Starting phenix.real_space_refine on Wed Feb 4 08:09:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9doh_47084/02_2026/9doh_47084.cif Found real_map, /net/cci-nas-00/data/ceres_data/9doh_47084/02_2026/9doh_47084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9doh_47084/02_2026/9doh_47084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9doh_47084/02_2026/9doh_47084.map" model { file = "/net/cci-nas-00/data/ceres_data/9doh_47084/02_2026/9doh_47084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9doh_47084/02_2026/9doh_47084.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 2 5.49 5 S 36 5.16 5 C 6024 2.51 5 N 1614 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9346 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "G" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2763 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 15, 'TRANS': 338} Chain: "F" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2777 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 17, 'TRANS': 344} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 15 Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 1.97, per 1000 atoms: 0.21 Number of scatterers: 9346 At special positions: 0 Unit cell: (70.2, 98.28, 146.88, 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 36 16.00 P 2 15.00 O 1670 8.00 N 1614 7.00 C 6024 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: 0.63 Conformation dependent library (CDL) restraints added in 272.7 milliseconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 56.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.560A pdb=" N ILE B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.598A pdb=" N LYS B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.596A pdb=" N LEU B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 removed outlier: 3.815A pdb=" N ARG B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.917A pdb=" N THR B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.501A pdb=" N ALA B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.705A pdb=" N ALA A 78 " --> pdb=" O GLY A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.501A pdb=" N ILE A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.816A pdb=" N LEU A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.606A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.835A pdb=" N ILE A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'G' and resid 2 through 37 removed outlier: 4.129A pdb=" N ASN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 55 through 82 removed outlier: 3.675A pdb=" N ARG G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Proline residue: G 65 - end of helix removed outlier: 3.524A pdb=" N LEU G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 94 through 119 removed outlier: 3.611A pdb=" N ILE G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) Proline residue: G 105 - end of helix removed outlier: 4.378A pdb=" N VAL G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU G 109 " --> pdb=" O PRO G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 137 Processing helix chain 'G' and resid 230 through 239 removed outlier: 3.716A pdb=" N VAL G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 removed outlier: 3.546A pdb=" N LEU G 244 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 260 removed outlier: 3.548A pdb=" N GLY G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 275 Processing helix chain 'G' and resid 275 through 293 Processing helix chain 'G' and resid 299 through 328 removed outlier: 3.676A pdb=" N GLY G 322 " --> pdb=" O GLN G 318 " (cutoff:3.500A) Proline residue: G 323 - end of helix removed outlier: 3.515A pdb=" N LEU G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 354 removed outlier: 4.088A pdb=" N ALA G 335 " --> pdb=" O PRO G 331 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 336 " --> pdb=" O PRO G 332 " (cutoff:3.500A) Proline residue: G 339 - end of helix Processing helix chain 'F' and resid 2 through 40 removed outlier: 3.746A pdb=" N VAL F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS F 33 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA F 36 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 Proline residue: F 57 - end of helix Processing helix chain 'F' and resid 