Starting phenix.real_space_refine on Fri Oct 10 19:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7m_36042/10_2025/8j7m_36042_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7m_36042/10_2025/8j7m_36042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j7m_36042/10_2025/8j7m_36042_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7m_36042/10_2025/8j7m_36042_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7m_36042/10_2025/8j7m_36042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7m_36042/10_2025/8j7m_36042.map" } resolution = 3.1 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= 0.004 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 44 5.16 5 C 6020 2.51 5 N 1316 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8806 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 119 Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'CLR': 3, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.36, per 1000 atoms: 0.27 Number of scatterers: 8806 At special positions: 0 Unit cell: (117.52, 117.52, 71.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 4 15.00 O 1422 8.00 N 1316 7.00 C 6020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 269.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.530A pdb=" N ASP A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 107 Processing helix chain 'A' and resid 114 through 140 Processing helix chain 'A' and resid 148 through 172 Processing helix chain 'A' and resid 176 through 191 removed outlier: 4.259A pdb=" N LEU A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 187 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.852A pdb=" N ARG A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 237 removed outlier: 3.779A pdb=" N ILE A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Proline residue: A 212 - end of helix removed outlier: 3.764A pdb=" N ASN A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.859A pdb=" N GLU A 309 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.531A pdb=" N ASP D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 107 Processing helix chain 'D' and resid 114 through 140 Processing helix chain 'D' and resid 148 through 172 Processing helix chain 'D' and resid 176 through 191 removed outlier: 4.258A pdb=" N LEU D 181 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG D 186 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 190 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 3.851A pdb=" N ARG D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 237 removed outlier: 3.780A pdb=" N ILE D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Proline residue: D 212 - end of helix removed outlier: 3.526A pdb=" N GLU D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 Processing helix chain 'D' and resid 290 through 303 Processing helix chain 'D' and resid 312 through 318 Processing helix chain 'D' and resid 324 through 337 Processing helix chain 'D' and resid 339 through 356 Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.530A pdb=" N ASP B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 107 Processing helix chain 'B' and resid 114 through 140 Processing helix chain 'B' and resid 148 through 172 Processing helix chain 'B' and resid 176 through 191 removed outlier: 4.258A pdb=" N LEU B 181 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG B 186 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.852A pdb=" N ARG B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 237 removed outlier: 3.779A pdb=" N ILE B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Proline residue: B 212 - end of helix removed outlier: 3.768A pdb=" N HIS B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 303 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.860A pdb=" N GLU B 309 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 356 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.531A pdb=" N ASP C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 107 Processing helix chain 'C' and resid 114 through 140 Processing helix chain 'C' and resid 148 through 172 Processing helix chain 'C' and resid 176 through 191 removed outlier: 4.258A pdb=" N LEU C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG C 186 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 187 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.851A pdb=" N ARG C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 236 removed outlier: 3.779A pdb=" N ILE C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 282 through 288 removed outlier: 3.616A pdb=" N GLU C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.858A pdb=" N GLU C 309 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 324 through 337 Processing helix chain 'C' and resid 337 through 356 614 hydrogen bonds defined for protein. 