Starting phenix.real_space_refine on Fri Jul 3 17:23:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpf_61698/07_2026/9jpf_61698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpf_61698/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jpf_61698/07_2026/9jpf_61698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpf_61698/07_2026/9jpf_61698.map" model { file = "/net/cci-nas-00/data/ceres_data/9jpf_61698/07_2026/9jpf_61698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpf_61698/07_2026/9jpf_61698.cif" } 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-dev-6108/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: 3.11, per 1000 atoms: 0.21 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: 0.73 Conformation dependent library (CDL) restraints added in 476.4 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: 1.35 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: 1.93 Time building geometry restraints manager: 1.05 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: 20643 2.48 - 4.97: 183 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=" 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 angle pdb=" CA LEU F 330 " pdb=" CB LEU F 330 " pdb=" CG LEU F 330 " ideal model delta sigma weight residual 116.30 128.72 -12.42 3.50e+00 8.16e-02 1.26e+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: 2110 0.071 - 0.142: 217 0.142 - 0.213: 3 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=" CB VAL B 249 " pdb=" CA VAL B 249 " pdb=" CG1 VAL B 249 " pdb=" CG2 VAL B 249 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.42e-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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.000 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- 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= 0.122 Angle : 0.573 12.421 20849 Z= 0.306 Chirality : 0.042 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 0.00261 / 0.12 (15262) covalent geometry : angle 0.57291 / 0.31 (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 : 0.510 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: 0.4152 time to fit residues: 74.9160 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 : 0.528 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** 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 = 0.4704 r_free = 0.4704 target = 0.231938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.188601 restraints weight = 21346.473| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.66 r_work: 0.4145 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15262 Z= 0.209 Angle : 0.635 10.806 20849 Z= 0.327 Chirality : 0.045 0.301 2331 Planarity : 0.005 0.048 2665 Dihedral : 12.680 89.180 2482 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 7.17 % Allowed : 24.88 % Favored : 67.95 % 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: -0.65 (0.19), residues: 1832 helix: 0.46 (0.22), residues: 543 sheet: -0.37 (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 0.016 0.002 TYR D 114 PHE 0.015 0.002 PHE C 95 TRP 0.016 0.002 TRP C 30 HIS 0.005 0.001 HIS B 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (15262) covalent geometry : angle 0.63488 / 0.33 (20849) hydrogen bonds : bond 0.04616 / 3.14 ( 446) hydrogen bonds : angle 5.35768 / 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 231 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 125 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7056 (pp20) cc_final: 0.6763 (pt0) REVERT: A 296 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: B 65 ARG cc_start: 0.7892 (ptp-110) cc_final: 0.7670 (ptp-110) REVERT: B 321 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5354 (t80) REVERT: C 57 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7211 (mp) REVERT: C 250 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6362 (mpt90) REVERT: C 291 GLN cc_start: 0.7631 (mp10) cc_final: 0.5882 (tp40) REVERT: D 305 TYR cc_start: 0.2402 (OUTLIER) cc_final: 0.1186 (m-80) REVERT: E 137 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7218 (mtp180) REVERT: E 338 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: F 15 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: F 55 ASN cc_start: 0.7760 (p0) cc_final: 0.6970 (p0) REVERT: F 174 TRP cc_start: 0.5485 (OUTLIER) cc_final: 0.4173 (m-10) outliers start: 106 outliers final: 42 residues processed: 214 average time/residue: 0.3839 time to fit residues: 93.8223 Evaluate side-chains 165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 A residue 296 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 170 ARG 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 250 ARG 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 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: 0.0370 chunk 10 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 178 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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 ** 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 = 0.4698 r_free = 0.4698 