Starting phenix.real_space_refine on Sun May 3 01:08:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xhi_66875/05_2026/9xhi_66875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xhi_66875/05_2026/9xhi_66875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xhi_66875/05_2026/9xhi_66875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xhi_66875/05_2026/9xhi_66875.map" model { file = "/net/cci-nas-00/data/ceres_data/9xhi_66875/05_2026/9xhi_66875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xhi_66875/05_2026/9xhi_66875.cif" } resolution = 3.2 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= 0.010 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6043 2.51 5 N 1601 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9449 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 540 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2432 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 297} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1743 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2565 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 383 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1758 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.25 Number of scatterers: 9449 At special positions: 0 Unit cell: (86.9, 119.488, 150.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1735 8.00 N 1601 7.00 C 6043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 52 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 298 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 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: 0.95 Conformation dependent library (CDL) restraints added in 306.5 milliseconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 37.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.536A pdb=" N GLN L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 87 Proline residue: R 62 - end of helix Processing helix chain 'R' and resid 91 through 120 removed outlier: 3.657A pdb=" N THR R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 125 through 159 removed outlier: 3.889A pdb=" N LYS R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 167 Processing helix chain 'R' and resid 167 through 190 Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'R' and resid 216 through 232 removed outlier: 4.195A pdb=" N PHE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 252 removed outlier: 3.906A pdb=" N GLN R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 291 removed outlier: 4.538A pdb=" N LYS R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 327 removed outlier: 4.183A pdb=" N ARG R 318 " --> pdb=" O LEU R 314 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS R 319 " --> pdb=" O ALA R 315 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 342 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.918A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 211' Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.536A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.589A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.946A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 22 through 28 removed outlier: 4.457A pdb=" N SER L 24 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU L 42 " --> pdb=" O SER L 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 197 through 200 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.210A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.581A pdb=" N ALA B 59 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 73 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 82 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS B 88 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 104 removed outlier: 6.193A pdb=" N CYS B 120 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 137 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 122 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 150 removed outlier: 3.766A pdb=" N CYS B 147 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP B 169 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN B 175 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 186 through 191 removed outlier: 7.183A pdb=" N GLY B 201 