63 through 82 Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 94 through 119 removed outlier: 3.920A pdb=" N ALA F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Proline residue: F 105 - end of helix removed outlier: 3.609A pdb=" N LEU F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 109 " --> pdb=" O PRO F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 136 removed outlier: 3.907A pdb=" N GLN F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 140 Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.505A pdb=" N GLU F 247 " --> pdb=" O GLU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 264 through 275 removed outlier: 3.790A pdb=" N LEU F 271 " --> pdb=" O TYR F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 292 removed outlier: 3.625A pdb=" N PHE F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) Proline residue: F 290 - end of helix Processing helix chain 'F' and resid 303 through 326 Processing helix chain 'F' and resid 336 through 352 removed outlier: 3.541A pdb=" N HIS F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 27 removed outlier: 6.264A pdb=" N VAL B 18 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG B 20 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 10 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL B 22 " --> pdb=" O HIS B 8 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU B 9 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN B 57 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 162 removed outlier: 3.819A pdb=" N THR B 193 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 206 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 207 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU B 218 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 27 removed outlier: 6.654A pdb=" N ARG A 20 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA A 10 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL A 22 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 8 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.546A pdb=" N LEU A 35 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 207 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 218 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 209 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 148 through 151 removed outlier: 7.377A pdb=" N GLU G 155 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG G 175 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 157 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG G 173 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE G 159 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL G 171 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL G 167 " --> pdb=" O GLN G 163 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL G 171 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE G 187 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ARG G 173 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA G 185 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG G 175 " --> pdb=" O GLU G 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 190 through 194 removed outlier: 3.566A pdb=" N GLU G 223 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR G 204 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS G 219 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR G 206 " --> pdb=" O VAL G 217 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL G 217 " --> pdb=" O THR G 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 216 through 217 473 hydrogen bonds defined for protein. 1368 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: 1.02 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1723 1.33 - 1.45: 2224 1.45 - 1.57: 5499 1.57 - 1.69: 4 1.69 - 1.81: 66 Bond restraints: 9516 Sorted by residual: bond pdb=" C21 3PE G 401 " pdb=" O21 3PE G 401 " ideal model delta sigma weight residual 1.316 1.450 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C31 3PE G 401 " pdb=" O31 3PE G 401 " ideal model delta sigma weight residual 1.331 1.453 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" CA LEU F 50 " pdb=" C LEU F 50 " ideal model delta sigma weight residual 1.524 1.496 0.027 1.26e-02 6.30e+03 4.71e+00 bond pdb=" C LEU F 50 " pdb=" N ILE F 51 