target = 0.231265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.187787 restraints weight = 21666.466| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.68 r_work: 0.4138 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15262 Z= 0.210 Angle : 0.641 11.467 20849 Z= 0.329 Chirality : 0.046 0.330 2331 Planarity : 0.005 0.047 2665 Dihedral : 12.265 89.869 2438 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 7.57 % Allowed : 23.94 % Favored : 68.49 % 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: -0.88 (0.19), residues: 1832 helix: 0.30 (0.21), residues: 543 sheet: -0.67 (0.30), residues: 305 loop : -1.04 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 166 TYR 0.015 0.002 TYR E 271 PHE 0.018 0.002 PHE A 59 TRP 0.016 0.002 TRP C 30 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (15262) covalent geometry : angle 0.64075 / 0.33 (20849) hydrogen bonds : bond 0.04452 / 3.02 ( 446) hydrogen bonds : angle 5.28928 / 3.59 ( 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 237 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 125 time to evaluate : 0.485 Fit side-chains REVERT: A 193 GLU cc_start: 0.3843 (OUTLIER) cc_final: 0.2901 (pp20) REVERT: A 201 ILE cc_start: 0.6044 (OUTLIER) cc_final: 0.5583 (tp) REVERT: A 247 GLU cc_start: 0.6955 (pp20) cc_final: 0.6676 (pt0) REVERT: B 65 ARG cc_start: 0.7941 (ptp-110) cc_final: 0.7737 (ptp-110) REVERT: B 161 MET cc_start: 0.6809 (mmm) cc_final: 0.5501 (pmm) REVERT: B 321 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5442 (t80) REVERT: C 172 ARG cc_start: 0.6616 (tpt-90) cc_final: 0.5446 (ptp-110) REVERT: C 246 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6889 (mp) REVERT: C 250 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6420 (mpt90) REVERT: C 291 GLN cc_start: 0.7573 (mp10) cc_final: 0.5799 (tp40) REVERT: D 305 TYR cc_start: 0.2384 (OUTLIER) cc_final: 0.1163 (m-80) REVERT: E 338 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: F 15 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: F 55 ASN cc_start: 0.7741 (p0) cc_final: 0.6923 (p0) REVERT: F 174 TRP cc_start: 0.5633 (OUTLIER) cc_final: 0.4441 (m-10) REVERT: F 230 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7310 (mm-30) REVERT: F 232 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.5439 (pp) REVERT: F 299 LYS cc_start: 0.7213 (tppt) cc_final: 0.6832 (tmmm) outliers start: 112 outliers final: 52 residues processed: 220 average time/residue: 0.3912 time to fit residues: 97.7996 Evaluate side-chains 178 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 115 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 298 LEU 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 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 170 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 250 ARG 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 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 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 32 GLN 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 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: 2.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.231525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.193126 restraints weight = 21319.198| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.29 r_work: 0.4157 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15262 Z= 0.194 Angle : 0.628 11.970 20849 Z= 0.323 Chirality : 0.045 0.344 2331 Planarity : 0.005 0.044 2665 Dihedral : 12.276 89.967 2438 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 7.78 % Allowed : 24.07 % Favored : 68.15 % 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: -0.95 (0.19), residues: 1832 helix: 0.29 (0.21), residues: 543 sheet: -0.76 (0.29), residues: 319 loop : -1.09 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 192 TYR 0.017 0.002 TYR D 114 PHE 0.012 0.002 PHE C 95 TRP 0.014 0.001 TRP C 30 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (15262) covalent geometry : angle 0.62776 / 0.32 (20849) hydrogen bonds : bond 0.04120 / 2.79 ( 446) hydrogen bonds : angle 5.19297 / 3.53 ( 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 240 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 125 time to evaluate : 0.543 Fit side-chains REVERT: A 192 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.6834 (ptm-80) REVERT: A 193 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.2326 (pp20) REVERT: B 161 MET cc_start: 0.6793 (mmm) cc_final: 0.5585 (pmm) REVERT: B 321 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.5441 (t80) REVERT: C 98 ARG cc_start: 0.5373 (OUTLIER) cc_final: 0.2978 (mtt90) REVERT: C 172 ARG cc_start: 0.6549 (tpt-90) cc_final: 0.5535 (ptp-110) REVERT: C 250 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6411 (mpt90) REVERT: C 291 GLN cc_start: 0.7620 (mp10) cc_final: 0.5929 (tp40) REVERT: D 305 TYR cc_start: 0.2560 (OUTLIER) cc_final: 0.1334 (m-80) REVERT: E 167 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6944 (mt0) REVERT: E 338 