1725 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: 1.36 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1255 1.30 - 1.42: 2666 1.42 - 1.55: 5101 1.55 - 1.68: 10 1.68 - 1.81: 72 Bond restraints: 9104 Sorted by residual: bond pdb=" CA TYR B 114 " pdb=" C TYR B 114 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.38e-02 5.25e+03 4.50e+01 bond pdb=" CA TYR D 114 " pdb=" C TYR D 114 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.38e-02 5.25e+03 4.28e+01 bond pdb=" C21 POV B 901 " pdb=" O21 POV B 901 " ideal model delta sigma weight residual 1.330 1.456 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C31 POV D 901 " pdb=" O31 POV D 901 " ideal model delta sigma weight residual 1.327 1.451 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 11864 2.74 - 5.48: 440 5.48 - 8.22: 97 8.22 - 10.97: 19 10.97 - 13.71: 6 Bond angle restraints: 12426 Sorted by residual: angle pdb=" N SER D 308 " pdb=" CA SER D 308 " pdb=" C SER D 308 " ideal model delta sigma weight residual 114.12 100.41 13.71 1.39e+00 5.18e-01 9.72e+01 angle pdb=" C ILE C 336 " pdb=" CA ILE C 336 " pdb=" CB ILE C 336 " ideal model delta sigma weight residual 111.97 100.06 11.91 1.28e+00 6.10e-01 8.66e+01 angle pdb=" N ILE C 336 " pdb=" CA ILE C 336 " pdb=" C ILE C 336 " ideal model delta sigma weight residual 110.42 119.28 -8.86 9.60e-01 1.09e+00 8.52e+01 angle pdb=" C ILE B 336 " pdb=" CA ILE B 336 " pdb=" CB ILE B 336 " ideal model delta sigma weight residual 112.14 100.08 12.06 1.35e+00 5.49e-01 7.98e+01 angle pdb=" N ILE B 336 " pdb=" CA ILE B 336 " pdb=" C ILE B 336 " ideal model delta sigma weight residual 110.62 119.23 -8.61 1.02e+00 9.61e-01 7.13e+01 ... (remaining 12421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 5225 26.04 - 52.09: 338 52.09 - 78.13: 63 78.13 - 104.17: 18 104.17 - 130.22: 4 Dihedral angle restraints: 5648 sinusoidal: 2632 harmonic: 3016 Sorted by residual: dihedral pdb=" C TRP D 307 " pdb=" N TRP D 307 " pdb=" CA TRP D 307 " pdb=" CB TRP D 307 " ideal model delta harmonic sigma weight residual -122.60 -107.20 -15.40 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" C GLU C 285 " pdb=" N GLU C 285 " pdb=" CA GLU C 285 " pdb=" CB GLU C 285 " ideal model delta harmonic sigma weight residual -122.60 -134.79 12.19 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" CA GLU D 305 " pdb=" C GLU D 305 " pdb=" N SER D 306 " pdb=" CA SER D 306 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1177 0.093 - 0.185: 134 0.185 - 0.278: 34 0.278 - 0.370: 18 0.370 - 0.463: 9 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA GLU C 285 " pdb=" N GLU C 285 " pdb=" C GLU C 285 " pdb=" CB GLU C 285 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C13 CLR B 902 " pdb=" C12 CLR B 902 " pdb=" C14 CLR B 902 " pdb=" C17 CLR B 902 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C13 CLR A 903 " pdb=" C12 CLR A 903 " pdb=" C14 CLR A 903 " pdb=" C17 CLR A 903 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1369 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 338 " 0.025 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C GLN C 338 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN C 338 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE C 339 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C ILE B 336 " -0.073 2.00e-02 2.50e+03 pdb=" O ILE B 336 " 0.027 2.00e-02 2.50e+03 pdb=" N CYS B 337 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 144 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.14e+00 pdb=" C PHE D 144 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE D 144 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP D 145 " 0.017 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 223 2.68 - 3.23: 9055 3.23 - 3.79: 13941 3.79 - 4.34: 18996 4.34 - 4.90: 31419 Nonbonded interactions: 73634 Sorted by model distance: nonbonded pdb=" O ILE B 339 " pdb=" ND2 ASN B 343 " model vdw 2.124 3.120 nonbonded pdb=" O CYS D 143 " pdb=" CE3 TRP D 145 " model vdw 2.223 3.340 nonbonded pdb=" O CYS A 143 " pdb=" CE3 TRP A 145 " model vdw 2.244 3.340 nonbonded pdb=" O LEU C 328 " pdb=" OG SER C 332 " model vdw 2.247 3.040 nonbonded pdb=" O LEU D 328 " pdb=" OG SER D 332 " model vdw 2.247 3.040 ... (remaining 73629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 61 through 356 or (resid 901 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or nam \ e O14 or name O21 or name O22 or name O31 or name O32 or name P or name C310 or \ name C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or \ resid 902 through 903)) selection = chain 'B' selection = (chain 'C' and (resid 61 through 356 or (resid 901 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C3 \ 6 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or nam \ e O14 or name O21 or name O22 or name O31 or name O32 or name P or name C310 or \ name C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or \ resid 902 through 903)) selection = (chain 'D' and resid 61 through 903) } 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=0.45 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.600 Find NCS groups from input model: 0.200 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.011 0.126 9104 Z= 0.614 Angle : 1.237 13.707 12426 Z= 0.685 Chirality : 0.082 0.463 1372 Planarity : 0.006 0.048 1456 Dihedral : 18.144 130.218 3712 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.27 % Allowed : 15.05 % Favored : 83.68 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.24), residues: 1012 helix: -0.93 (0.17), residues: 732 sheet: None (None), residues: 0 loop : -2.73 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.014 0.003 TYR B 114 PHE 0.022 0.002 PHE C 144 TRP 0.019 0.002 TRP D 149 HIS 0.004 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.01096 ( 9104) covalent geometry : angle 1.23678 (12426) hydrogen bonds : bond 0.10663 ( 614) hydrogen bonds : angle 6.63026 ( 1725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 142 PHE cc_start: 0.8284 (m-80) cc_final: 0.8074 (m-80) REVERT: A 185 LEU cc_start: 0.8595 (mt) cc_final: 0.8218 (tt) REVERT: A 209 LYS cc_start: 0.7860 (mmpt) cc_final: 0.7628 (mttm) REVERT: A 286 GLU cc_start: 0.7924 (tt0) cc_final: 0.7723 (tt0) REVERT: A 288 TYR cc_start: 0.8550 (m-80) cc_final: 0.8201 (m-80) REVERT: A 328 LEU cc_start: 0.8459 (mt) cc_final: 0.8226 (mt) REVERT: D 185 LEU cc_start: 0.8587 (mt) cc_final: 0.8224 (tt) REVERT: D 288 TYR cc_start: 0.8591 (m-80) cc_final: 0.8240 (m-80) REVERT: D 328 LEU cc_start: 0.8464 (mt) cc_final: 0.8232 (mt) REVERT: B 123 PHE cc_start: 0.7560 (t80) cc_final: 0.7271 (t80) REVERT: B 142 PHE cc_start: 0.8124 (m-80) cc_final: 0.7836 (m-10) REVERT: B 288 TYR cc_start: 0.8465 (m-80) cc_final: 0.8113 (m-80) REVERT: B 328 LEU cc_start: 0.8473 (mt) cc_final: 0.8239 (mt) REVERT: C 288 TYR cc_start: 0.8579 (m-80) cc_final: 0.8221 (m-80) REVERT: C 328 LEU cc_start: 0.8536 (mt) cc_final: 0.8328 (mt) outliers start: 11 outliers final: 7 residues processed: 203 average time/residue: 0.0940 time to fit residues: 26.8774 Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN D 72 HIS D 126 ASN B 72 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN C 72 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.184598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147123 restraints weight = 8754.209| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.79 r_work: 0.3458 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9104 Z= 0.149 Angle : 0.617 6.632 12426 Z= 0.310 Chirality : 0.044 0.187 1372 Planarity : 0.005 0.058 1456 Dihedral : 12.420 116.680 1902 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.93 % Allowed : 17.36 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.26), residues: 1012 helix: 0.16 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 313 TYR 0.013 0.002 TYR C 283 PHE 0.018 0.001 PHE C 144 TRP 0.021 0.001 TRP D 145 HIS 0.002 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9104) covalent geometry : angle 0.61744 (12426) hydrogen bonds : bond 0.04539 ( 614) hydrogen bonds : angle 5.42770 ( 1725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 174 time to evaluate : 0.398 Fit side-chains REVERT: A 145 TRP cc_start: 0.8347 (p90) cc_final: 0.7989 (p90) REVERT: A 185 LEU