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.26e-02 6.30e+03 1.61e+00 bond pdb=" CA PHE F 49 " pdb=" C PHE F 49 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.27e-02 6.20e+03 1.54e+00 ... (remaining 9511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12665 1.95 - 3.89: 165 3.89 - 5.84: 31 5.84 - 7.78: 5 7.78 - 9.73: 3 Bond angle restraints: 12869 Sorted by residual: angle pdb=" N LEU F 48 " pdb=" CA LEU F 48 " pdb=" C LEU F 48 " ideal model delta sigma weight residual 112.54 108.13 4.41 1.22e+00 6.72e-01 1.30e+01 angle pdb=" C2 3PE G 401 " pdb=" O21 3PE G 401 " pdb=" C21 3PE G 401 " ideal model delta sigma weight residual 121.04 111.31 9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" N ILE B 102 " pdb=" CA ILE B 102 " pdb=" C ILE B 102 " ideal model delta sigma weight residual 111.81 109.18 2.63 8.60e-01 1.35e+00 9.38e+00 angle pdb=" C32 3PE G 401 " pdb=" C31 3PE G 401 " pdb=" O31 3PE G 401 " ideal model delta sigma weight residual 111.17 120.25 -9.08 3.00e+00 1.11e-01 9.16e+00 angle pdb=" N GLU G 118 " pdb=" CA GLU G 118 " pdb=" C GLU G 118 " ideal model delta sigma weight residual 113.97 110.34 3.63 1.28e+00 6.10e-01 8.04e+00 ... (remaining 12864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 5238 24.12 - 48.25: 426 48.25 - 72.37: 61 72.37 - 96.49: 6 96.49 - 120.62: 1 Dihedral angle restraints: 5732 sinusoidal: 2326 harmonic: 3406 Sorted by residual: dihedral pdb=" O21 3PE G 401 " pdb=" C2 3PE G 401 " pdb=" C3 3PE G 401 " pdb=" O31 3PE G 401 " ideal model delta sinusoidal sigma weight residual 60.47 -60.15 120.62 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA ARG G 146 " pdb=" CB ARG G 146 " pdb=" CG ARG G 146 " pdb=" CD ARG G 146 " ideal model delta sinusoidal sigma weight residual -60.00 -119.82 59.82 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 152 " pdb=" CA LEU A 152 " pdb=" CB LEU A 152 " pdb=" CG LEU A 152 " ideal model delta sinusoidal sigma weight residual -60.00 -119.50 59.50 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 829 0.027 - 0.054: 423 0.054 - 0.081: 131 0.081 - 0.108: 84 0.108 - 0.135: 17 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CB ILE F 346 " pdb=" CA ILE F 346 " pdb=" CG1 ILE F 346 " pdb=" CG2 ILE F 346 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 80 " pdb=" N ILE A 80 " pdb=" C ILE A 80 " pdb=" CB ILE A 80 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1481 not shown) Planarity restraints: 1631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP F 44 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" CG ASP F 44 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP F 44 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 44 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 202 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" CG ASP A 202 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP A 202 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 202 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 277 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO F 278 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 278 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 278 " -0.016 5.00e-02 4.00e+02 ... (remaining 1628 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2171 2.79 - 3.32: 8689 3.32 - 3.84: 14850 3.84 - 4.37: 16810 4.37 - 4.90: 29999 Nonbonded interactions: 72519 Sorted by model distance: nonbonded pdb=" OH TYR F 76 " pdb=" OG1 THR F 102 " model vdw 2.262 3.040 nonbonded pdb=" O GLY G 138 " pdb=" ND2 ASN G 160 " model vdw 2.313 3.120 nonbonded pdb=" O SER F 262 " pdb=" NE2 GLN F 268 " model vdw 2.323 3.120 nonbonded pdb=" O ASP G 140 " pdb=" ND2 ASN G 160 " model vdw 2.326 3.120 nonbonded pdb=" OG SER F 249 " pdb=" OD1 ASP F 252 " model vdw 2.328 3.040 ... (remaining 72514 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.004 0.134 9516 Z= 0.182 Angle : 0.577 9.728 12869 Z= 0.291 Chirality : 0.040 0.135 1484 Planarity : 0.003 0.028 1631 Dihedral : 16.411 120.616 3550 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.21 % Allowed : 20.68 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1186 helix: 1.32 (0.23), residues: 621 sheet: -1.13 (0.52), residues: 107 loop : -1.74 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 217 TYR 0.011 0.001 