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: F 15 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: F 29 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6176 (m-30) REVERT: F 55 ASN cc_start: 0.7681 (p0) cc_final: 0.6916 (p0) REVERT: F 174 TRP cc_start: 0.5772 (OUTLIER) cc_final: 0.4682 (m-10) REVERT: F 230 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7350 (mm-30) REVERT: F 232 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5590 (pp) REVERT: F 260 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.7036 (mt) REVERT: F 299 LYS cc_start: 0.7133 (tppt) cc_final: 0.6771 (tmmm) outliers start: 115 outliers final: 67 residues processed: 221 average time/residue: 0.3752 time to fit residues: 94.8436 Evaluate side-chains 195 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 115 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 193 GLU 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 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 313 ILE 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 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 201 SER 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 230 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 ARG 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 18 LEU 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 179 LEU 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 29 ASP Chi-restraints excluded: chain F residue 32 GLN 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 79 VAL 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 231 LEU 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: 8.9990 chunk 96 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** C 129 GLN ** D 141 ASN ** 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 = 0.4715 r_free = 0.4715 target = 0.231981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.189240 restraints weight = 21392.157| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.61 r_work: 0.4157 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15262 Z= 0.178 Angle : 0.619 12.447 20849 Z= 0.317 Chirality : 0.045 0.349 2331 Planarity : 0.004 0.038 2665 Dihedral : 12.224 89.774 2437 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 7.78 % Allowed : 24.48 % 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: -0.92 (0.19), residues: 1832 helix: 0.36 (0.22), residues: 543 sheet: -0.79 (0.30), residues: 309 loop : -1.08 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.014 0.002 TYR E 271 PHE 0.020 0.002 PHE A 59 TRP 0.012 0.001 TRP C 30 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (15262) covalent geometry : angle 0.61921 / 0.32 (20849) hydrogen bonds : bond 0.03953 / 2.69 ( 446) hydrogen bonds : angle 5.10499 / 3.47 ( 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 246 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 131 time to evaluate : 0.528 Fit side-chains REVERT: A 193 GLU cc_start: 0.3770 (OUTLIER) cc_final: 0.2852 (pp20) REVERT: B 161 MET cc_start: 0.6787 (mmm) cc_final: 0.5675 (pmm) REVERT: B 321 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5518 (t80) REVERT: C 98 ARG cc_start: 0.5344 (OUTLIER) cc_final: 0.3100 (mtt90) REVERT: C 172 ARG cc_start: 0.6582 (tpt-90) cc_final: 0.5535 (ptp-110) REVERT: C 250 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.7012 (mpt90) REVERT: C 291 GLN cc_start: 0.7588 (mp10) cc_final: 0.5914 (tp40) REVERT: C 335 VAL cc_start: 0.5919 (t) cc_final: 0.5351 (t) REVERT: D 305 TYR cc_start: 0.2589 (OUTLIER) cc_final: 0.1370 (m-80) REVERT: E 167 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: E 338 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: F 15 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: F 29 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6351 (m-30) REVERT: F 55 ASN cc_start: 0.7636 (p0) cc_final: 0.6867 (p0) REVERT: F 174 TRP cc_start: 0.5870 (OUTLIER) cc_final: 0.4855 (m-10) REVERT: F 230 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: F 232 ILE cc_start: 0.5959 (OUTLIER) cc_final: 0.5734 (pp) REVERT: F 260 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7100 (mt) REVERT: F 299 LYS cc_start: 0.7080 (tppt) cc_final: 0.6829 (tmmm) outliers start: 115 outliers final: 65 residues processed: 228 average time/residue: 0.4121 time to fit residues: 107.2179 Evaluate side-chains 192 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 114 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 298 LEU 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 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 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 228 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 ARG 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 8 THR Chi-restraints excluded: chain D residue 18 LEU 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 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 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 21 SER Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 32 GLN 