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 189 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 199 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU B 191 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 197 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP B 211 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS B 217 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 228 through 233 removed outlier: 6.816A pdb=" N GLY B 243 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE B 231 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA B 241 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE B 233 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA B 239 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS B 249 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 262 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 251 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 272 through 277 removed outlier: 6.737A pdb=" N ASP B 297 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG B 303 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.529A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.599A pdb=" N THR D 129 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 148 " --> pdb=" O THR D 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 182 through 183 removed outlier: 5.309A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1386 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: 1.34 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3017 1.34 - 1.46: 2339 1.46 - 1.58: 4189 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 9643 Sorted by residual: bond pdb=" C2 CLR R 601 " pdb=" C3 CLR R 601 " ideal model delta sigma weight residual 1.515 1.558 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" C3 CLR R 601 " pdb=" C4 CLR R 601 " ideal model delta sigma weight residual 1.526 1.553 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C VAL R 234 " pdb=" N PRO R 235 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.40e+00 bond pdb=" C13 CLR R 601 " pdb=" C18 CLR R 601 " ideal model delta sigma weight residual 1.532 1.555 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" CA LEU R 111 " pdb=" C LEU R 111 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.23e-02 6.61e+03 1.30e+00 ... (remaining 9638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 12713 1.63 - 3.27: 289 3.27 - 4.90: 43 4.90 - 6.53: 16 6.53 - 8.16: 6 Bond angle restraints: 13067 Sorted by residual: angle pdb=" C CYS R 319 " pdb=" N CYS R 320 " pdb=" CA CYS R 320 " ideal model delta sigma weight residual 122.06 116.63 5.43 1.86e+00 2.89e-01 8.52e+00 angle pdb=" C GLN L 14 " pdb=" N ARG L 15 " pdb=" CA ARG L 15 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.82e+00 angle pdb=" C GLN L 28 " pdb=" N GLU L 29 " pdb=" CA GLU L 29 " ideal model delta sigma weight residual 120.97 128.69 -7.72 2.84e+00 1.24e-01 7.40e+00 angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 122.82 126.58 -3.76 1.42e+00 4.96e-01 7.00e+00 angle pdb=" CA LEU B 189 " pdb=" CB LEU B 189 " pdb=" CG LEU B 189 " ideal model delta sigma weight residual 116.30 124.46 -8.16 3.50e+00 8.16e-02 5.44e+00 ... (remaining 13062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.59: 5266 19.59 - 39.18: 448 39.18 - 58.78: 59 58.78 - 78.37: 11 78.37 - 97.96: 6 Dihedral angle restraints: 5790 sinusoidal: 2261 harmonic: 3529 Sorted by residual: dihedral pdb=" CB CYS L 8 " pdb=" SG CYS L 8 " pdb=" SG CYS L 34 " pdb=" CB CYS L 34 " ideal model delta sinusoidal sigma weight residual 93.00 153.16 -60.16 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 298 " pdb=" CB CYS R 298 " ideal model delta sinusoidal sigma weight residual 93.00 147.37 -54.37 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" SG CYS L 8 " pdb=" CB CYS L 34 " pdb=" SG CYS L 34 " pdb=" CA CYS L 34 " ideal model delta sinusoidal sigma weight residual 79.00 5.13 73.87 1 2.00e+01 2.50e-03 1.73e+01 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1298 0.067 - 0.134: 194 0.134 - 0.201: 9 0.201 - 0.268: 1 0.268 - 0.335: 2 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C9 CLR R 601 " pdb=" C10 CLR R 601 " pdb=" C11 