TYR F 314 PHE 0.013 0.001 PHE F 301 TRP 0.009 0.001 TRP F 338 HIS 0.010 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9516) covalent geometry : angle 0.57734 (12869) hydrogen bonds : bond 0.14569 ( 473) hydrogen bonds : angle 5.41777 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.338 Fit side-chains REVERT: B 202 ASP cc_start: 0.8801 (t0) cc_final: 0.8397 (t0) REVERT: B 214 GLN cc_start: 0.8948 (mt0) cc_final: 0.8731 (mt0) REVERT: B 220 ASP cc_start: 0.8542 (p0) cc_final: 0.8327 (p0) REVERT: A 47 TYR cc_start: 0.9157 (m-10) cc_final: 0.8782 (m-10) REVERT: A 124 GLU cc_start: 0.7798 (tt0) cc_final: 0.7451 (mt-10) REVERT: A 228 ASP cc_start: 0.7961 (t0) cc_final: 0.7553 (m-30) REVERT: G 34 ASP cc_start: 0.8703 (t0) cc_final: 0.8434 (m-30) REVERT: F 152 MET cc_start: 0.7157 (tpp) cc_final: 0.6689 (tpp) REVERT: F 192 ILE cc_start: 0.4821 (mt) cc_final: 0.4443 (mt) outliers start: 2 outliers final: 2 residues processed: 169 average time/residue: 0.0751 time to fit residues: 17.8563 Evaluate side-chains 132 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain F residue 332 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 195 HIS G 37 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105168 restraints weight = 14022.384| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.71 r_work: 0.3158 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9516 Z= 0.118 Angle : 0.519 7.057 12869 Z= 0.266 Chirality : 0.040 0.156 1484 Planarity : 0.004 0.029 1631 Dihedral : 8.794 129.667 1420 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.28 % Allowed : 20.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1186 helix: 1.53 (0.23), residues: 615 sheet: -0.90 (0.53), residues: 107 loop : -1.68 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 78 TYR 0.019 0.001 TYR F 314 PHE 0.009 0.001 PHE G 330 TRP 0.009 0.001 TRP F 338 HIS 0.008 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9516) covalent geometry : angle 0.51860 (12869) hydrogen bonds : bond 0.03960 ( 473) hydrogen bonds : angle 4.34685 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.287 Fit side-chains REVERT: B 202 ASP cc_start: 0.8769 (t0) cc_final: 0.8449 (t0) REVERT: A 47 TYR cc_start: 0.9026 (m-10) cc_final: 0.8625 (m-10) REVERT: A 119 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: A 124 GLU cc_start: 0.7714 (tt0) cc_final: 0.7346 (mt-10) REVERT: F 31 PHE cc_start: 0.8293 (t80) cc_final: 0.7963 (m-80) REVERT: F 103 MET cc_start: 0.8935 (tpp) cc_final: 0.8517 (mmt) REVERT: F 164 LEU cc_start: 0.6203 (mt) cc_final: 0.5835 (mt) REVERT: F 192 ILE cc_start: 0.5033 (mt) cc_final: 0.4733 (mt) outliers start: 22 outliers final: 14 residues processed: 143 average time/residue: 0.0679 time to fit residues: 14.3226 Evaluate side-chains 136 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 324 GLN Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN G 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101317 restraints weight = 14334.406| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.57 r_work: 0.3095 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9516 Z= 0.248 Angle : 0.594 6.580 12869 Z= 0.308 Chirality : 0.043 0.162 1484 Planarity : 0.004 0.036 1631 Dihedral : 8.504 128.474 1415 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.62 % Allowed : 19.86 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1186 helix: 1.32 (0.22), residues: 616 sheet: -1.06 (0.50), residues: 111 loop : -1.96 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.018 0.001 TYR F 314 PHE 0.017 0.002 PHE F 301 TRP 0.011 0.001 TRP G 349 HIS 0.014 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 9516) covalent geometry : angle 0.59400 (12869) hydrogen bonds : bond 0.04767 ( 473) hydrogen bonds : angle 4.35334 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.242 Fit side-chains REVERT: B 202 ASP cc_start: 0.8756 (t0) cc_final: 0.8479 (t0) REVERT: A 124 GLU cc_start: 0.7742 (tt0) cc_final: 0.7364 (mt-10) REVERT: G 149 TRP cc_start: 0.8109 (m100) cc_final: 0.7744 (m100) REVERT: F 164 LEU cc_start: 0.6115 (mt) cc_final: 0.5794 (mt) REVERT: F 192 ILE cc_start: 0.5004 (mt) cc_final: 0.4709 (mt) outliers start: 35 outliers final: 21 residues processed: 152 average time/residue: 0.0747 time to fit residues: 16.6702 Evaluate