cc_start: 0.8702 (mt) cc_final: 0.8364 (tt) REVERT: A 209 LYS cc_start: 0.8250 (mmpt) cc_final: 0.7618 (mtpp) REVERT: A 288 TYR cc_start: 0.8649 (m-80) cc_final: 0.8424 (m-80) REVERT: A 328 LEU cc_start: 0.8469 (mt) cc_final: 0.8263 (mt) REVERT: D 145 TRP cc_start: 0.8285 (p90) cc_final: 0.7987 (p90) REVERT: D 185 LEU cc_start: 0.8671 (mt) cc_final: 0.8347 (tt) REVERT: D 328 LEU cc_start: 0.8494 (mt) cc_final: 0.8264 (mt) REVERT: B 123 PHE cc_start: 0.8078 (t80) cc_final: 0.7652 (t80) REVERT: B 142 PHE cc_start: 0.8317 (m-80) cc_final: 0.8049 (m-80) REVERT: B 145 TRP cc_start: 0.8363 (p90) cc_final: 0.7886 (p90) REVERT: B 209 LYS cc_start: 0.8203 (mttm) cc_final: 0.7923 (mtpp) REVERT: B 328 LEU cc_start: 0.8526 (mt) cc_final: 0.8295 (mt) REVERT: C 145 TRP cc_start: 0.8281 (p90) cc_final: 0.7923 (p90) outliers start: 8 outliers final: 7 residues processed: 179 average time/residue: 0.0976 time to fit residues: 24.5790 Evaluate side-chains 173 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144784 restraints weight = 8664.444| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.75 r_work: 0.3449 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9104 Z= 0.178 Angle : 0.590 5.951 12426 Z= 0.299 Chirality : 0.045 0.196 1372 Planarity : 0.005 0.039 1456 Dihedral : 11.280 108.253 1898 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.74 % Allowed : 18.29 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.27), residues: 1012 helix: 0.16 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -3.73 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 192 TYR 0.015 0.002 TYR D 283 PHE 0.019 0.002 PHE A 144 TRP 0.009 0.001 TRP D 145 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9104) covalent geometry : angle 0.58989 (12426) hydrogen bonds : bond 0.04340 ( 614) hydrogen bonds : angle 5.27524 ( 1725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.321 Fit side-chains REVERT: A 145 TRP cc_start: 0.8420 (p90) cc_final: 0.8008 (p90) REVERT: A 185 LEU cc_start: 0.8623 (mt) cc_final: 0.8390 (tt) REVERT: A 209 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7801 (mtpt) REVERT: A 328 LEU cc_start: 0.8531 (mt) cc_final: 0.8297 (mt) REVERT: D 145 TRP cc_start: 0.8339 (p90) cc_final: 0.7951 (p90) REVERT: D 185 LEU cc_start: 0.8671 (mt) cc_final: 0.8452 (tt) REVERT: D 209 LYS cc_start: 0.8167 (mmpt) cc_final: 0.7895 (mmtt) REVERT: D 328 LEU cc_start: 0.8502 (mt) cc_final: 0.8254 (mt) REVERT: B 142 PHE cc_start: 0.8410 (m-80) cc_final: 0.8209 (m-80) REVERT: B 145 TRP cc_start: 0.8445 (p90) cc_final: 0.7990 (p90) REVERT: B 209 LYS cc_start: 0.8193 (mttm) cc_final: 0.7910 (mtpp) REVERT: C 145 TRP cc_start: 0.8360 (p90) cc_final: 0.7999 (p90) REVERT: C 209 LYS cc_start: 0.8276 (mmpt) cc_final: 0.7938 (mmtt) outliers start: 15 outliers final: 10 residues processed: 184 average time/residue: 0.0976 time to fit residues: 24.9143 Evaluate side-chains 181 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 80 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.185268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147846 restraints weight = 8750.164| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.80 r_work: 0.3484 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9104 Z= 0.128 Angle : 0.538 5.801 12426 Z= 0.274 Chirality : 0.042 0.159 1372 Planarity : 0.004 0.031 1456 Dihedral : 10.431 98.868 1896 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.20 % Allowed : 18.17 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.27), residues: 1012 helix: 0.79 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.79 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 192 TYR 0.011 0.001 TYR D 138 PHE 0.018 0.001 PHE C 144 TRP 0.010 0.001 TRP D 145 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9104) covalent geometry : angle 0.53830 (12426) hydrogen bonds : bond 0.03894 ( 614) hydrogen bonds : angle 5.12548 ( 1725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.347 Fit side-chains REVERT: A 145 TRP cc_start: 0.8356 (p90) cc_final: 0.8018 (p90) REVERT: A 209 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7758 (mtpt) REVERT: A 286 GLU cc_start: 0.8849 (tt0) cc_final: 0.8545 (tt0) REVERT: A 328 LEU cc_start: 0.8493 (mt) cc_final: 0.8258 (mt) REVERT: D 145 TRP cc_start: 0.8324 (p90) cc_final: 0.8082 (p90) REVERT: D 209 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7702 (mtpt) REVERT: D 328 LEU cc_start: 0.8560 (mt) cc_final: 0.8334 (mt) REVERT: B 145 TRP cc_start: 0.8471 (p90) cc_final: 0.8077 (p90) REVERT: B 209 LYS cc_start: 0.8176 (mttm) cc_final: 0.7886 (mtpp) REVERT: B 328 LEU cc_start: 0.8549 (mt) cc_final: 0.8313 (mt) REVERT: C 145 TRP cc_start: 0.8297 (p90) cc_final: 0.7969 (p90) REVERT: C 209 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7926 (mmtt) outliers start: 19 outliers final: 10 residues processed: 183 average time/residue: 0.1047 time to fit residues: 26.0868 Evaluate side-chains 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 46 optimal weight: 0.5980 chunk 71 optimal weight: 0.0570 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.186538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149198 restraints weight = 8648.273| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.73 r_work: 0.3509 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9104 Z= 0.118 Angle : 0.520 5.080 12426 Z= 0.266 Chirality : 0.041 0.158 1372 Planarity : 0.004 0.057 1456 Dihedral : 10.067 89.862 1894 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.39 % Allowed : 18.17 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.27), residues: 1012 helix: 0.96 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.55 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.011 0.001 TYR D 138 PHE 0.017 0.001 PHE C 144 TRP 0.008 0.001 TRP D 145 HIS 0.001 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9104) covalent geometry : angle 0.52034 (12426) hydrogen bonds : bond 0.03780 ( 614) hydrogen bonds : angle 5.05569 ( 1725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.322 Fit side-chains REVERT: A 145 TRP cc_start: 0.8376 (p90) cc_final: 0.8106 (p90) REVERT: A 209 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7765 (mtpt) REVERT: A 225 MET cc_start: 0.8670 (mtp) cc_final: 0.8457 (mtp) REVERT: A 286 GLU cc_start: 0.8571 (tt0) cc_final: 0.8271 (tt0) REVERT: A 328 LEU cc_start: 0.8516 (mt) cc_final: 0.8270 (mt) REVERT: D 145 TRP cc_start: 0.8264 (p90) cc_final: 0.8029 (p90) REVERT: D 328 LEU cc_start: 0.8538 (mt) cc_final: 0.8303 (mt) REVERT: B 145 TRP cc_start: 0.8420 (p90) cc_final: 0.8065 (p90) REVERT: B 209 LYS cc_start: 0.8018 (mttm) cc_final: 0.7797 (mtpp) REVERT: B 286 GLU cc_start: 0.8548 (tt0) cc_final: 0.8311 (tt0) REVERT: B 328 LEU cc_start: 0.8524 (mt) cc_final: 0.8280 (mt) REVERT: C 145 TRP cc_start: 0.8307 (p90) cc_final: 0.8067 (p90) REVERT: C 209 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7749 (mtpt) outliers start: 12 outliers final: 10 residues processed: 190 average time/residue: 0.0982 time to fit residues: 25.8755 Evaluate side-chains 190 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149175 restraints weight = 8685.395| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.76 r_work: 0.3505 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9104 Z= 0.127 Angle : 0.530 6.017 12426 Z= 0.269 Chirality : 0.041 0.157 1372 Planarity : 0.004 0.034 1456 Dihedral : 9.870 79.440 1892 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.50 % Allowed : 19.68 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.28), residues: 1012 helix: 1.03 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.013 0.001 TYR C 138 PHE 0.017 0.001 PHE C 144 TRP 0.008 0.001 TRP D 145 HIS 0.002 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9104) covalent geometry : angle 0.53040 (12426) hydrogen bonds : bond 0.03784 ( 614) hydrogen bonds : angle 5.02287 ( 1725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.342 Fit side-chains REVERT: A 209 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7775 (mtpt) REVERT: A 286 GLU cc_start: 0.8830 (tt0) cc_final: 0.8524 (tt0) REVERT: A 328 LEU cc_start: 0.8549 (mt) cc_final: 0.8304 (mt) REVERT: D 209 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7820 (mttm) REVERT: D 328 LEU cc_start: 0.8579 (mt) cc_final: 0.8343 (mt) REVERT: B 145 TRP cc_start: 0.8434 (p90) cc_final: 0.8124 (p90) REVERT: B 209 LYS cc_start: 0.8103 (mttm) cc_final: 0.7886 (mtpp) REVERT: B 286 GLU cc_start: 0.8828 (tt0) cc_final: 0.8504 (tt0) REVERT: B 328 LEU cc_start: 0.8558 (mt) cc_final: 0.8322 (mt) REVERT: C 145 TRP cc_start: 0.8304 (p90) cc_final: 0.8037 (p90) REVERT: C 209 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7762 (mtpt) outliers