Starting phenix.real_space_refine on Thu Jul 2 08:51:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyt_60578/07_2026/8zyt_60578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyt_60578/07_2026/8zyt_60578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zyt_60578/07_2026/8zyt_60578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyt_60578/07_2026/8zyt_60578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zyt_60578/07_2026/8zyt_60578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyt_60578/07_2026/8zyt_60578.map" } resolution = 2.65 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= -0.000 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 25 5.16 5 C 5046 2.51 5 N 1360 2.21 5 O 1492 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 7930 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2648 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 28, 'TRANS': 332} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 15, 'ARG:plan': 6, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 145 Chain: "D" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1629 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1598 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 1931 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 142} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 654 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASN:plan1': 9, 'ASP:plan': 7, 'TYR:plan': 6, 'PHE:plan': 9, 'GLN:plan1': 6, 'GLU:plan': 4, 'HIS:plan': 6, 'TRP:plan': 2, 'ARG:plan': 6, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 263 Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 51 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'PIO': 1, 'SRW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 1.84, per 1000 atoms: 0.23 Number of scatterers: 7930 At special positions: 0 Unit cell: (84.872, 104.648, 160.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 6 15.00 F 1 9.00 O 1492 8.00 N 1360 7.00 C 5046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS D 119 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 155 " - pdb=" SG CYS Q 215 " distance=2.03 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 443.7 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 17 sheets defined 26.1% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.995A pdb=" N LYS B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.503A pdb=" N ASP D 113 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 114 " --> pdb=" O ALA D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 114' Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 215 through 219 removed outlier: 3.711A pdb=" N SER D 218 " --> pdb=" O PRO D 215 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 219 " --> pdb=" O SER D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 219' Processing helix chain 'Q' and resid 100 through 104 removed outlier: 3.533A pdb=" N PHE Q 104 " --> pdb=" O PRO Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 148 Processing helix chain 'Q' and resid 205 through 210 Processing helix chain 'R' and resid 59 through 90 removed outlier: 3.757A pdb=" N ARG R 90 " --> pdb=" O PHE R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 119 removed outlier: 3.747A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 127 removed outlier: 3.804A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 172 Processing helix chain 'R' and resid 172 through 179 removed outlier: 3.800A pdb=" N ALA R 176 " --> pdb=" O HIS R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 199 removed outlier: 3.734A pdb=" N ALA R 197 " --> pdb=" O TRP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 207 removed outlier: 3.728A pdb=" N LEU R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 246 through 267 removed outlier: 3.658A pdb=" N VAL R 265 " --> pdb=" O ASN R 261 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 304 through 326 removed outlier: 3.608A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE R 310 " --> pdb=" O ARG R 306 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS R 315 " --> pdb=" O ALA R 311 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU R 317 " --> pdb=" O VAL R 313 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.836A pdb=" N LEU R 324 " --> pdb=" O HIS R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 368 removed outlier: 4.013A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 378 removed outlier: 3.593A pdb=" N THR R 378 " --> pdb=" O ILE R 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 111 through 115 Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.924A pdb=" N TYR B 143 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS B 169 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N VAL B 141 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 79 