side-chains 140 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 116 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN G 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103875 restraints weight = 14246.769| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.71 r_work: 0.3134 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9516 Z= 0.111 Angle : 0.497 6.221 12869 Z= 0.257 Chirality : 0.040 0.145 1484 Planarity : 0.003 0.028 1631 Dihedral : 8.017 124.966 1415 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.10 % Allowed : 20.27 % Favored : 76.63 % 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 are not related in a simple way. whole: 0.11 (0.26), residues: 1186 helix: 1.54 (0.23), residues: 619 sheet: -0.78 (0.50), residues: 106 loop : -1.82 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 78 TYR 0.015 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.012 0.001 TRP F 338 HIS 0.007 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9516) covalent geometry : angle 0.49745 (12869) hydrogen bonds : bond 0.03553 ( 473) hydrogen bonds : angle 4.05725 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.357 Fit side-chains REVERT: B 202 ASP cc_start: 0.8746 (t0) cc_final: 0.8477 (t0) REVERT: A 47 TYR cc_start: 0.9026 (m-10) cc_final: 0.8629 (m-10) REVERT: A 119 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: A 124 GLU cc_start: 0.7831 (tt0) cc_final: 0.7429 (mt-10) REVERT: G 239 MET cc_start: 0.7993 (mmm) cc_final: 0.7729 (mmm) REVERT: F 31 PHE cc_start: 0.8361 (t80) cc_final: 0.7999 (m-80) REVERT: F 136 ASP cc_start: 0.6541 (OUTLIER) cc_final: 0.5871 (t0) REVERT: F 164 LEU cc_start: 0.5732 (mt) cc_final: 0.5328 (mt) REVERT: F 192 ILE cc_start: 0.5052 (mt) cc_final: 0.4772 (mt) outliers start: 30 outliers final: 20 residues processed: 150 average time/residue: 0.0705 time to fit residues: 15.8005 Evaluate side-chains 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 259 GLN Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS G 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104115 restraints weight = 14315.878| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.71 r_work: 0.3135 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9516 Z= 0.108 Angle : 0.497 6.856 12869 Z= 0.256 Chirality : 0.040 0.303 1484 Planarity : 0.003 0.029 1631 Dihedral : 7.718 122.433 1415 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.10 % Allowed : 20.68 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.26), residues: 1186 helix: 1.61 (0.23), residues: 619 sheet: -0.67 (0.50), residues: 106 loop : -1.79 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 78 TYR 0.016 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.007 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9516) covalent geometry : angle 0.49674 (12869) hydrogen bonds : bond 0.03448 ( 473) hydrogen bonds : angle 3.95900 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.209 Fit side-chains REVERT: B 202 ASP cc_start: 0.8741 (t0) cc_final: 0.8491 (t0) REVERT: A 47 TYR cc_start: 0.9015 (m-10) cc_final: 0.8642 (m-10) REVERT: A 119 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: A 124 GLU cc_start: 0.7878 (tt0) cc_final: 0.7492 (mt-10) REVERT: G 149 TRP cc_start: 0.8061 (m100) cc_final: 0.7755 (m100) REVERT: G 239 MET cc_start: 0.8007 (mmm) cc_final: 0.7731 (mmm) REVERT: F 31 PHE cc_start: 0.8323 (t80) cc_final: 0.7936 (m-80) REVERT: F 192 ILE cc_start: 0.5043 (mt) cc_final: 0.4763 (mt) outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.0652 time to fit residues: 14.4978 Evaluate side-chains 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103648 restraints weight = 14250.370| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.71 r_work: 0.3130 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9516 Z= 0.128 Angle : 0.508 7.029 12869 Z= 0.261 Chirality : 0.041 0.281 1484 Planarity : 0.003 0.030 1631 Dihedral : 7.580 120.718 1415 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.90 % Allowed : 21.20 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1186 helix: 1.64 (0.23), residues: 619 sheet: -0.66 (0.51), residues: 106 loop : -1.80 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.019 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.009 0.001 TRP F 338 