Starting phenix.real_space_refine on Thu Mar 13 08:32:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7m_36042/03_2025/8j7m_36042_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7m_36042/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7m_36042/03_2025/8j7m_36042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7m_36042/03_2025/8j7m_36042.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7m_36042/03_2025/8j7m_36042_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7m_36042/03_2025/8j7m_36042_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.73, per 1000 atoms: 0.65 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: 2.46 Conformation dependent library (CDL) restraints added in 958.3 milliseconds 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: 0.70 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: 2.18 Time building geometry restraints manager: 2.84 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 356 or resid 901 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: 0.720 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.440 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- 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= 0.685 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP D 149 HIS 0.004 0.001 HIS C 237 PHE 0.022 0.002 PHE C 144 TYR 0.014 0.003 TYR B 114 ARG 0.002 0.000 ARG B 293 *********************** 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 : 0.801 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: 0.7621 (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: 0.8202 (m-80) REVERT: A 328 LEU cc_start: 0.8459 (mt) cc_final: 0.8227 (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: 0.8233 (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: 0.7837 (m-10) REVERT: B 209 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7649 (mttm) 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: 0.1944 time to fit residues: 55.0405 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 : 0.904 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4113 r_free = 0.4113 target = 0.185775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147301 restraints weight = 8650.022| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.86 r_work: 0.3478 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9104 Z= 0.187 Angle : 0.610 6.788 12426 Z= 0.308 Chirality : 0.043 0.169 1372 Planarity : 0.005 0.060 1456 Dihedral : 12.335 117.310 1902 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.58 % Allowed : 17.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1012 helix: 0.21 (0.18), residues: 732 sheet: None (None), residues: 0 loop : -2.28 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 145 HIS 0.001 0.001 HIS C 237 PHE 0.019 0.001 PHE D 218 TYR 0.012 0.002 TYR C 283 ARG 0.003 0.000 ARG D 313 *********************** 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 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 145 TRP cc_start: 0.8348 (p90) cc_final: 0.7936 (p90) REVERT: A 185 LEU cc_start: 0.8681 (mt) cc_final: 0.8335 (tt) REVERT: A 209 LYS cc_start: 0.8219 (mmpt) cc_final: 0.7572 (mtpp) REVERT: A 286 GLU cc_start: 0.8766 (tt0) cc_final: 0.8538 (tt0) REVERT: A 288 TYR cc_start: 0.8672 (m-80) cc_final: 0.8447 (m-80) REVERT: A 328 LEU cc_start: 0.8406 (mt) cc_final: 0.8199 (mt) REVERT: D 145 TRP cc_start: 0.8267 (p90) cc_final: 0.7913 (p90) REVERT: D 185 LEU cc_start: 0.8648 (mt) cc_final: 0.8316 (tt) REVERT: D 209 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7924 (mmtt) REVERT: D 328 LEU cc_start: 0.8541 (mt) cc_final: 0.8307 (mt) REVERT: B 123 PHE cc_start: 0.8045 (t80) cc_final: 0.7629 (t80) REVERT: B 142 PHE cc_start: 0.8270 (m-80) cc_final: 0.8011 (m-80) REVERT: B 145 TRP cc_start: 0.8327 (p90) cc_final: 0.7822 (p90) REVERT: B 209 LYS cc_start: 0.8198 (mmpt) cc_final: 0.7594 (mtpp) REVERT: B 328 LEU cc_start: 0.8508 (mt) cc_final: 0.8284 (mt) REVERT: C 145 TRP cc_start: 0.8258 (p90) cc_final: 0.7917 (p90) REVERT: C 288 TYR cc_start: 0.8610 (m-80) cc_final: 0.8388 (m-80) outliers start: 5 outliers final: 4 residues processed: 174 average time/residue: 0.2216 time to fit residues: 54.0745 Evaluate side-chains 168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain B residue 211 ILE 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 14 