.7577 (p0) cc_final: 0.6841 (p0) REVERT: F 174 TRP cc_start: 0.5724 (OUTLIER) cc_final: 0.4570 (m-10) REVERT: F 230 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: F 232 ILE cc_start: 0.5962 (OUTLIER) cc_final: 0.5745 (pp) REVERT: F 299 LYS cc_start: 0.7171 (tppt) cc_final: 0.6933 (tttm) outliers start: 89 outliers final: 44 residues processed: 200 average time/residue: 0.3630 time to fit residues: 82.6179 Evaluate side-chains 175 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 146 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.230136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.192586 restraints weight = 21336.989| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.77 r_work: 0.4142 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15262 Z= 0.232 Angle : 0.703 15.034 20849 Z= 0.356 Chirality : 0.048 0.391 2331 Planarity : 0.005 0.049 2665 Dihedral : 12.152 90.380 2430 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 6.09 % Allowed : 26.77 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1832 helix: 0.25 (0.21), residues: 536 sheet: -0.93 (0.29), residues: 305 loop : -1.14 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 192 TYR 0.017 0.002 TYR D 114 PHE 0.016 0.002 PHE C 95 TRP 0.019 0.002 TRP C 30 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (15262) covalent geometry : angle 0.70254 / 0.36 (20849) hydrogen bonds : bond 0.04222 / 2.86 ( 446) hydrogen bonds : angle 5.19116 / 3.55 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 122 time to evaluate : 0.397 Fit side-chains REVERT: A 193 GLU cc_start: 0.3506 (OUTLIER) cc_final: 0.2553 (pp20) REVERT: A 201 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5783 (tp) REVERT: B 161 MET cc_start: 0.6945 (mmm) cc_final: 0.5761 (pmm) REVERT: B 206 GLU cc_start: 0.4139 (OUTLIER) cc_final: 0.3698 (tp30) REVERT: B 321 PHE cc_start: 0.6114 (OUTLIER) cc_final: 0.5484 (t80) REVERT: C 98 ARG cc_start: 0.5452 (OUTLIER) cc_final: 0.3214 (mtt90) REVERT: C 172 ARG cc_start: 0.6580 (tpt-90) cc_final: 0.5553 (ptp-170) REVERT: C 192 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5551 (mm) REVERT: C 193 ASP cc_start: 0.6651 (m-30) cc_final: 0.6289 (m-30) REVERT: C 233 LEU cc_start: 0.7394 (mt) cc_final: 0.7178 (tp) REVERT: C 291 GLN cc_start: 0.7712 (mp10) cc_final: 0.5996 (tp40) REVERT: D 305 TYR cc_start: 0.2793 (OUTLIER) cc_final: 0.1743 (m-80) REVERT: E 167 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: E 332 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8191 (ttt90) REVERT: E 338 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: F 15 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: F 55 ASN cc_start: 0.7650 (p0) cc_final: 0.6820 (p0) REVERT: F 174 TRP cc_start: 0.5851 (OUTLIER) cc_final: 0.4628 (m-10) REVERT: F 230 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7315 (mt-10) REVERT: F 260 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6864 (mm) REVERT: F 299 LYS cc_start: 0.7185 (tppt) cc_final: 0.6809 (tmmm) outliers start: 90 outliers final: 47 residues processed: 198 average time/residue: 0.3771 time to fit residues: 84.4764 Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 329 ASN D 141 ASN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.234541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.196532 restraints weight = 21322.770| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 3.12 r_work: 0.4202 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15262 Z= 0.122 Angle : 0.596 12.214 20849 Z= 0.304 Chirality : 0.043 0.321 2331 Planarity : 0.004 0.062 2665 Dihedral : 11.881 88.147 2427 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.80 % Allowed : 28.40 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1832 helix: 0.65 (0.22), residues: 537 sheet: -1.01 (0.29), residues: 315 loop : -0.91 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 192 TYR 0.015 0.001 TYR D 114 PHE 0.022 0.001 PHE A 59 TRP 0.010 0.001 TRP F 174 HIS 0.006 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15262) covalent geometry : angle 0.59576 / 0.30 (20849) hydrogen bonds : bond 0.03435 / 2.36 ( 446) hydrogen bonds : angle 4.78348 / 3.26 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 122 time to evaluate : 0.557 Fit side-chains REVERT: A 91 TRP cc_start: 0.2682 (OUTLIER) cc_final: 0.2448 (t60) REVERT: A 193 GLU cc_start: 0.3367 (OUTLIER) cc_final: 0.2373 (pp20) REVERT: A 247 GLU cc_start: 0.7186 (pp20) cc_final: 0.6903 (pt0) REVERT: B 161 MET cc_start: 0.6849 (mmm) cc_final: 0.5669 (pmm) REVERT: B 206 GLU cc_start: 0.4135 (OUTLIER) cc_final: 0.3894 (tp30) REVERT: B 244 LYS cc_start: 0.6609 (mttt) cc_final: 0.6183 (mtpt) REVERT: B 274 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6645 (pp20) REVERT: B 321 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5445 (t80) REVERT: C 37 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: C 98 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.3046 (mtt90) REVERT: C 172 ARG cc_start: 0.6566 (tpt-90) cc_final: 0.5402 (ptp-170) REVERT: C 192 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5318 (mm) REVERT: C 193 ASP cc_start: 0.6545 (m-30) cc_final: 0.6204 (m-30) REVERT: C 291 GLN cc_start: 0.7528 (mp10) cc_final: 