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.45 -2.73 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C17 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C16 CLR R 601 " pdb=" C20 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.55 2.80 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1501 not shown) Planarity restraints: 1637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 234 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO B 235 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 83 " 0.015 2.00e-02 2.50e+03 1.19e-02 2.83e+00 pdb=" CG TYR R 83 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR R 83 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR R 83 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 83 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR R 83 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 83 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 83 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 61 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO R 62 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 62 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 62 " -0.022 5.00e-02 4.00e+02 ... (remaining 1634 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 637 2.74 - 3.28: 9395 3.28 - 3.82: 16270 3.82 - 4.36: 19041 4.36 - 4.90: 33231 Nonbonded interactions: 78574 Sorted by model distance: nonbonded pdb=" O ILE B 57 " pdb=" OG SER B 315 " model vdw 2.198 3.040 nonbonded pdb=" O ALA R 103 " pdb=" OG SER R 139 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP B 162 " pdb=" OG1 THR B 164 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR B 273 " pdb=" O VAL B 314 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 274 " pdb=" O SER B 315 " model vdw 2.275 3.040 ... (remaining 78569 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 9649 Z= 0.146 Angle : 0.631 8.165 13079 Z= 0.328 Chirality : 0.047 0.335 1504 Planarity : 0.004 0.058 1637 Dihedral : 14.540 97.961 3492 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.24), residues: 1195 helix: 0.74 (0.25), residues: 416 sheet: -0.06 (0.31), residues: 264 loop : -1.41 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 62 TYR 0.028 0.001 TYR R 83 PHE 0.014 0.002 PHE A 189 TRP 0.020 0.002 TRP R 59 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9643) covalent geometry : angle 0.63051 (13067) SS BOND : bond 0.00480 ( 6) SS BOND : angle 1.27741 ( 12) hydrogen bonds : bond 0.12511 ( 471) hydrogen bonds : angle 6.33064 ( 1386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 6 GLN cc_start: 0.7905 (mt0) cc_final: 0.7573 (mt0) REVERT: L 42 LEU cc_start: 0.8963 (mm) cc_final: 0.8566 (mm) REVERT: L 61 GLN cc_start: 0.9457 (mp10) cc_final: 0.9009 (mp10) REVERT: R 44 PHE cc_start: 0.6756 (m-80) cc_final: 0.6470 (m-80) REVERT: R 65 TYR cc_start: 0.7466 (m-10) cc_final: 0.7070 (m-10) REVERT: R 120 LYS cc_start: 0.7724 (mttt) cc_final: 0.7299 (mmtt) REVERT: R 135 ILE cc_start: 0.8436 (tp) cc_final: 0.8119 (tp) REVERT: R 210 CYS cc_start: 0.5980 (t) cc_final: 0.5576 (t) REVERT: A 247 MET cc_start: 0.8286 (ttt) cc_final: 0.7936 (ttt) REVERT: A 251 ASP cc_start: 0.7270 (m-30) cc_final: 0.6816 (m-30) REVERT: A 269 ASN cc_start: 0.7425 (p0) cc_final: 0.7224 (p0) REVERT: A 270 LYS cc_start: 0.7207 (ptpp) cc_final: 0.6601 (ttpt) REVERT: A 302 TYR cc_start: 0.7665 (t80) cc_final: 0.7416 (t80) REVERT: B 296 TRP cc_start: 0.7927 (m100) cc_final: 0.7706 (m100) REVERT: C 18 GLN cc_start: 0.8422 (tp40) cc_final: 0.8068 (tp-100) REVERT: C 31 SER cc_start: 0.7463 (t) cc_final: 0.7214 (m) REVERT: C 47 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8638 (mt-10) REVERT: D 113 GLN cc_start: 0.7004 (mm110) cc_final: 0.6170 (mt0) REVERT: D 126 ILE cc_start: 0.8136 (mt) cc_final: 0.7794 (mt) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1129 time to fit residues: 39.3011 Evaluate side-chains 204 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN R 99 ASN R 322 ASN R 335 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 175 GLN B 229 ASN C 24 ASN D 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.188717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156488 