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.186230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149780 restraints weight = 8723.571| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.80 r_work: 0.3496 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9104 Z= 0.176 Angle : 0.532 5.081 12426 Z= 0.272 Chirality : 0.042 0.166 1372 Planarity : 0.004 0.036 1456 Dihedral : 10.698 103.290 1896 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.85 % Allowed : 17.94 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 1012 helix: 0.77 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.80 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 145 HIS 0.002 0.001 HIS A 72 PHE 0.019 0.001 PHE A 144 TYR 0.014 0.001 TYR D 283 ARG 0.002 0.000 ARG B 192 *********************** 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 182 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.963 Fit side-chains REVERT: A 145 TRP cc_start: 0.8354 (p90) cc_final: 0.8027 (p90) REVERT: A 209 LYS cc_start: 0.8037 (mmpt) cc_final: 0.7692 (mtpt) REVERT: D 145 TRP cc_start: 0.8260 (p90) cc_final: 0.7951 (p90) REVERT: D 209 LYS cc_start: 0.7934 (mmpt) cc_final: 0.7645 (mtpt) REVERT: D 225 MET cc_start: 0.8552 (mtp) cc_final: 0.8308 (mtp) REVERT: D 286 GLU cc_start: 0.8430 (tt0) cc_final: 0.8195 (tm-30) REVERT: D 328 LEU cc_start: 0.8480 (mt) cc_final: 0.8229 (mt) REVERT: B 142 PHE cc_start: 0.8322 (m-80) cc_final: 0.8075 (m-80) REVERT: B 145 TRP cc_start: 0.8419 (p90) cc_final: 0.7928 (p90) REVERT: B 209 LYS cc_start: 0.8006 (mmpt) cc_final: 0.7653 (mtpt) REVERT: B 328 LEU cc_start: 0.8470 (mt) cc_final: 0.8225 (mt) REVERT: C 145 TRP cc_start: 0.8309 (p90) cc_final: 0.8002 (p90) REVERT: C 209 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7755 (mmtt) REVERT: C 286 GLU cc_start: 0.8501 (tt0) cc_final: 0.8237 (tm-30) outliers start: 16 outliers final: 11 residues processed: 178 average time/residue: 0.2523 time to fit residues: 60.7607 Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 164 LEU Chi-restraints excluded: chain C residue 185 LEU 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 46 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.181786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143390 restraints weight = 8687.337| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.78 r_work: 0.3450 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9104 Z= 0.294 Angle : 0.600 5.549 12426 Z= 0.302 Chirality : 0.046 0.189 1372 Planarity : 0.004 0.032 1456 Dihedral : 10.522 101.559 1894 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.85 % Allowed : 18.40 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1012 helix: 0.75 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.72 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 69 HIS 0.003 0.001 HIS A 237 PHE 0.019 0.002 PHE A 329 TYR 0.012 0.002 TYR A 283 ARG 0.003 0.000 ARG C 192 *********************** 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 197 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.854 Fit side-chains REVERT: A 145 TRP cc_start: 0.8376 (p90) cc_final: 0.8000 (p90) REVERT: A 209 LYS cc_start: 0.8256 (mmpt) cc_final: 0.7831 (mtpt) REVERT: A 286 GLU cc_start: 0.8864 (tt0) cc_final: 0.8585 (tt0) REVERT: A 328 LEU cc_start: 0.8570 (mt) cc_final: 0.8339 (mt) REVERT: D 145 TRP cc_start: 0.8368 (p90) cc_final: 0.8107 (p90) REVERT: D 328 LEU cc_start: 0.8550 (mt) cc_final: 0.8309 (mt) REVERT: B 145 TRP cc_start: 0.8485 (p90) cc_final: 0.8042 (p90) REVERT: B 209 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7754 (mtpt) REVERT: C 145 TRP cc_start: 0.8348 (p90) cc_final: 0.8044 (p90) REVERT: C 209 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7788 (mtpt) outliers start: 16 outliers final: 12 residues processed: 193 average time/residue: 0.2250 time to fit residues: 58.9082 Evaluate side-chains 191 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 135 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.184946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147518 restraints weight = 8609.082| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.71 r_work: 0.3502 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 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 = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2237 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= 0.190 Angle : 0.535 6.496 12426 Z= 0.270 Chirality : 0.042 