start: 13 outliers final: 9 residues processed: 181 average time/residue: 0.0926 time to fit residues: 23.5385 Evaluate side-chains 182 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 50 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.184279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145938 restraints weight = 8735.445| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.71 r_work: 0.3494 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9104 Z= 0.153 Angle : 0.549 6.443 12426 Z= 0.276 Chirality : 0.043 0.160 1372 Planarity : 0.004 0.031 1456 Dihedral : 9.833 74.544 1892 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.08 % Allowed : 19.79 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.27), residues: 1012 helix: 1.01 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.48 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.013 0.002 TYR A 236 PHE 0.017 0.001 PHE A 144 TRP 0.007 0.001 TRP C 69 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9104) covalent geometry : angle 0.54921 (12426) hydrogen bonds : bond 0.03861 ( 614) hydrogen bonds : angle 5.04375 ( 1725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.334 Fit side-chains REVERT: A 209 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7824 (mtpt) REVERT: A 286 GLU cc_start: 0.8835 (tt0) cc_final: 0.8540 (tt0) REVERT: D 328 LEU cc_start: 0.8596 (mt) cc_final: 0.8348 (mt) REVERT: B 145 TRP cc_start: 0.8471 (p90) cc_final: 0.8244 (p90) REVERT: B 328 LEU cc_start: 0.8577 (mt) cc_final: 0.8346 (mt) REVERT: C 145 TRP cc_start: 0.8310 (p90) cc_final: 0.8035 (p90) REVERT: C 209 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7822 (mtpt) outliers start: 18 outliers final: 13 residues processed: 196 average time/residue: 0.0893 time to fit residues: 24.9116 Evaluate side-chains 189 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147098 restraints weight = 8674.560| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.73 r_work: 0.3479 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9104 Z= 0.159 Angle : 0.554 6.777 12426 Z= 0.279 Chirality : 0.043 0.162 1372 Planarity : 0.004 0.030 1456 Dihedral : 9.733 66.754 1892 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.55 % Allowed : 19.56 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.27), residues: 1012 helix: 1.01 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 192 TYR 0.015 0.002 TYR A 236 PHE 0.017 0.001 PHE A 144 TRP 0.007 0.001 TRP D 69 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9104) covalent geometry : angle 0.55358 (12426) hydrogen bonds : bond 0.03920 ( 614) hydrogen bonds : angle 5.06133 ( 1725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.319 Fit side-chains REVERT: A 92 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8174 (mp) REVERT: A 145 TRP cc_start: 0.8396 (p90) cc_final: 0.8170 (p90) REVERT: A 209 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7798 (mtpt) REVERT: A 286 GLU cc_start: 0.8836 (tt0) cc_final: 0.8513 (tt0) REVERT: A 328 LEU cc_start: 0.8549 (mt) cc_final: 0.8318 (mt) REVERT: D 92 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8161 (mp) REVERT: D 114 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.6859 (m-80) REVERT: D 209 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7933 (mmtm) REVERT: B 123 PHE cc_start: 0.8302 (t80) cc_final: 0.7957 (t80) REVERT: B 145 TRP cc_start: 0.8464 (p90) cc_final: 0.8241 (p90) REVERT: B 286 GLU cc_start: 0.8775 (tt0) cc_final: 0.8444 (tt0) REVERT: B 328 LEU cc_start: 0.8577 (mt) cc_final: 0.8347 (mt) REVERT: C 92 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 123 PHE cc_start: 0.8269 (t80) cc_final: 0.7945 (t80) REVERT: C 145 TRP cc_start: 0.8393 (p90) cc_final: 0.8190 (p90) REVERT: C 209 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7786 (mtpt) outliers start: 22 outliers final: 15 residues processed: 192 average time/residue: 0.0877 time to fit residues: 24.0855 Evaluate side-chains 196 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.186002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148373 restraints weight = 8570.378| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.67 r_work: 0.3525 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9104 Z= 0.123 Angle : 0.521 6.599 12426 Z= 0.262 Chirality : 0.041 0.156 1372 Planarity : 0.004 0.031 1456 Dihedral : 