restraints weight = 12910.577| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.16 r_work: 0.3693 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9649 Z= 0.157 Angle : 0.589 9.009 13079 Z= 0.305 Chirality : 0.043 0.200 1504 Planarity : 0.004 0.046 1637 Dihedral : 5.257 34.968 1374 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.96 % Allowed : 11.18 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.24 (0.24), residues: 1195 helix: 1.12 (0.25), residues: 423 sheet: -0.17 (0.31), residues: 258 loop : -1.22 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 148 TYR 0.017 0.002 TYR C 40 PHE 0.015 0.002 PHE A 334 TRP 0.021 0.001 TRP R 59 HIS 0.004 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9643) covalent geometry : angle 0.58841 (13067) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.21568 ( 12) hydrogen bonds : bond 0.04540 ( 471) hydrogen bonds : angle 5.11630 ( 1386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.8066 (ptp-110) cc_final: 0.7831 (ptp-170) REVERT: L 61 GLN cc_start: 0.9411 (mp10) cc_final: 0.9122 (mp10) REVERT: R 120 LYS cc_start: 0.7801 (mttt) cc_final: 0.7435 (mmtt) REVERT: R 135 ILE cc_start: 0.7924 (tp) cc_final: 0.7658 (tp) REVERT: R 200 GLN cc_start: 0.6800 (tt0) cc_final: 0.6506 (tt0) REVERT: R 324 PHE cc_start: 0.8519 (m-10) cc_final: 0.8299 (m-10) REVERT: A 200 ASP cc_start: 0.7499 (t0) cc_final: 0.7285 (t0) REVERT: A 270 LYS cc_start: 0.7168 (ptpp) cc_final: 0.6725 (ptmt) REVERT: A 302 TYR cc_start: 0.7645 (t80) cc_final: 0.7442 (t80) REVERT: A 346 ASN cc_start: 0.8142 (t0) cc_final: 0.7497 (m110) REVERT: C 18 GLN cc_start: 0.8442 (tp40) cc_final: 0.8183 (tp-100) REVERT: C 31 SER cc_start: 0.7540 (t) cc_final: 0.7147 (m) REVERT: C 47 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8651 (mt-10) REVERT: D 113 GLN cc_start: 0.7018 (mm110) cc_final: 0.5970 (mt0) REVERT: D 126 ILE cc_start: 0.8153 (mt) cc_final: 0.7833 (mt) REVERT: D 233 LEU cc_start: 0.8150 (mt) cc_final: 0.7941 (mt) outliers start: 20 outliers final: 16 residues processed: 228 average time/residue: 0.1132 time to fit residues: 34.7633 Evaluate side-chains 219 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN B 294 ASN C 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.188849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.156551 restraints weight = 12911.755| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.19 r_work: 0.3695 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9649 Z= 0.143 Angle : 0.563 7.256 13079 Z= 0.294 Chirality : 0.042 0.184 1504 Planarity : 0.004 0.045 1637 Dihedral : 4.904 33.569 1374 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.25 % Allowed : 13.63 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.14 (0.24), residues: 1195 helix: 1.37 (0.25), residues: 420 sheet: -0.15 (0.32), residues: 256 loop : -1.27 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.016 0.001 TYR R 83 PHE 0.013 0.001 PHE A 334 TRP 0.022 0.001 TRP R 59 HIS 0.004 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9643) covalent geometry : angle 0.56243 (13067) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.94150 ( 12) hydrogen bonds : bond 0.04315 ( 471) hydrogen bonds : angle 4.95088 ( 1386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.8100 (ptp-110) cc_final: 0.7849 (ptp-170) REVERT: L 42 LEU cc_start: 0.8937 (mm) cc_final: 0.8559 (mm) REVERT: R 48 CYS cc_start: 0.2739 (OUTLIER) cc_final: 0.2452 (m) REVERT: R 120 LYS cc_start: 0.7830 (mttt) cc_final: 0.7461 (mmtt) REVERT: A 251 ASP cc_start: 0.6944 (m-30) cc_final: 0.6331 (m-30) REVERT: A 270 LYS cc_start: 0.7104 (ptpp) cc_final: 0.6735 (ptmt) REVERT: A 330 LYS cc_start: 0.8076 (ptpp) cc_final: 0.7542 (tptt) REVERT: A 346 ASN cc_start: 0.8145 (t0) cc_final: 0.7522 (m110) REVERT: B 18 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.8365 (tmm-80) REVERT: C 18 GLN cc_start: 0.8483 (tp40) cc_final: 0.8271 (tp40) REVERT: C 31 SER cc_start: 0.7554 (t) cc_final: 0.7229 (m) REVERT: C 47 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8641 (mt-10) REVERT: D 113 GLN cc_start: 0.7128 (mm110) cc_final: 0.6103 (mt0) REVERT: D 126 ILE cc_start: 0.8140 (mt) cc_final: 0.7832 (mt) outliers start: 