0.157 1372 Planarity : 0.004 0.054 1456 Dihedral : 10.060 92.181 1894 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.50 % Allowed : 18.98 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1012 helix: 0.97 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.61 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 145 HIS 0.002 0.001 HIS D 237 PHE 0.017 0.001 PHE A 144 TYR 0.012 0.001 TYR A 138 ARG 0.002 0.000 ARG C 192 *********************** 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 190 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.927 Fit side-chains REVERT: A 145 TRP cc_start: 0.8433 (p90) cc_final: 0.8157 (p90) REVERT: A 209 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7819 (mtpt) REVERT: A 286 GLU cc_start: 0.8858 (tt0) cc_final: 0.8571 (tt0) REVERT: A 328 LEU cc_start: 0.8558 (mt) cc_final: 0.8324 (mt) REVERT: D 145 TRP cc_start: 0.8336 (p90) cc_final: 0.8077 (p90) REVERT: D 209 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7810 (mttm) REVERT: D 328 LEU cc_start: 0.8593 (mt) cc_final: 0.8358 (mt) REVERT: B 145 TRP cc_start: 0.8415 (p90) cc_final: 0.8029 (p90) REVERT: B 209 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7767 (mtpt) REVERT: B 328 LEU cc_start: 0.8578 (mt) cc_final: 0.8349 (mt) REVERT: B 352 LYS cc_start: 0.8227 (tppt) cc_final: 0.7965 (tppt) REVERT: C 145 TRP cc_start: 0.8350 (p90) cc_final: 0.8101 (p90) REVERT: C 209 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7806 (mtpt) outliers start: 13 outliers final: 12 residues processed: 184 average time/residue: 0.2316 time to fit residues: 57.5879 Evaluate side-chains 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 128 MET 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 Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.182924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144819 restraints weight = 8618.297| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.75 r_work: 0.3477 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9104 Z= 0.251 Angle : 0.565 6.265 12426 Z= 0.284 Chirality : 0.043 0.168 1372 Planarity : 0.004 0.036 1456 Dihedral : 9.989 83.646 1892 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.97 % Allowed : 19.33 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1012 helix: 1.00 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.58 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.003 0.001 HIS D 237 PHE 0.018 0.001 PHE C 144 TYR 0.011 0.002 TYR D 138 ARG 0.002 0.000 ARG D 192 *********************** 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 193 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.801 Fit side-chains REVERT: A 145 TRP cc_start: 0.8444 (p90) cc_final: 0.8196 (p90) REVERT: A 209 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7832 (mtpt) REVERT: D 114 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: D 145 TRP cc_start: 0.8347 (p90) cc_final: 0.8097 (p90) REVERT: D 209 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7829 (mttm) REVERT: D 328 LEU cc_start: 0.8565 (mt) cc_final: 0.8316 (mt) REVERT: B 145 TRP cc_start: 0.8408 (p90) cc_final: 0.8004 (p90) REVERT: B 209 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7772 (mtpt) REVERT: C 145 TRP cc_start: 0.8408 (p90) cc_final: 0.8137 (p90) REVERT: C 209 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7809 (mtpt) outliers start: 17 outliers final: 14 residues processed: 184 average time/residue: 0.2134 time to fit residues: 53.9670 Evaluate side-chains 191 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 135 ILE 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 352 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.184243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146526 restraints weight = 8737.360| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.75 r_work: 0.3491 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 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 = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9104 Z= 0.206 Angle : 0.541 6.549 12426 Z= 0.271 Chirality : 0.042 0.158 1372 Planarity : 0.004 0.031 1456 Dihedral : 9.711 67.681 1892 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.97 % Allowed : 20.02 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.27), residues: 1012 helix: 1.10 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 69 HIS 0.002 0.001 HIS A 237 PHE 0.017 