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B 60 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP B 77 " --> pdb=" O PHE B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 126 through 128 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.579A pdb=" N SER B 265 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 206 through 208 removed outlier: 4.162A pdb=" N TYR B 320 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B 350 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N VAL B 318 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 229 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 230 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 256 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 232 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET B 254 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 234 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 249 " --> pdb=" O GLN R 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN R 95 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 26 through 30 Processing sheet with id=AA7, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.507A pdb=" N TRP D 59 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 73 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE D 57 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR D 132 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.507A pdb=" N TRP D 59 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 73 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE D 57 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.710A pdb=" N GLY D 169 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR D 206 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.710A pdb=" N GLY D 169 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR D 206 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 184 removed outlier: 4.477A pdb=" N TYR D 224 " --> pdb=" O VAL D 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 25 through 27 Processing sheet with id=AB4, first strand: chain 'Q' and resid 31 through 34 removed outlier: 6.336A pdb=" N LEU Q 32 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL Q 54 " --> pdb=" O TYR Q 70 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR Q 70 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP Q 56 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 31 through 34 removed outlier: 6.336A pdb=" N LEU Q 32 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR Q 118 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 135 through 139 removed outlier: 3.721A pdb=" N PHE Q 139 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL Q 154 " --> pdb=" O PHE Q 139 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR Q 194 " --> pdb=" O ASN Q 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 167 through 168 Processing sheet with id=AB8, first strand: chain 'R' and resid 209 through 210 removed outlier: 3.689A pdb=" N GLN R 210 " --> pdb=" O VAL R 223 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL R 223 " --> pdb=" O GLN R 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 406 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1257 1.30 - 1.43: 2124 1.43 - 1.56: 4679 1.56 - 1.68: 19 1.68 - 1.81: 32 Bond restraints: 8111 Sorted by residual: bond pdb=" C23 SRW R 502 " pdb=" O2 SRW R 502 " ideal model delta sigma weight residual 1.429 1.188 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C13 SRW R 502 " pdb=" N1 SRW R 502 " ideal model delta sigma weight residual 1.357 1.487 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" OG1 TPO R 407 " pdb=" P TPO R 407 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C3 SRW R 502 " pdb=" C8 SRW R 502 " ideal model delta sigma weight residual 1.519 1.627 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C1A PIO R 501 " pdb=" O2C PIO R 501 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 8106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 10988 2.84 - 5.67: 102 5.67 - 8.51: 19 8.51 - 11.34: 5 11.34 - 14.18: 4 Bond angle restraints: 11118 Sorted by residual: angle pdb=" C14 SRW R 502 " pdb=" C24 SRW R 502 " pdb=" C26 SRW R 502 " ideal model delta sigma weight residual 122.08 136.26 -14.18 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O11 PIO R 501 " pdb=" P1 PIO R 501 " pdb=" O12 PIO R 501 " ideal model delta sigma weight residual 121.09 109.33 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O1 PIO R 501 " pdb=" P1 PIO R 501 " pdb=" O13 PIO R 501 " ideal model delta sigma weight residual 97.64 109.24 -11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CB TPO R 407 " pdb=" OG1 TPO R 407 " pdb=" P TPO R 407 " ideal model delta sigma weight residual 119.31 107.97 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C22 SRW R 502 " pdb=" C23 SRW R 502 " pdb=" O2 SRW R 502 " ideal model delta sigma weight residual 109.10 119.75 -10.65 3.00e+00 1.11e-01 1.26e+01 ... (remaining 11113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 4604 30.68 - 61.36: 174 61.36 - 92.05: 22 92.05 - 122.73: 3 122.73 - 153.41: 5 Dihedral angle restraints: 4808 sinusoidal: 1572 harmonic: 3236 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual 93.00 159.97 -66.97 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" C25 SRW R 502 " pdb=" C24 SRW R 502 " pdb=" C26 SRW R 502 " pdb=" F1 SRW R 502 " ideal model delta sinusoidal sigma weight residual 106.02 -100.57 -153.41 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C12 SRW R 502 " pdb=" C11 SRW R 502 " pdb=" N1 SRW R 502 " pdb=" C13 SRW R 502 " ideal model delta sinusoidal sigma weight residual 130.69 -82.86 -146.45 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 4805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.021: 1318 1.021 - 2.043: 0 2.043 - 3.064: 0 3.064 - 4.085: 0 4.085 - 5.106: 1 Chirality restraints: 1319 Sorted by residual: chirality pdb=" C8 SRW R 502 " pdb=" C12 SRW R 502 " pdb=" C3 SRW R 502 " pdb=" C9 SRW R 502 " both_signs ideal model delta sigma weight residual False -2.46 2.65 -5.11 2.00e-01 2.50e+01 6.52e+02 chirality pdb=" C24 SRW R 502 " pdb=" C14 SRW R 502 " pdb=" C25 SRW R 502 " pdb=" F1 SRW R 502 " both_signs ideal model delta sigma weight residual True 1.45 1.99 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" C4 PIO R 501 " pdb=" C3 PIO R 501 " pdb=" C5 PIO R 501 " pdb=" O4 PIO R 501 " both_signs ideal model delta sigma weight residual False 2.50 2.35 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1316 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 12 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO B 13 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 194 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO B 195 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 148 " -0.038 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO D 149 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.031 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 183 2.69 - 3.24: 7296 3.24 - 3.79: 12205 3.79 - 4.35: 15694 4.35 - 4.90: 26984 Nonbonded interactions: 62362 Sorted by model distance: nonbonded pdb=" O PRO D 153 " pdb=" OG SER Q 142 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASP B 203 " pdb=" OH TYR B 207 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP B 296 " pdb=" OH TYR D 80 " model vdw 2.236 3.040 nonbonded pdb=" O PRO B 123 " pdb=" OH TYR B 143 " model vdw 2.254 3.040 nonbonded pdb=" N GLU Q 102 " pdb=" OE1 GLU Q 102 " model vdw 2.264 3.120 ... (remaining 62357 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.190 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.006 0.241 8114 Z= 0.302 Angle : 0.735 14.178 11124 Z= 0.330 Chirality : 0.148 5.106 1319 Planarity : 0.005 0.065 1412 Dihedral : 17.394 153.408 2711 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.27 % Allowed : 26.16 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.27), residues: 1086 helix: 2.21 (0.34), residues: 253 sheet: -0.11 (0.30), residues: 340 loop : -1.20 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 372 TYR 0.015 0.001 TYR R 167 PHE 0.025 0.002 PHE D 125 TRP 0.007 0.001 TRP R 316 HIS 0.011 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.30 ( 8111) covalent geometry : angle 0.73559 / 0.33 (11118) SS BOND : bond 0.00152 / 0.06 ( 3) SS BOND : angle 0.52826 / 0.29 ( 6) hydrogen bonds : bond 0.21219 / 14.24 ( 377) hydrogen bonds : angle 8.18320 / 5.72 ( 1131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.304 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 120 average time/residue: 0.3822 time to fit residues: 49.8287 Evaluate side-chains 115 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS R 320 HIS R 365 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.196562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129787 restraints weight = 9760.105| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.26 r_work: 0.3471 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 8114 Z= 0.314 Angle : 0.732 7.857 11124 Z= 0.372 Chirality : 0.049 0.284 1319 Planarity : 0.006 0.073 1412 Dihedral : 13.917 148.999 1239 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.04 % Allowed : 21.25 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.26), residues: 1086 helix: 1.97 (0.33), residues: 251 sheet: -0.08 (0.29), residues: 331 loop : -1.37 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 24 TYR 0.016 0.002 TYR Q 112 PHE 0.046 0.003 PHE D 125 TRP 0.008 0.002 TRP Q 169 HIS 0.004 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.31 ( 8111) covalent geometry : angle 0.73143 / 0.37 (11118) SS BOND : bond 0.00368 / 0.17 ( 3) SS BOND : angle 