23 outliers final: 16 residues processed: 223 average time/residue: 0.1105 time to fit residues: 33.4023 Evaluate side-chains 212 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 48 CYS Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.185333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152838 restraints weight = 13006.840| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.34 r_work: 0.3640 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9649 Z= 0.216 Angle : 0.614 7.110 13079 Z= 0.319 Chirality : 0.045 0.211 1504 Planarity : 0.004 0.042 1637 Dihedral : 5.022 35.244 1374 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.24 % Allowed : 15.29 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.29 (0.24), residues: 1195 helix: 1.22 (0.25), residues: 425 sheet: -0.46 (0.31), residues: 265 loop : -1.24 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.019 0.002 TYR R 83 PHE 0.017 0.002 PHE A 199 TRP 0.022 0.002 TRP R 59 HIS 0.006 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 9643) covalent geometry : angle 0.61356 (13067) SS BOND : bond 0.00252 ( 6) SS BOND : angle 1.09321 ( 12) hydrogen bonds : bond 0.04746 ( 471) hydrogen bonds : angle 5.05077 ( 1386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.8126 (ptp-110) cc_final: 0.7818 (ptp-170) REVERT: L 42 LEU cc_start: 0.8995 (mm) cc_final: 0.8704 (mm) REVERT: L 61 GLN cc_start: 0.9400 (mp10) cc_final: 0.9082 (mp10) REVERT: R 120 LYS cc_start: 0.7734 (mttt) cc_final: 0.7425 (mmtt) REVERT: A 247 MET cc_start: 0.8300 (ttt) cc_final: 0.7863 (ttt) REVERT: A 251 ASP cc_start: 0.7006 (m-30) cc_final: 0.6717 (m-30) REVERT: A 270 LYS cc_start: 0.7077 (ptpp) cc_final: 0.6702 (ptmt) REVERT: A 346 ASN cc_start: 0.8182 (t0) cc_final: 0.7531 (m110) REVERT: B 18 ARG cc_start: 0.8632 (tmm-80) cc_final: 0.8382 (tmm-80) REVERT: C 18 GLN cc_start: 0.8508 (tp40) cc_final: 0.8194 (tp40) REVERT: C 31 SER cc_start: 0.7530 (t) cc_final: 0.7218 (m) REVERT: C 47 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8679 (mt-10) REVERT: D 126 ILE cc_start: 0.8216 (mt) cc_final: 0.7906 (mt) outliers start: 33 outliers final: 26 residues processed: 228 average time/residue: 0.1138 time to fit residues: 34.6763 Evaluate side-chains 229 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.183564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150578 restraints weight = 13032.253| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.33 r_work: 0.3605 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9649 Z= 0.249 Angle : 0.654 7.813 13079 Z= 0.339 Chirality : 0.045 0.202 1504 Planarity : 0.004 0.040 1637 Dihedral : 5.132 35.825 1374 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.82 % Allowed : 15.98 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.45 (0.24), residues: 1195 helix: 1.09 (0.25), residues: 425 sheet: -0.47 (0.32), residues: 259 loop : -1.38 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.024 0.002 TYR D 95 PHE 0.018 0.002 PHE A 334 TRP 0.023 0.002 TRP R 59 HIS 0.005 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 9643) covalent geometry : angle 0.65264 (13067) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.60378 ( 12) hydrogen bonds : bond 0.04933 ( 471) hydrogen bonds : angle 5.18213 ( 1386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.8098 (ptp-110) cc_final: 0.7780 (ptp-170) REVERT: L 50 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8106 (mt-10) REVERT: L 61 GLN cc_start: 0.9404 (mp10) cc_final: 0.9080 (mp10) REVERT: R 120 LYS cc_start: 0.7776 (mttt) cc_final: 0.7460 (mmtt) REVERT: R 318 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7445 (ptt-90) REVERT: A 270 LYS cc_start: 0.7019 (ptpp) cc_final: 0.6620 (ptmt) REVERT: A 346 ASN cc_start: 0.8240 (t0) cc_final: 0.7585 (m110) REVERT: B 17 ILE cc_start: 0.9069 (tt) cc_final: 0.8843 (tp) REVERT: B 18 ARG cc_start: 0.8711 (tmm-80) cc_final: 0.8425 (tmm-80) REVERT: C 18 GLN cc_start: 0.8515 (tp40) cc_final: 0.8186 (tp40) REVERT: C 31 SER cc_start: 0.7543 (t) cc_final: 0.7225 (m) REVERT: C 47 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8711 (mt-10) REVERT: D 79 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4915 (tt) REVERT: D 113 