0.001 PHE C 144 TYR 0.012 0.001 TYR A 236 ARG 0.004 0.000 ARG C 192 *********************** 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 196 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.801 Fit side-chains REVERT: A 145 TRP cc_start: 0.8427 (p90) cc_final: 0.8189 (p90) REVERT: A 209 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7790 (mtpt) REVERT: A 286 GLU cc_start: 0.8895 (tt0) cc_final: 0.8598 (tt0) REVERT: D 75 LYS cc_start: 0.8732 (pttt) cc_final: 0.8502 (pttt) REVERT: D 145 TRP cc_start: 0.8347 (p90) cc_final: 0.8143 (p90) REVERT: D 209 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7763 (mttm) REVERT: D 328 LEU cc_start: 0.8594 (mt) cc_final: 0.8350 (mt) REVERT: B 145 TRP cc_start: 0.8479 (p90) cc_final: 0.8232 (p90) REVERT: B 209 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7742 (mtpt) REVERT: B 328 LEU cc_start: 0.8569 (mt) cc_final: 0.8334 (mt) REVERT: C 145 TRP cc_start: 0.8354 (p90) cc_final: 0.8091 (p90) REVERT: C 209 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7787 (mtpt) outliers start: 17 outliers final: 13 residues processed: 191 average time/residue: 0.1987 time to fit residues: 52.8721 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 : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain D residue 128 MET 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 352 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.181266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144464 restraints weight = 8812.341| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.78 r_work: 0.3476 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 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 = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9104 Z= 0.296 Angle : 0.587 7.158 12426 Z= 0.293 Chirality : 0.045 0.178 1372 Planarity : 0.004 0.031 1456 Dihedral : 9.745 71.078 1892 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.08 % Allowed : 19.91 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.27), residues: 1012 helix: 0.56 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -3.40 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.003 0.001 HIS D 237 PHE 0.018 0.002 PHE D 329 TYR 0.013 0.002 TYR A 236 ARG 0.002 0.000 ARG C 192 *********************** 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 202 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.049 Fit side-chains REVERT: A 145 TRP cc_start: 0.8455 (p90) cc_final: 0.8212 (p90) REVERT: A 184 ASN cc_start: 0.7925 (m110) cc_final: 0.7721 (m-40) REVERT: A 209 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7714 (mtpt) REVERT: A 286 GLU cc_start: 0.8862 (tt0) cc_final: 0.8542 (tt0) REVERT: D 114 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: D 145 TRP cc_start: 0.8397 (p90) cc_final: 0.8179 (p90) REVERT: D 209 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7774 (mttm) REVERT: B 123 PHE cc_start: 0.8256 (t80) cc_final: 0.7904 (t80) REVERT: B 145 TRP cc_start: 0.8461 (p90) cc_final: 0.8212 (p90) REVERT: B 209 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7749 (mtpt) REVERT: B 286 GLU cc_start: 0.8798 (tt0) cc_final: 0.8465 (tt0) REVERT: C 123 PHE cc_start: 0.8283 (t80) cc_final: 0.7960 (t80) REVERT: C 145 TRP cc_start: 0.8421 (p90) cc_final: 0.8114 (p90) REVERT: C 209 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7792 (mtpt) outliers start: 18 outliers final: 13 residues processed: 193 average time/residue: 0.2620 time to fit residues: 69.7866 Evaluate side-chains 194 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 219 VAL 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 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 185 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 352 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.184943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147955 restraints weight = 8672.767| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.70 r_work: 0.3522 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 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 = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9104 Z= 0.182 Angle : 0.525 6.792 12426 Z= 0.264 Chirality : 0.041 0.158 1372 Planarity : 0.004 0.032 1456 Dihedral : 9.371 67.014 1892 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.39 % Allowed : 20.95 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 145 