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 231 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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** B 173 GLN ** 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** ** 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 = 0.4719 r_free = 0.4719 target = 0.232480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.194400 restraints weight = 21152.541| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 3.26 r_work: 0.4171 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15262 Z= 0.162 Angle : 0.608 12.953 20849 Z= 0.312 Chirality : 0.045 0.355 2331 Planarity : 0.004 0.048 2665 Dihedral : 12.183 89.822 2437 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 7.44 % Allowed : 25.15 % Favored : 67.41 % 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: -0.88 (0.19), residues: 1832 helix: 0.44 (0.22), residues: 542 sheet: -0.86 (0.29), residues: 314 loop : -1.05 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 192 TYR 0.015 0.002 TYR C 285 PHE 0.009 0.001 PHE C 95 TRP 0.011 0.001 TRP C 30 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (15262) covalent geometry : angle 0.60818 / 0.31 (20849) hydrogen bonds : bond 0.03844 / 2.64 ( 446) hydrogen bonds : angle 5.00404 / 3.40 ( 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 236 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 126 time to evaluate : 0.427 Fit side-chains REVERT: A 193 GLU cc_start: 0.3618 (OUTLIER) cc_final: 0.2705 (pp20) REVERT: B 161 MET cc_start: 0.6801 (mmm) cc_final: 0.5614 (pmm) REVERT: B 206 GLU cc_start: 0.4085 (OUTLIER) cc_final: 0.3758 (tp30) REVERT: B 274 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6815 (pp20) REVERT: B 321 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5528 (t80) REVERT: C 37 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: C 98 ARG cc_start: 0.5356 (OUTLIER) cc_final: 0.3093 (mtt90) REVERT: C 159 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: C 172 ARG cc_start: 0.6538 (tpt-90) cc_final: 0.5441 (ptp-110) REVERT: C 192 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5326 (mm) REVERT: C 193 ASP cc_start: 0.6529 (m-30) cc_final: 0.6323 (m-30) REVERT: C 250 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.7037 (mpt90) REVERT: C 291 GLN cc_start: 0.7565 (mp10) cc_final: 0.5952 (tp40) REVERT: C 335 VAL cc_start: 0.5929 (t) cc_final: 0.5419 (t) REVERT: D 305 TYR cc_start: 0.2614 (OUTLIER) cc_final: 0.1547 (m-80) REVERT: E 167 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: E 297 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7405 (tm-30) REVERT: E 327 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.7033 (mp) REVERT: E 338 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: F 15 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: F 29 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6262 (m-30) REVERT: F 55 ASN cc_start: 0.7616 (p0) cc_final: 0.6834 (p0) REVERT: F 174 TRP cc_start: 0.5803 (OUTLIER) cc_final: 0.4859 (m-10) REVERT: F 230 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: F 232 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5708 (pp) REVERT: F 260 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6966 (mt) REVERT: F 299 LYS cc_start: 0.7151 (tppt) cc_final: 0.6897 (tmmm) outliers start: 110 outliers final: 60 residues processed: 218 average time/residue: 0.4282 time to fit residues: 106.4777 Evaluate side-chains 193 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 114 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 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 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 298 LEU 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 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 159 GLU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 201 SER 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 230 GLU Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 321 GLU 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 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 287 SER Chi-restraints excluded: chain E residue 300 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 11 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 32 GLN 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 79 VAL 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 Chi-restraints excluded: chain F residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 129 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.232124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.189554 restraints weight = 21061.107| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.60 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: 0.6974 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15262 Z= 0.172 Angle : 0.619 13.675 20849 Z= 0.316 Chirality : 0.045 0.356 2331 Planarity : 0.004 0.050 2665 Dihedral : 12.144 90.213 2432 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 7.44 % Allowed : 25.15 % Favored : 67.41 % 