0.5891 (tp40) REVERT: D 305 TYR cc_start: 0.2857 (OUTLIER) cc_final: 0.1875 (m-80) REVERT: E 167 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6864 (mt0) REVERT: E 327 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6965 (mp) REVERT: E 332 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8250 (ttt90) REVERT: E 338 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: F 15 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: F 55 ASN cc_start: 0.7575 (p0) cc_final: 0.6788 (p0) REVERT: F 174 TRP cc_start: 0.5596 (OUTLIER) cc_final: 0.4631 (m-10) REVERT: F 230 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: F 299 LYS cc_start: 0.7100 (tppt) cc_final: 0.6808 (tmmm) outliers start: 71 outliers final: 37 residues processed: 184 average time/residue: 0.4428 time to fit residues: 93.0148 Evaluate side-chains 167 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 114 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A 301 ASN C 329 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.231521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.188733 restraints weight = 21346.570| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.61 r_work: 0.4163 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15262 Z= 0.199 Angle : 0.679 14.485 20849 Z= 0.343 Chirality : 0.046 0.385 2331 Planarity : 0.005 0.056 2665 Dihedral : 11.984 90.518 2426 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.06 % Allowed : 29.34 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.19), residues: 1832 helix: 0.47 (0.22), residues: 536 sheet: -0.96 (0.29), residues: 312 loop : -1.07 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 192 TYR 0.018 0.002 TYR C 285 PHE 0.013 0.002 PHE C 95 TRP 0.017 0.002 TRP C 30 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (15262) covalent geometry : angle 0.67869 / 0.34 (20849) hydrogen bonds : bond 0.03975 / 2.73 ( 446) hydrogen bonds : angle 4.99621 / 3.41 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 115 time to evaluate : 0.401 Fit side-chains REVERT: A 91 TRP cc_start: 0.2858 (OUTLIER) cc_final: 0.2610 (t60) REVERT: A 193 GLU cc_start: 0.3562 (OUTLIER) cc_final: 0.2488 (pp20) REVERT: A 247 GLU cc_start: 0.7325 (pp20) cc_final: 0.7001 (pt0) REVERT: B 161 MET cc_start: 0.6859 (mmm) cc_final: 0.5735 (pmm) REVERT: B 206 GLU cc_start: 0.4190 (OUTLIER) cc_final: 0.3769 (tp30) REVERT: B 321 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5448 (t80) REVERT: C 98 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.3162 (mtt90) REVERT: C 172 ARG cc_start: 0.6498 (tpt-90) cc_final: 0.5513 (ptp-110) REVERT: C 192 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5595 (mm) REVERT: C 193 ASP cc_start: 0.6671 (m-30) cc_final: 0.6306 (m-30) REVERT: C 233 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7201 (tp) REVERT: C 291 GLN cc_start: 0.7563 (mp10) cc_final: 0.5938 (tp40) REVERT: D 305 TYR cc_start: 0.2808 (OUTLIER) cc_final: 0.1767 (m-80) REVERT: E 167 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6973 (mt0) REVERT: E 332 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8191 (ttt90) REVERT: E 338 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: F 15 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: F 29 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: F 55 ASN cc_start: 0.7610 (p0) cc_final: 0.6818 (p0) REVERT: F 174 TRP cc_start: 0.5751 (OUTLIER) cc_final: 0.4673 (m-10) REVERT: F 230 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: F 299 LYS cc_start: 0.7105 (tppt) cc_final: 0.6840 (tmmm) outliers start: 60 outliers final: 37 residues processed: 164 average time/residue: 0.4146 time to fit residues: 77.3026 Evaluate side-chains 160 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 108 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 332 ARG Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 174 TRP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 34 optimal weight: 0.3980 chunk 133 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 28 optimal weight: 0.0770 chunk 79 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN D 141 ASN ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.235080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.197351 restraints weight = 21103.185| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.25 r_work: 0.4204 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15262 Z= 0.118 Angle : 0.599 12.358 20849 Z= 0.304 Chirality : 0.043 0.323 2331 Planarity : 0.004 0.065 2665 Dihedral : 11.808 88.443 2426 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.92 % Allowed : 29.61 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 1832 helix: 0.78 (0.22), residues: 537 sheet: -0.93 (0.29), residues: 318 loop : -0.89 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 192 TYR 0.015 0.001 TYR C 285 PHE 0.022 0.001 PHE A 59 TRP 0.010 0.001 TRP F 270 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15262) covalent geometry : angle 0.59873 / 0.30 (20849) hydrogen bonds : bond 0.03391 / 2.35 ( 446) hydrogen bonds : angle 4.69780 / 3.20 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3927.58 seconds wall clock time: 67 minutes 46.77 seconds (4066.77 seconds total)