HIS 0.002 0.001 HIS D 72 PHE 0.017 0.001 PHE B 144 TYR 0.013 0.001 TYR A 236 ARG 0.005 0.000 ARG D 192 *********************** 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 198 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.830 Fit side-chains REVERT: A 145 TRP cc_start: 0.8382 (p90) cc_final: 0.8178 (p90) REVERT: A 209 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7797 (mtpt) REVERT: A 286 GLU cc_start: 0.8837 (tt0) cc_final: 0.8548 (tt0) REVERT: D 209 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7782 (mttm) REVERT: D 328 LEU cc_start: 0.8574 (mt) cc_final: 0.8343 (mt) REVERT: B 123 PHE cc_start: 0.8241 (t80) cc_final: 0.7908 (t80) REVERT: B 145 TRP cc_start: 0.8424 (p90) cc_final: 0.8223 (p90) REVERT: B 209 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7731 (mtpt) REVERT: B 286 GLU cc_start: 0.8764 (tt0) cc_final: 0.8456 (tt0) REVERT: B 328 LEU cc_start: 0.8565 (mt) cc_final: 0.8337 (mt) REVERT: C 123 PHE cc_start: 0.8270 (t80) cc_final: 0.7950 (t80) REVERT: C 209 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7799 (mtpt) outliers start: 12 outliers final: 11 residues processed: 194 average time/residue: 0.1984 time to fit residues: 53.0899 Evaluate side-chains 189 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 352 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 92 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 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 = 0.4112 r_free = 0.4112 target = 0.185198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149570 restraints weight = 8713.125| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.76 r_work: 0.3518 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9104 Z= 0.185 Angle : 0.533 7.041 12426 Z= 0.267 Chirality : 0.041 0.157 1372 Planarity : 0.004 0.032 1456 Dihedral : 9.214 65.578 1892 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.27 % Allowed : 20.72 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 1012 helix: 1.23 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.34 (0.44), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 145 HIS 0.003 0.001 HIS B 72 PHE 0.017 0.001 PHE A 144 TYR 0.012 0.001 TYR A 236 ARG 0.004 0.000 ARG A 192 ********************** 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 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.893 Fit side-chains REVERT: A 145 TRP cc_start: 0.8296 (p90) cc_final: 0.8075 (p90) REVERT: A 209 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7817 (mtpt) REVERT: A 286 GLU cc_start: 0.8854 (tt0) cc_final: 0.8542 (tt0) REVERT: D 145 TRP cc_start: 0.8210 (p90) cc_final: 0.7998 (p90) REVERT: D 209 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7791 (mttm) REVERT: D 328 LEU cc_start: 0.8591 (mt) cc_final: 0.8362 (mt) REVERT: B 123 PHE cc_start: 0.8278 (t80) cc_final: 0.7943 (t80) REVERT: B 145 TRP cc_start: 0.8353 (p90) cc_final: 0.8111 (p90) REVERT: B 209 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7741 (mtpt) REVERT: B 286 GLU cc_start: 0.8803 (tt0) cc_final: 0.8502 (tt0) REVERT: B 328 LEU cc_start: 0.8586 (mt) cc_final: 0.8364 (mt) REVERT: C 123 PHE cc_start: 0.8297 (t80) cc_final: 0.7965 (t80) REVERT: C 145 TRP cc_start: 0.8233 (p90) cc_final: 0.8027 (p90) REVERT: C 209 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7712 (mtpp) outliers start: 11 outliers final: 11 residues processed: 186 average time/residue: 0.1964 time to fit residues: 51.3207 Evaluate side-chains 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 352 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.168315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124720 restraints weight = 9007.219| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.56 r_work: 0.3394 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2630 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= 0.275 Angle : 0.579 7.667 12426 Z= 0.288 Chirality : 0.044 0.162 1372 Planarity : 0.004 0.031 1456 Dihedral : 9.411 68.287 1892 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 1012 helix: 1.13 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.44 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 145 HIS 0.003 0.001 HIS B 72 PHE 0.018 0.002 PHE C 144 TYR 0.014 0.002 TYR D 236 ARG 0.003 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5718.48 seconds wall clock time: 101 minutes 39.46 seconds (6099.46 seconds total)