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: -0.92 (0.19), residues: 1832 helix: 0.43 (0.22), residues: 542 sheet: -0.98 (0.29), residues: 307 loop : -1.04 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 192 TYR 0.015 0.002 TYR D 114 PHE 0.024 0.002 PHE A 59 TRP 0.015 0.001 TRP B 239 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (15262) covalent geometry : angle 0.61853 / 0.32 (20849) hydrogen bonds : bond 0.03832 / 2.61 ( 446) hydrogen bonds : angle 5.00109 / 3.41 ( 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 237 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 127 time to evaluate : 0.623 Fit side-chains REVERT: A 193 GLU cc_start: 0.3636 (OUTLIER) cc_final: 0.2627 (pp20) REVERT: B 65 ARG cc_start: 0.7921 (ptp-110) cc_final: 0.7713 (ptp-110) REVERT: B 161 MET cc_start: 0.6772 (mmm) cc_final: 0.5682 (pmm) REVERT: B 206 GLU cc_start: 0.4106 (OUTLIER) cc_final: 0.3677 (tp30) REVERT: B 321 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5528 (t80) REVERT: C 37 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: C 98 ARG cc_start: 0.5325 (OUTLIER) cc_final: 0.3070 (mtt90) REVERT: C 159 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6714 (tt0) REVERT: C 172 ARG cc_start: 0.6640 (tpt-90) cc_final: 0.5457 (ptp-170) REVERT: C 192 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5589 (mm) REVERT: C 193 ASP cc_start: 0.6568 (m-30) cc_final: 0.6325 (m-30) REVERT: C 291 GLN cc_start: 0.7595 (mp10) cc_final: 0.5950 (tp40) REVERT: C 335 VAL cc_start: 0.5874 (t) cc_final: 0.5390 (t) REVERT: D 305 TYR cc_start: 0.2715 (OUTLIER) cc_final: 0.1610 (m-80) REVERT: E 167 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6954 (mt0) REVERT: E 327 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7172 (mp) REVERT: E 338 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: F 15 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: F 29 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.6300 (m-30) REVERT: F 55 ASN cc_start: 0.7624 (p0) cc_final: 0.6869 (p0) REVERT: F 174 TRP cc_start: 0.5872 (OUTLIER) cc_final: 0.4947 (m-10) REVERT: F 230 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: F 232 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5809 (pp) REVERT: F 260 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.7061 (mt) outliers start: 110 outliers final: 62 residues processed: 220 average time/residue: 0.4399 time to fit residues: 109.6052 Evaluate side-chains 189 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 110 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 193 GLU 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 298 LEU 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 77 GLN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 230 GLU 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 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 179 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 287 SER 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 11 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 32 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 146 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 93 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 141 ASN ** D 164 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.234916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.197396 restraints weight = 21238.724| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 3.19 r_work: 0.4196 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15262 Z= 0.116 Angle : 0.576 12.444 20849 Z= 0.295 Chirality : 0.043 0.314 2331 Planarity : 0.004 0.058 2665 Dihedral : 12.014 89.319 2432 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.41 % Allowed : 27.65 % Favored : 66.94 % 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: -0.66 (0.19), residues: 1832 helix: 0.70 (0.22), residues: 543 sheet: -0.91 (0.29), residues: 315 loop : -0.89 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 192 TYR 0.011 0.001 TYR C 285 PHE 0.008 0.001 PHE A 250 TRP 0.009 0.001 TRP F 270 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15262) covalent geometry : angle 0.57634 / 0.30 (20849) hydrogen bonds : bond 0.03403 / 2.34 ( 446) hydrogen bonds : angle 4.73521 / 3.22 ( 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 205 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 125 time to evaluate : 0.541 Fit side-chains REVERT: A 91 TRP cc_start: 0.2643 (OUTLIER) cc_final: 0.2413 (t60) REVERT: A 193 GLU cc_start: 0.3469 (OUTLIER) cc_final: 0.2536 (pp20) REVERT: A 247 GLU cc_start: 0.7196 (pp20) cc_final: 0.6905 (pt0) REVERT: B 65 ARG cc_start: 0.7956 (ptp-110) cc_final: 0.7730 (ptp-110) REVERT: B 161 MET cc_start: 0.6680 (mmm) cc_final: 0.5490 (pmm) REVERT: B 244 LYS cc_start: 0.6427 (mttt) cc_final: 0.5682 (mtpt) REVERT: B 274 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6680 (pp20) REVERT: B 286 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7082 (tp) REVERT: B 321 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.5442 (t80) REVERT: C 37 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6644 (mp10) REVERT: C 98 ARG cc_start: 0.5224 (OUTLIER) cc_final: 0.2945 (mtt90) REVERT: C 172 ARG cc_start: 0.6538 (tpt-90) cc_final: 0.5337 (ptp-170) REVERT: C 291 GLN cc_start: 0.7510 (mp10) cc_final: 0.5897 (tp40) REVERT: D 305 TYR cc_start: 0.2754 (OUTLIER) cc_final: 0.1779 (m-80) REVERT: E 167 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: E 327 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6995 (mp) REVERT: F 15 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: F 29 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6291 (m-30) REVERT: F 55 ASN cc_start: 0.7535 (p0) cc_final: 0.6777 (p0) REVERT: F 230 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7205 (mm-30) outliers start: 80 outliers final: 36 residues processed: 191 average time/residue: 0.4420 time to fit residues: 96.0750 Evaluate side-chains 165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 B residue 274 GLU 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 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 170 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 233 LEU 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 134 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 21 SER 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 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: 5.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 154 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN A 301 ASN D 141 ASN ** 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 = 0.4739 r_free = 0.4739 target = 0.235122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.197594 restraints weight = 21342.335| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.72 r_work: 0.4202 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15262 Z= 0.118 Angle : 0.579 13.429 20849 Z= 0.295 Chirality : 0.043 0.348 2331 Planarity : 0.004 0.060 2665 Dihedral : 11.804 90.427 2425 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.19 % Allowed : 29.14 % Favored : 66.67 % 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: -0.54 (0.20), residues: 1832 helix: 0.78 (0.22), residues: 543 sheet: -0.80 (0.30), residues: 309 loop : -0.82 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 192 TYR 0.016 0.001 TYR D 114 PHE 0.025 0.001 PHE A 59 TRP 0.021 0.001 TRP F 174 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15262) covalent geometry : angle 0.57856 / 0.29 (20849) hydrogen bonds : bond 0.03316 / 2.28 ( 446) hydrogen bonds : angle 4.65308 / 3.17 ( 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 183 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 121 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.2626 (OUTLIER) cc_final: 0.2396 (t60) REVERT: A 193 GLU cc_start: 0.3456 (OUTLIER) cc_final: 0.2514 (pp20) REVERT: B 65 ARG cc_start: 0.7924 (ptp-110) cc_final: 0.7702 (ptp-110) REVERT: B 161 MET cc_start: 0.6606 (mmm) cc_final: 0.4938 (ppp) REVERT: B 244 LYS cc_start: 0.6581 (mttt) cc_final: 0.6125 (mtpt) REVERT: B 274 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6633 (pp20) REVERT: B 286 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7019 (tp) REVERT: B 321 PHE cc_start: 0.6071 (OUTLIER) cc_final: 0.5413 (t80) REVERT: C 37 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6598 (mp10) REVERT: C 98 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.2981 (mtt90) REVERT: C 172 ARG cc_start: 0.6519 (tpt-90) cc_final: 0.5349 (ptp-170) REVERT: C 193 ASP cc_start: 0.6582 (m-30) cc_final: 0.6268 (m-30) REVERT: C 291 GLN cc_start: 0.7495 (mp10) cc_final: 0.5938 (tp40) REVERT: D 305 TYR cc_start: 0.2766 (OUTLIER) cc_final: 0.1743 (m-80) REVERT: E 327 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6990 (mp) REVERT: F 29 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.6228 (m-30) REVERT: F 55 ASN cc_start: 0.7481 (p0) cc_final: 0.6714 (p0) REVERT: F 230 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: F 299 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7072 (tppt) outliers start: 62 outliers final: 40 residues processed: 173 average time/residue: 0.4479 time to fit residues: 88.5146 Evaluate side-chains 167 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 115 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 274 GLU 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 37 GLN Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 83 ASN 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 170 VAL Chi-restraints excluded: chain C residue 201 SER 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 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 179 LEU Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 21 SER 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 273 ASP Chi-restraints excluded: chain F residue 299 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.0270 chunk 78 optimal weight: 0.