GLN cc_start: 0.7381 (mm110) cc_final: 0.6204 (mt0) REVERT: D 126 ILE cc_start: 0.8270 (mt) cc_final: 0.7970 (mt) outliers start: 39 outliers final: 28 residues processed: 228 average time/residue: 0.1116 time to fit residues: 34.2409 Evaluate side-chains 233 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 318 ARG Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 111 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.188571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.155948 restraints weight = 12919.783| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.17 r_work: 0.3690 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9649 Z= 0.122 Angle : 0.571 7.530 13079 Z= 0.296 Chirality : 0.042 0.178 1504 Planarity : 0.004 0.041 1637 Dihedral : 4.890 36.149 1374 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.55 % Allowed : 18.04 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.19 (0.24), residues: 1195 helix: 1.42 (0.25), residues: 420 sheet: -0.38 (0.32), residues: 260 loop : -1.29 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.028 0.002 TYR D 95 PHE 0.015 0.001 PHE A 334 TRP 0.026 0.002 TRP R 59 HIS 0.003 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9643) covalent geometry : angle 0.57128 (13067) SS BOND : bond 0.00326 ( 6) SS BOND : angle 0.52515 ( 12) hydrogen bonds : bond 0.04145 ( 471) hydrogen bonds : angle 4.87057 ( 1386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.8088 (ptp-110) cc_final: 0.7726 (ptp-170) REVERT: L 50 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7970 (mt-10) REVERT: L 61 GLN cc_start: 0.9417 (mp10) cc_final: 0.9098 (mp10) REVERT: R 120 LYS cc_start: 0.7748 (mttt) cc_final: 0.7455 (mmtt) REVERT: A 247 MET cc_start: 0.8251 (ttt) cc_final: 0.7846 (ttt) REVERT: A 270 LYS cc_start: 0.6948 (ptpp) cc_final: 0.6560 (ptmt) REVERT: C 18 GLN cc_start: 0.8552 (tp40) cc_final: 0.8271 (tp40) REVERT: C 31 SER cc_start: 0.7505 (t) cc_final: 0.7194 (m) REVERT: C 47 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8671 (mt-10) REVERT: D 126 ILE cc_start: 0.8284 (mt) cc_final: 0.7932 (mt) REVERT: D 148 ARG cc_start: 0.6314 (mtm110) cc_final: 0.6085 (mtm-85) REVERT: D 162 LEU cc_start: 0.6251 (tp) cc_final: 0.5954 (tp) outliers start: 26 outliers final: 18 residues processed: 224 average time/residue: 0.1131 time to fit residues: 34.0237 Evaluate side-chains 210 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 335 ASN ** A 244 HIS ** 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 = 0.4330 r_free = 0.4330 target = 0.188151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155305 restraints weight = 12922.397| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 3.42 r_work: 0.3682 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9649 Z= 0.146 Angle : 0.588 8.568 13079 Z= 0.305 Chirality : 0.042 0.186 1504 Planarity : 0.004 0.040 1637 Dihedral : 4.913 36.490 1374 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.65 % Allowed : 19.12 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.22 (0.24), residues: 1195 helix: 1.32 (0.25), residues: 426 sheet: -0.36 (0.32), residues: 264 loop : -1.28 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 208 TYR 0.030 0.002 TYR D 95 PHE 0.028 0.002 PHE A 199 TRP 0.026 0.002 TRP R 59 HIS 0.004 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9643) covalent geometry : angle 0.58763 (13067) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.71347 ( 12) hydrogen bonds : bond 0.04238 ( 471) hydrogen bonds : angle 4.84935 ( 1386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.8107 (ptp-110) cc_final: 0.7749 (ptp-170) REVERT: R 120 LYS cc_start: 0.7739 (mttt) cc_final: 0.7467 (mmtt) REVERT: R 335 ASN cc_start: 0.8008 (m-40) cc_final: 0.7692 (m110) REVERT: A 207 GLU cc_start: 0.7766 (tt0) cc_final: 0.7497 (tp30) REVERT: A 247 MET cc_start: 0.8289 (ttt) cc_final: 0.7908 (ttt) REVERT: A 270 LYS cc_start: 0.6971 (ptpp) cc_final: 0.6565 (ptmt) REVERT: A 330 LYS cc_start: 0.8139 (ptpp) cc_final: 0.7648 (mmmm) REVERT: B 18 ARG cc_start: 0.8664 (tmm-80) cc_final: 0.8279 (tmm-80) REVERT: C 18 GLN cc_start: 0.8544 (tp40) cc_final: 0.8285 (tp40) REVERT: C 31 SER cc_start: 0.7532 (t) cc_final: 