1.03151 / 0.61 ( 6) hydrogen bonds : bond 0.04545 / 3.02 ( 377) hydrogen bonds : angle 5.74110 / 4.03 ( 1131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: D 36 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7462 (mm110) outliers start: 37 outliers final: 15 residues processed: 146 average time/residue: 0.3624 time to fit residues: 57.3746 Evaluate side-chains 130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 231 ASN R 172 HIS R 365 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.200049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.133708 restraints weight = 9651.576| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.32 r_work: 0.3523 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8114 Z= 0.142 Angle : 0.592 7.602 11124 Z= 0.298 Chirality : 0.044 0.258 1319 Planarity : 0.005 0.066 1412 Dihedral : 13.644 148.016 1235 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.50 % Allowed : 22.21 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.26), residues: 1086 helix: 2.28 (0.33), residues: 252 sheet: -0.02 (0.28), residues: 338 loop : -1.31 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 160 TYR 0.012 0.001 TYR Q 112 PHE 0.028 0.002 PHE D 125 TRP 0.007 0.001 TRP Q 169 HIS 0.004 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8111) covalent geometry : angle 0.59200 / 0.30 (11118) SS BOND : bond 0.00186 / 0.08 ( 3) SS BOND : angle 0.63999 / 0.38 ( 6) hydrogen bonds : bond 0.03309 / 2.23 ( 377) hydrogen bonds : angle 5.05822 / 3.55 ( 1131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: B 220 THR cc_start: 0.7457 (OUTLIER) cc_final: 0.7181 (p) REVERT: B 361 HIS cc_start: 0.4742 (m90) cc_final: 0.4413 (m90) REVERT: Q 154 VAL cc_start: 0.7855 (m) cc_final: 0.7604 (t) REVERT: R 90 ARG cc_start: 0.3890 (ptt180) cc_final: 0.3541 (tmm160) REVERT: R 378 THR cc_start: 0.5855 (p) cc_final: 0.5294 (p) outliers start: 33 outliers final: 12 residues processed: 145 average time/residue: 0.3129 time to fit residues: 49.8005 Evaluate side-chains 128 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 59 GLN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS ** R 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.200690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134215 restraints weight = 9799.553| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.36 r_work: 0.3525 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8114 Z= 0.134 Angle : 0.586 7.865 11124 Z= 0.291 Chirality : 0.044 0.225 1319 Planarity : 0.005 0.063 1412 Dihedral : 13.592 147.931 1235 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.36 % Allowed : 23.02 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.26), residues: 1086 helix: 2.40 (0.33), residues: 251 sheet: 0.12 (0.28), residues: 346 loop : -1.27 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 160 TYR 0.013 0.001 TYR B 248 PHE 0.025 0.001 PHE D 125 TRP 0.008 0.001 TRP R 316 HIS 0.005 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8111) covalent geometry : angle 0.58599 / 0.29 (11118) SS BOND : bond 0.00173 / 0.08 ( 3) SS BOND : angle 0.54331 / 0.32 ( 6) hydrogen bonds : bond 0.02945 / 1.98 ( 377) hydrogen bonds : angle 4.75526 / 3.34 ( 1131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 220 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7228 (p) REVERT: R 90 ARG cc_start: 0.3832 (ptt180) cc_final: 0.3455 (tmm160) REVERT: R 378 THR cc_start: 0.5930 (p) cc_final: 0.5351 (p) outliers start: 32 outliers final: 14 residues processed: 141 average time/residue: 0.2795 time to fit residues: 43.2891 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS R 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.199267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134702 restraints weight = 9760.745| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.66 r_work: 0.3484 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8114 Z= 0.187 Angle : 0.619 9.027 11124 Z= 0.309 Chirality : 0.045 0.211 1319 Planarity : 0.005 0.063 1412 Dihedral : 13.629 148.164 1235 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.31 % Allowed : 22.75 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.26), residues: 1086 helix: 2.36 (0.33), residues: 252 sheet: 0.14 (0.28), residues: 353 loop : -1.39 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 372 TYR 0.015 0.002 TYR Q 112 PHE 0.032 0.002 PHE D 125 TRP 0.007 0.001 TRP D 126 HIS 0.005 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 8111) covalent geometry : angle 0.61907 / 0.31 (11118) SS BOND : bond 0.00204 / 0.08 ( 3) SS BOND : angle 0.64869 / 0.37 ( 6) hydrogen bonds : bond 0.03119 / 2.08 ( 377) hydrogen bonds : angle 4.73234 / 3.33 ( 1131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 220 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7252 (p) REVERT: D 36 