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 ASN D 144 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 = 0.4742 r_free = 0.4742 target = 0.235360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.197321 restraints weight = 21284.171| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 3.22 r_work: 0.4207 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1492 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= 0.120 Angle : 0.580 13.160 20849 Z= 0.296 Chirality : 0.042 0.349 2331 Planarity : 0.004 0.060 2665 Dihedral : 11.756 90.713 2425 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.39 % Allowed : 29.07 % Favored : 66.53 % 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: -0.46 (0.20), residues: 1832 helix: 0.88 (0.22), residues: 537 sheet: -0.79 (0.30), residues: 309 loop : -0.77 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 192 TYR 0.017 0.001 TYR C 285 PHE 0.007 0.001 PHE E 95 TRP 0.027 0.001 TRP F 174 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15262) covalent geometry : angle 0.58001 / 0.30 (20849) hydrogen bonds : bond 0.03284 / 2.26 ( 446) hydrogen bonds : angle 4.60953 / 3.15 ( 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 191 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 126 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.2587 (OUTLIER) cc_final: 0.2375 (t60) REVERT: A 193 GLU cc_start: 0.3449 (OUTLIER) cc_final: 0.2504 (pp20) REVERT: A 247 GLU cc_start: 0.7261 (pp20) cc_final: 0.6929 (pt0) REVERT: B 65 ARG cc_start: 0.7942 (ptp-110) cc_final: 0.7718 (ptp-110) REVERT: B 161 MET cc_start: 0.6723 (mmm) cc_final: 0.4989 (ppp) REVERT: B 244 LYS cc_start: 0.6468 (mttt) cc_final: 0.5733 (mtpt) REVERT: B 274 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6617 (pp20) REVERT: B 286 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.6972 (tp) REVERT: B 321 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.5380 (t80) REVERT: C 37 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6699 (mp10) REVERT: C 98 ARG cc_start: 0.5243 (OUTLIER) cc_final: 0.2877 (mtt90) REVERT: C 172 ARG cc_start: 0.6503 (tpt-90) cc_final: 0.5356 (ptp-170) REVERT: C 193 ASP cc_start: 0.6587 (m-30) cc_final: 0.6273 (m-30) REVERT: C 291 GLN cc_start: 0.7490 (mp10) cc_final: 0.5939 (tp40) REVERT: D 305 TYR cc_start: 0.2785 (OUTLIER) cc_final: 0.1875 (m-80) REVERT: E 167 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: E 327 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6981 (mp) REVERT: F 29 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6230 (m-30) REVERT: F 55 ASN cc_start: 0.7490 (p0) cc_final: 0.6712 (p0) REVERT: F 174 TRP cc_start: 0.5419 (OUTLIER) cc_final: 0.4315 (m-10) REVERT: F 230 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: F 299 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7063 (tppt) outliers start: 65 outliers final: 42 residues processed: 180 average time/residue: 0.4610 time to fit residues: 94.1683 Evaluate side-chains 174 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 274 GLU 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 37 GLN Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 83 ASN 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 170 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 209 VAL 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 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 D residue 320 VAL Chi-restraints excluded: chain E residue 24 LEU 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 179 LEU Chi-restraints excluded: chain E residue 297 GLN Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 32 GLN 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 230 GLU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 299 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 34 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 chunk 165 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 301 ASN C 329 ASN D 262 ASN ** E 229 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 = 0.4745 r_free = 0.4745 target = 0.235741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.197964 restraints weight = 21152.881| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.27 r_work: 0.4208 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15262 Z= 0.116 Angle : 0.581 12.916 20849 Z= 0.295 Chirality : 0.042 0.354 2331 Planarity : 0.004 0.059 2665 Dihedral : 11.694 90.751 2422 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.19 % Allowed : 29.41 % Favored : 66.40 % 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: -0.40 (0.20), residues: 1832 helix: 0.94 (0.22), residues: 537 sheet: -0.77 (0.30), residues: 309 loop : -0.74 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 192 TYR 0.028 0.001 TYR C 247 PHE 0.022 0.001 PHE A 59 TRP 0.022 0.001 TRP F 174 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15262) covalent geometry : angle 0.58053 / 0.30 (20849) hydrogen bonds : bond 0.03226 / 2.21 ( 446) hydrogen bonds : angle 4.59049 / 3.13 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4366.08 seconds wall clock time: 75 minutes 28.53 seconds (4528.53 seconds total)