9.317 62.685 1892 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.50 % Allowed : 20.72 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.28), residues: 1012 helix: 1.17 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.012 0.001 TYR C 138 PHE 0.016 0.001 PHE A 144 TRP 0.007 0.001 TRP B 145 HIS 0.002 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9104) covalent geometry : angle 0.52123 (12426) hydrogen bonds : bond 0.03715 ( 614) hydrogen bonds : angle 4.96533 ( 1725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.332 Fit side-chains REVERT: A 209 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7803 (mtpt) REVERT: A 286 GLU cc_start: 0.8829 (tt0) cc_final: 0.8526 (tt0) REVERT: A 328 LEU cc_start: 0.8533 (mt) cc_final: 0.8288 (mt) REVERT: D 209 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7964 (mmtm) REVERT: D 328 LEU cc_start: 0.8552 (mt) cc_final: 0.8315 (mt) REVERT: B 123 PHE cc_start: 0.8255 (t80) cc_final: 0.7922 (t80) REVERT: B 145 TRP cc_start: 0.8411 (p90) cc_final: 0.8197 (p90) REVERT: B 286 GLU cc_start: 0.8773 (tt0) cc_final: 0.8459 (tt0) REVERT: B 328 LEU cc_start: 0.8567 (mt) cc_final: 0.8336 (mt) REVERT: C 123 PHE cc_start: 0.8255 (t80) cc_final: 0.7926 (t80) REVERT: C 209 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7812 (mtpt) outliers start: 13 outliers final: 13 residues processed: 191 average time/residue: 0.0897 time to fit residues: 24.6057 Evaluate side-chains 190 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 71 optimal weight: 0.0470 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149236 restraints weight = 8600.440| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.70 r_work: 0.3500 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9104 Z= 0.117 Angle : 0.521 7.667 12426 Z= 0.262 Chirality : 0.041 0.157 1372 Planarity : 0.004 0.032 1456 Dihedral : 9.064 60.803 1892 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.39 % Allowed : 21.30 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.27), residues: 1012 helix: 1.22 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.33 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.013 0.001 TYR C 138 PHE 0.016 0.001 PHE B 144 TRP 0.044 0.001 TRP C 145 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9104) covalent geometry : angle 0.52145 (12426) hydrogen bonds : bond 0.03649 ( 614) hydrogen bonds : angle 4.91899 ( 1725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.301 Fit side-chains REVERT: A 209 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7723 (mtpt) REVERT: A 225 MET cc_start: 0.8692 (mtp) cc_final: 0.8471 (mtp) REVERT: A 286 GLU cc_start: 0.8595 (tt0) cc_final: 0.8277 (tt0) REVERT: A 328 LEU cc_start: 0.8492 (mt) cc_final: 0.8240 (mt) REVERT: D 209 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7849 (mmtm) REVERT: D 328 LEU cc_start: 0.8504 (mt) cc_final: 0.8257 (mt) REVERT: B 123 PHE cc_start: 0.8129 (t80) cc_final: 0.7809 (t80) REVERT: B 286 GLU cc_start: 0.8507 (tt0) cc_final: 0.8183 (tt0) REVERT: B 328 LEU cc_start: 0.8538 (mt) cc_final: 0.8299 (mt) REVERT: C 123 PHE cc_start: 0.8163 (t80) cc_final: 0.7837 (t80) outliers start: 12 outliers final: 12 residues processed: 184 average time/residue: 0.0829 time to fit residues: 22.2912 Evaluate side-chains 186 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.171918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128401 restraints weight = 8884.912| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.62 r_work: 0.3355 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9104 Z= 0.120 Angle : 0.522 6.669 12426 Z= 0.263 Chirality : 0.041 0.156 1372 Planarity : 0.004 0.032 1456 Dihedral : 8.967 60.117 1892 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.85 % Allowed : 20.95 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.27), residues: 1012 helix: 1.27 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.32 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.013 0.001 TYR D 138 PHE 0.016 0.001 PHE B 144 TRP 0.062 0.001 TRP C 145 HIS 0.002 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9104) covalent geometry : angle 0.52243 (12426) hydrogen bonds : bond 0.03639 ( 614) hydrogen bonds : angle 4.89765 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2888.97 seconds wall clock time: 50 minutes 1.19 seconds (3001.19 seconds total)