0.7205 (m) REVERT: C 47 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8691 (mt-10) REVERT: D 126 ILE cc_start: 0.8297 (mt) cc_final: 0.7953 (mt) outliers start: 27 outliers final: 23 residues processed: 219 average time/residue: 0.1102 time to fit residues: 32.5184 Evaluate side-chains 212 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 318 ARG Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.0040 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.190661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.157693 restraints weight = 12932.694| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.05 r_work: 0.3725 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9649 Z= 0.122 Angle : 0.577 9.807 13079 Z= 0.299 Chirality : 0.042 0.177 1504 Planarity : 0.003 0.041 1637 Dihedral : 4.787 36.733 1374 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.94 % Allowed : 19.22 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.13 (0.24), residues: 1195 helix: 1.39 (0.25), residues: 429 sheet: -0.29 (0.32), residues: 268 loop : -1.27 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 208 TYR 0.029 0.001 TYR D 95 PHE 0.032 0.001 PHE A 199 TRP 0.030 0.002 TRP R 59 HIS 0.003 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9643) covalent geometry : angle 0.57663 (13067) SS BOND : bond 0.00265 ( 6) SS BOND : angle 0.77323 ( 12) hydrogen bonds : bond 0.03959 ( 471) hydrogen bonds : angle 4.72812 ( 1386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.8048 (ptp-110) cc_final: 0.7702 (ptp-170) REVERT: L 50 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7777 (mt-10) REVERT: R 120 LYS cc_start: 0.7705 (mttt) cc_final: 0.7446 (mmtt) REVERT: A 270 LYS cc_start: 0.6978 (ptpp) cc_final: 0.6494 (ptmt) REVERT: A 330 LYS cc_start: 0.8086 (ptpp) cc_final: 0.7615 (mmmm) REVERT: B 18 ARG cc_start: 0.8635 (tmm-80) cc_final: 0.8241 (tmm-80) REVERT: C 18 GLN cc_start: 0.8551 (tp40) cc_final: 0.8267 (tp40) REVERT: C 31 SER cc_start: 0.7539 (t) cc_final: 0.7219 (m) REVERT: C 47 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8676 (mt-10) REVERT: D 126 ILE cc_start: 0.8297 (mt) cc_final: 0.7945 (mt) outliers start: 30 outliers final: 22 residues processed: 220 average time/residue: 0.1091 time to fit residues: 32.7844 Evaluate side-chains 215 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 318 ARG Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 2 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 43 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 103 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 335 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN D 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.187939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156192 restraints weight = 12513.033| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.39 r_work: 0.3581 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9649 Z= 0.126 Angle : 0.582 7.715 13079 Z= 0.302 Chirality : 0.042 0.186 1504 Planarity : 0.004 0.040 1637 Dihedral : 4.766 36.875 1374 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.65 % Allowed : 19.80 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.09 (0.24), residues: 1195 helix: 1.41 (0.25), residues: 429 sheet: -0.22 (0.32), residues: 261 loop : -1.25 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.033 0.002 TYR D 95 PHE 0.023 0.001 PHE A 199 TRP 0.030 0.002 TRP R 59 HIS 0.003 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9643) covalent geometry : angle 0.58179 (13067) SS BOND : bond 0.00246 ( 6) SS BOND : angle 0.79040 ( 12) hydrogen bonds : bond 0.03965 ( 471) hydrogen bonds : angle 4.72661 ( 1386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.7926 (ptp-110) cc_final: 0.7619 (ptp-170) REVERT: R 44 PHE cc_start: 0.7066 (m-80) cc_final: 0.6754 (m-80) REVERT: R 120 LYS cc_start: 0.7676 (mttt) cc_final: 0.7438 (mmtt) REVERT: R 291 PHE cc_start: 0.6704 (m-80) cc_final: 0.6390 (m-80) REVERT: A 247 MET cc_start: 0.8346 (ttt) cc_final: 0.7918 (ttt) REVERT: A 270 LYS cc_start: 0.6945 (ptpp) cc_final: 0.6555 (ptmt) REVERT: A 330 LYS cc_start: 0.8020 (ptpp) cc_final: 0.7565 (mmmm) REVERT: B 18 ARG cc_start: 0.8600 (tmm-80) cc_final: 