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7401 (mm110) REVERT: R 90 ARG cc_start: 0.3809 (ptt180) cc_final: 0.3507 (tmm160) REVERT: R 378 THR cc_start: 0.6038 (p) cc_final: 0.5448 (p) outliers start: 39 outliers final: 19 residues processed: 142 average time/residue: 0.2786 time to fit residues: 43.5301 Evaluate side-chains 136 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.200567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134090 restraints weight = 9696.997| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.33 r_work: 0.3525 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8114 Z= 0.140 Angle : 0.586 9.234 11124 Z= 0.291 Chirality : 0.044 0.193 1319 Planarity : 0.005 0.060 1412 Dihedral : 13.562 147.507 1235 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.22 % Allowed : 24.11 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.26), residues: 1086 helix: 2.43 (0.33), residues: 252 sheet: 0.23 (0.28), residues: 353 loop : -1.36 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 372 TYR 0.012 0.001 TYR Q 112 PHE 0.027 0.002 PHE D 125 TRP 0.007 0.001 TRP D 70 HIS 0.006 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8111) covalent geometry : angle 0.58579 / 0.29 (11118) SS BOND : bond 0.00176 / 0.08 ( 3) SS BOND : angle 0.56710 / 0.33 ( 6) hydrogen bonds : bond 0.02819 / 1.88 ( 377) hydrogen bonds : angle 4.54556 / 3.19 ( 1131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7219 (p) REVERT: R 90 ARG cc_start: 0.3839 (ptt180) cc_final: 0.3545 (tmm160) REVERT: R 378 THR cc_start: 0.6021 (p) cc_final: 0.5444 (p) outliers start: 31 outliers final: 18 residues processed: 140 average time/residue: 0.2826 time to fit residues: 43.2505 Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 61 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.201029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134529 restraints weight = 9758.102| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.35 r_work: 0.3521 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8114 Z= 0.135 Angle : 0.581 8.658 11124 Z= 0.290 Chirality : 0.044 0.185 1319 Planarity : 0.005 0.060 1412 Dihedral : 13.514 147.469 1235 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.50 % Allowed : 23.84 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.27), residues: 1086 helix: 2.46 (0.33), residues: 252 sheet: 0.34 (0.28), residues: 353 loop : -1.34 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 372 TYR 0.013 0.001 TYR Q 112 PHE 0.025 0.002 PHE D 125 TRP 0.007 0.001 TRP R 316 HIS 0.008 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8111) covalent geometry : angle 0.58153 / 0.29 (11118) SS BOND : bond 0.00161 / 0.07 ( 3) SS BOND : angle 0.49944 / 0.29 ( 6) hydrogen bonds : bond 0.02740 / 1.83 ( 377) hydrogen bonds : angle 4.41875 / 3.09 ( 1131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 228 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8085 (tttp) REVERT: B 361 HIS cc_start: 0.5014 (m90) cc_final: 0.4688 (m90) REVERT: R 90 ARG cc_start: 0.3932 (ptt180) cc_final: 0.3394 (tmm160) REVERT: R 102 HIS cc_start: 0.7506 (p90) cc_final: 0.7292 (p90) REVERT: R 378 THR cc_start: 0.6035 (p) cc_final: 0.5436 (p) outliers start: 33 outliers final: 22 residues processed: 138 average time/residue: 0.2726 time to fit residues: 41.5945 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 63 LYS Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 0.0030 chunk 11 optimal weight: 0.9980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.199295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.132768 restraints weight = 9738.974| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.28 r_work: 0.3501 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8114 Z= 0.197 Angle : 0.634 9.300 11124 Z= 0.317 Chirality : 0.045 0.179 1319 Planarity : 0.005 0.060 1412 Dihedral : 13.569 147.682 1235 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.77 % Allowed : 23.57 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.26), residues: 1086 helix: 2.33 (0.33), residues: 252 sheet: 0.25 (0.28), residues: 353 loop : -1.41 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 372 TYR 0.016 0.002 TYR R 167 PHE 0.034 0.002 PHE D 125 TRP 0.007 0.001 TRP D 126 HIS 0.011 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 8111) covalent geometry : angle 0.63356 / 0.32 (11118) SS BOND : bond 0.00230 / 0.10 ( 3) SS BOND : angle 0.69383 / 0.40 ( 6) hydrogen bonds : bond 0.03019 / 2.00 ( 377) hydrogen bonds : angle 4.57901 / 3.20 ( 1131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: D 36 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7384 (mm110) REVERT: Q 45 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6928 (ttm110) REVERT: R 90 ARG cc_start: 0.3778 (ptt180) cc_final: 0.3542 (tmm160) REVERT: R 378 THR cc_start: 