HIS 0.008 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9516) covalent geometry : angle 0.50838 (12869) hydrogen bonds : bond 0.03533 ( 473) hydrogen bonds : angle 3.92560 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.212 Fit side-chains REVERT: B 202 ASP cc_start: 0.8745 (t0) cc_final: 0.8497 (t0) REVERT: A 119 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: A 124 GLU cc_start: 0.7885 (tt0) cc_final: 0.7494 (mt-10) REVERT: G 63 MET cc_start: 0.8009 (mtp) cc_final: 0.7666 (mtp) REVERT: G 149 TRP cc_start: 0.8075 (m100) cc_final: 0.7781 (m100) REVERT: G 239 MET cc_start: 0.8075 (mmm) cc_final: 0.7767 (mmm) REVERT: F 192 ILE cc_start: 0.5086 (mt) cc_final: 0.4810 (mt) outliers start: 28 outliers final: 22 residues processed: 149 average time/residue: 0.0677 time to fit residues: 15.0124 Evaluate side-chains 145 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103509 restraints weight = 14253.622| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.61 r_work: 0.3133 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9516 Z= 0.134 Angle : 0.512 7.049 12869 Z= 0.263 Chirality : 0.041 0.260 1484 Planarity : 0.004 0.074 1631 Dihedral : 7.484 118.694 1415 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.00 % Allowed : 20.68 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1186 helix: 1.65 (0.23), residues: 619 sheet: -0.62 (0.51), residues: 106 loop : -1.80 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 78 TYR 0.017 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.009 0.001 TRP F 338 HIS 0.008 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9516) covalent geometry : angle 0.51177 (12869) hydrogen bonds : bond 0.03611 ( 473) hydrogen bonds : angle 3.90436 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8679 (t0) cc_final: 0.8466 (t0) REVERT: A 47 TYR cc_start: 0.8948 (m-10) cc_final: 0.8578 (m-10) REVERT: A 119 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 124 GLU cc_start: 0.7825 (tt0) cc_final: 0.7443 (mt-10) REVERT: G 63 MET cc_start: 0.8043 (mtp) cc_final: 0.7761 (mtp) REVERT: G 239 MET cc_start: 0.8006 (mmm) cc_final: 0.7748 (mmm) REVERT: F 31 PHE cc_start: 0.8355 (t80) cc_final: 0.8024 (m-80) REVERT: F 33 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8575 (tmtt) REVERT: F 136 ASP cc_start: 0.6298 (OUTLIER) cc_final: 0.5858 (t0) outliers start: 29 outliers final: 25 residues processed: 145 average time/residue: 0.0714 time to fit residues: 15.3816 Evaluate side-chains 152 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS G 37 ASN G 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104551 restraints weight = 14240.956| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.61 r_work: 0.3146 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9516 Z= 0.112 Angle : 0.503 7.025 12869 Z= 0.259 Chirality : 0.040 0.252 1484 Planarity : 0.004 0.066 1631 Dihedral : 7.341 116.024 1415 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.69 % Allowed : 20.99 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1186 helix: 1.72 (0.23), residues: 619 sheet: -0.57 (0.51), residues: 106 loop : -1.75 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 78 TYR 0.021 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.008 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9516) covalent geometry : angle 0.50290 (12869) hydrogen bonds : bond 0.03347 ( 473) hydrogen bonds : angle 3.83196 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 47 TYR cc_start: 0.8916 (m-10) cc_final: 0.8587 (m-10) REVERT: A 119 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: A 124 GLU cc_start: 0.7782 (tt0) cc_final: 0.7402 (mt-10) REVERT: G 63 MET cc_start: 0.8043 (mtp) cc_final: 0.7773 (mtp) REVERT: G 239 MET cc_start: 0.8134 (mmm) cc_final: 0.7894 (mmm) REVERT: F 31 PHE cc_start: 0.8333 (t80) cc_final: 0.8016 (m-80) REVERT: F 33 LYS cc_start: 0.8905 (tmtt) cc_final: 0.8516 (tmtt) REVERT: F 103 MET cc_start: 0.8940 (tpp) cc_final: 0.8470 (mmt) outliers start: 26 outliers final: 21 residues processed: 145 average time/residue: 0.0634 time to fit residues: 13.6533 Evaluate side-chains 148 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104506 restraints weight = 14135.025| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.73 r_work: 0.3137 