0.8220 (tmm-80) REVERT: B 300 LYS cc_start: 0.7198 (mttm) cc_final: 0.6998 (mttm) REVERT: C 18 GLN cc_start: 0.8500 (tp40) cc_final: 0.8287 (tp40) REVERT: C 31 SER cc_start: 0.7648 (t) cc_final: 0.7312 (m) REVERT: C 47 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8654 (mt-10) REVERT: D 126 ILE cc_start: 0.8303 (mt) cc_final: 0.7964 (mt) REVERT: D 148 ARG cc_start: 0.6198 (mtm110) cc_final: 0.5979 (mtm-85) outliers start: 27 outliers final: 24 residues processed: 212 average time/residue: 0.1091 time to fit residues: 31.5797 Evaluate side-chains 216 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 318 ARG Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 GLN D 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154211 restraints weight = 12510.822| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.25 r_work: 0.3562 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9649 Z= 0.154 Angle : 0.612 7.699 13079 Z= 0.317 Chirality : 0.044 0.185 1504 Planarity : 0.004 0.040 1637 Dihedral : 4.845 37.077 1374 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.65 % Allowed : 19.90 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.17 (0.24), residues: 1195 helix: 1.28 (0.25), residues: 429 sheet: -0.24 (0.32), residues: 261 loop : -1.24 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.025 0.002 TYR D 95 PHE 0.025 0.002 PHE R 60 TRP 0.029 0.002 TRP R 59 HIS 0.005 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9643) covalent geometry : angle 0.61153 (13067) SS BOND : bond 0.00258 ( 6) SS BOND : angle 0.96213 ( 12) hydrogen bonds : bond 0.04184 ( 471) hydrogen bonds : angle 4.84033 ( 1386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 ARG cc_start: 0.7947 (ptp-110) cc_final: 0.7633 (ptp-170) REVERT: L 50 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7651 (mt-10) REVERT: R 44 PHE cc_start: 0.7114 (m-80) cc_final: 0.6831 (m-80) REVERT: R 120 LYS cc_start: 0.7691 (mttt) cc_final: 0.7472 (mmtt) REVERT: R 206 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7222 (mp-120) REVERT: A 247 MET cc_start: 0.8381 (ttt) cc_final: 0.7976 (ttt) REVERT: A 270 LYS cc_start: 0.6939 (ptpp) cc_final: 0.6562 (ptmt) REVERT: A 330 LYS cc_start: 0.8025 (ptpp) cc_final: 0.7617 (mmmm) REVERT: B 18 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8196 (tmm-80) REVERT: B 255 ARG cc_start: 0.7020 (mpp80) cc_final: 0.6792 (mpp80) REVERT: C 31 SER cc_start: 0.7623 (t) cc_final: 0.7229 (m) REVERT: C 47 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8653 (mt-10) REVERT: D 126 ILE cc_start: 0.8304 (mt) cc_final: 0.7984 (mt) REVERT: D 148 ARG cc_start: 0.6138 (mtm110) cc_final: 0.5926 (mtm-85) REVERT: D 167 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.6986 (tt0) outliers start: 27 outliers final: 25 residues processed: 212 average time/residue: 0.1101 time to fit residues: 31.5069 Evaluate side-chains 219 residues out of total 1046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 128 PHE Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 318 ARG Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.183876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151441 restraints weight = 12423.164| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.26 r_work: 0.3520 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9649 Z= 0.194 Angle : 0.647 13.770 13079 Z= 0.335 Chirality : 0.045 0.185 1504 Planarity : 0.004 0.039 1637 Dihedral : 4.997 37.663 1374 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.04 % Allowed : 20.10 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.21 (0.24), residues: 1195 helix: 1.20 (0.25), residues: 428 sheet: -0.28 (0.32), residues: 255 loop : -1.20 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 208 TYR 0.027 0.002 TYR D 95 PHE 0.027 0.002 PHE R 60 TRP 0.028 0.002 TRP R 59 HIS 0.005 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 9643) covalent geometry : angle 0.64641 (13067) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.09311 ( 12) hydrogen bonds : bond 0.04474 ( 471) hydrogen bonds : angle 4.98672 ( 1386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2721.09 seconds wall clock time: 47 minutes 29.29 seconds (2849.29 seconds total)