0.6221 (p) cc_final: 0.5631 (p) outliers start: 35 outliers final: 21 residues processed: 141 average time/residue: 0.3174 time to fit residues: 48.9742 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 98 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.199656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133231 restraints weight = 9642.422| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.27 r_work: 0.3510 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8114 Z= 0.184 Angle : 0.632 9.123 11124 Z= 0.316 Chirality : 0.045 0.161 1319 Planarity : 0.005 0.060 1412 Dihedral : 13.542 147.675 1235 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.09 % Allowed : 24.80 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.27), residues: 1086 helix: 2.24 (0.33), residues: 253 sheet: 0.24 (0.28), residues: 353 loop : -1.42 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 166 TYR 0.017 0.002 TYR R 167 PHE 0.032 0.002 PHE D 125 TRP 0.007 0.001 TRP D 126 HIS 0.012 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 8111) covalent geometry : angle 0.63198 / 0.32 (11118) SS BOND : bond 0.00216 / 0.10 ( 3) SS BOND : angle 0.65977 / 0.38 ( 6) hydrogen bonds : bond 0.02930 / 1.94 ( 377) hydrogen bonds : angle 4.54199 / 3.17 ( 1131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 36 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7383 (mm110) REVERT: Q 45 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6889 (ttm110) REVERT: R 90 ARG cc_start: 0.3792 (ptt180) cc_final: 0.3562 (tmm160) REVERT: R 378 THR cc_start: 0.6244 (p) cc_final: 0.5668 (p) outliers start: 30 outliers final: 23 residues processed: 136 average time/residue: 0.3198 time to fit residues: 47.6707 Evaluate side-chains 141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 36 GLN Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 95 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.198190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131305 restraints weight = 9638.445| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.28 r_work: 0.3481 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 8114 Z= 0.238 Angle : 0.682 9.524 11124 Z= 0.343 Chirality : 0.047 0.181 1319 Planarity : 0.005 0.060 1412 Dihedral : 13.648 147.347 1235 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.50 % Allowed : 24.80 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.26), residues: 1086 helix: 2.05 (0.33), residues: 254 sheet: 0.13 (0.28), residues: 353 loop : -1.50 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 166 TYR 0.016 0.002 TYR Q 112 PHE 0.038 0.002 PHE D 125 TRP 0.008 0.002 TRP Q 56 HIS 0.013 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 ( 8111) covalent geometry : angle 0.68235 / 0.34 (11118) SS BOND : bond 0.00272 / 0.13 ( 3) SS BOND : angle 0.85732 / 0.49 ( 6) hydrogen bonds : bond 0.03196 / 2.11 ( 377) hydrogen bonds : angle 4.70616 / 3.28 ( 1131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: Q 45 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6998 (ttm110) REVERT: R 90 ARG cc_start: 0.3670 (ptt180) cc_final: 0.3440 (tmm160) REVERT: R 378 THR cc_start: 0.6335 (p) cc_final: 0.5731 (p) outliers start: 33 outliers final: 20 residues processed: 135 average time/residue: 0.3346 time to fit residues: 49.3847 Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 90 ARG Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 LYS Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 172 HIS Chi-restraints excluded: chain R residue 370 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 89 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN Q 121 GLN ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.201049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134333 restraints weight = 9714.348| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.36 r_work: 0.3523 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8114 Z= 0.132 Angle : 0.614 8.964 11124 Z= 0.304 Chirality : 0.044 0.153 1319 Planarity : 0.005 0.059 1412 Dihedral : 13.501 147.291 1235 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.13 % Allowed : 26.16 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.27), residues: 1086 helix: 2.23 (0.33), residues: 253 sheet: 0.31 (0.28), residues: 353 loop : -1.46 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 372 TYR 0.015 0.001 TYR R 167 PHE 0.026 0.001 PHE D 125 TRP 0.009 0.001 TRP D 70 HIS 0.013 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8111) covalent geometry : angle 0.61415 / 0.30 (11118) SS BOND : bond 0.00150 / 0.07 ( 3) SS BOND : angle 0.53592 / 0.31 ( 6) hydrogen bonds : bond 0.02703 / 1.80 ( 377) hydrogen bonds : angle 4.45646 / 3.10 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.53 seconds wall clock time: 61 minutes 32.98 seconds (3692.98 seconds total)