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9516 Z= 0.105 Angle : 0.504 7.022 12869 Z= 0.260 Chirality : 0.040 0.241 1484 Planarity : 0.003 0.057 1631 Dihedral : 7.241 113.944 1415 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.48 % Allowed : 21.41 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1186 helix: 1.78 (0.23), residues: 619 sheet: -0.51 (0.51), residues: 106 loop : -1.73 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 78 TYR 0.018 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.010 0.001 TRP F 338 HIS 0.009 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9516) covalent geometry : angle 0.50443 (12869) hydrogen bonds : bond 0.03227 ( 473) hydrogen bonds : angle 3.77976 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 47 TYR cc_start: 0.8962 (m-10) cc_final: 0.8631 (m-10) REVERT: A 119 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: A 124 GLU cc_start: 0.7880 (tt0) cc_final: 0.7472 (mt-10) REVERT: G 63 MET cc_start: 0.8136 (mtp) cc_final: 0.7861 (mtp) REVERT: G 239 MET cc_start: 0.8128 (mmm) cc_final: 0.7869 (mmm) REVERT: F 31 PHE cc_start: 0.8283 (t80) cc_final: 0.7958 (m-80) REVERT: F 103 MET cc_start: 0.9005 (tpp) cc_final: 0.8492 (mmt) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.0659 time to fit residues: 13.9705 Evaluate side-chains 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 110 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.0010 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS G 37 ASN G 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.105734 restraints weight = 14249.745| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.57 r_work: 0.3160 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9516 Z= 0.110 Angle : 0.526 7.671 12869 Z= 0.269 Chirality : 0.040 0.241 1484 Planarity : 0.004 0.055 1631 Dihedral : 7.097 111.538 1415 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.17 % Allowed : 22.13 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1186 helix: 1.79 (0.23), residues: 619 sheet: -0.40 (0.51), residues: 106 loop : -1.70 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 78 TYR 0.017 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.009 0.001 TRP F 338 HIS 0.008 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9516) covalent geometry : angle 0.52576 (12869) hydrogen bonds : bond 0.03284 ( 473) hydrogen bonds : angle 3.76191 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 47 TYR cc_start: 0.8909 (m-10) cc_final: 0.8566 (m-10) REVERT: A 119 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: A 124 GLU cc_start: 0.7802 (tt0) cc_final: 0.7417 (mt-10) REVERT: G 63 MET cc_start: 0.8126 (mtp) cc_final: 0.7888 (mtp) REVERT: G 239 MET cc_start: 0.8112 (mmm) cc_final: 0.7831 (mmm) REVERT: G 242 GLU cc_start: 0.7974 (mp0) cc_final: 0.7773 (mp0) REVERT: F 31 PHE cc_start: 0.8294 (t80) cc_final: 0.8002 (m-80) REVERT: F 103 MET cc_start: 0.8919 (tpp) cc_final: 0.8421 (mmt) outliers start: 21 outliers final: 18 residues processed: 142 average time/residue: 0.0633 time to fit residues: 13.4850 Evaluate side-chains 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 215 SER Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 76 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 chunk 89 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104998 restraints weight = 14133.842| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.59 r_work: 0.3159 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9516 Z= 0.117 Angle : 0.523 7.050 12869 Z= 0.269 Chirality : 0.040 0.237 1484 Planarity : 0.003 0.029 1631 Dihedral : 7.006 109.977 1415 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.07 % Allowed : 22.34 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1186 helix: 1.81 (0.23), residues: 619 sheet: -0.37 (0.52), residues: 106 loop : -1.71 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 78 TYR 0.020 0.001 TYR F 314 PHE 0.011 0.001 PHE G 330 TRP 0.009 0.001 TRP F 338 HIS 0.008 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9516) covalent geometry : angle 0.52305 (12869) hydrogen bonds : bond 0.03326 ( 473) hydrogen bonds : angle 3.77448 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1960.37 seconds wall clock time: 34 minutes 8.54 seconds (2048.54 seconds total)