Starting phenix.real_space_refine on Wed Aug 5 05:00:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7s_73879/08_2026/9z7s_73879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7s_73879/08_2026/9z7s_73879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z7s_73879/08_2026/9z7s_73879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7s_73879/08_2026/9z7s_73879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z7s_73879/08_2026/9z7s_73879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7s_73879/08_2026/9z7s_73879.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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: 6 Type Number sf(0) Gaussians Mg 2 5.21 5 S 21 5.16 5 C 2814 2.51 5 N 678 2.21 5 O 744 1.98 5 H 4117 0.53 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8376 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4310 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 9, 'TRANS': 284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 7, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 4060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4060 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 4} Link IDs: {None: 5} Time building chain proxies: 1.76, per 1000 atoms: 0.21 Number of scatterers: 8376 At special positions: 0 Unit cell: (57.186, 101.664, 67.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 Mg 2 11.99 O 744 8.00 N 678 7.00 C 2814 6.00 H 4117 1.00 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: 0.82 Conformation dependent library (CDL) restraints added in 422.9 milliseconds 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1062 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 8 through 43 removed outlier: 3.666A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.700A pdb=" N LEU B 54 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 77 removed outlier: 4.056A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.594A pdb=" N THR B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 90 through 103 removed outlier: 4.118A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.859A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 178 through 209 removed outlier: 3.818A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 243 removed outlier: 4.324A pdb=" N TRP B 219 " --> pdb=" O HIS B 215 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 269 through 274 removed outlier: 4.046A pdb=" N ASP B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 299 removed outlier: 3.741A pdb=" N SER B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 37 removed outlier: 3.891A pdb=" N ILE A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 55 Processing helix chain 'A' and resid 56 through 78 removed outlier: 3.747A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 88 through 104 Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.539A pdb=" N HIS A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.927A pdb=" N HIS A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 removed outlier: 3.717A pdb=" N PHE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 4.324A pdb=" N ARG A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 208 removed outlier: 3.817A pdb=" N ILE A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 241 removed outlier: 4.568A pdb=" N TRP A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 275 through 299 removed outlier: 3.880A pdb=" N PHE A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1065 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: 1.85 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4107 1.03 - 1.23: 10 1.23 - 1.42: 1802 1.42 - 1.62: 2519 1.62 - 1.81: 32 Bond restraints: 8470 Sorted by residual: bond pdb=" CA LEU A 88 " pdb=" C LEU A 88 " ideal model delta sigma weight residual 1.518 1.548 -0.030 4.01e-02 6.22e+02 5.55e-01 bond pdb=" C THR B 249 " pdb=" O THR B 249 " ideal model delta sigma weight residual 1.244 1.237 0.006 1.00e-02 1.00e+04 4.16e-01 bond pdb=" C LEU A 88 " pdb=" O LEU A 88 " ideal model delta sigma weight residual 1.239 1.255 -0.016 2.50e-02 1.60e+03 4.16e-01 bond pdb=" CG1 ILE B 29 " pdb=" CD1 ILE B 29 " ideal model delta sigma weight residual 1.513 1.490 0.023 3.90e-02 6.57e+02 3.45e-01 bond pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " ideal model delta sigma weight residual 1.808 1.790 0.018 3.30e-02 9.18e+02 3.10e-01 ... (remaining 8465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 14086 1.02 - 2.05: 1145 2.05 - 3.07: 34 3.07 - 4.09: 8 4.09 - 5.11: 6 Bond angle restraints: 15279 Sorted by residual: angle pdb=" N GLY A 89 " pdb=" CA GLY A 89 " pdb=" C GLY A 89 " ideal model delta sigma weight residual 113.99 109.70 4.29 1.28e+00 6.10e-01 1.12e+01 angle pdb=" CA LYS B 300 " pdb=" C LYS B 300 " pdb=" O LYS B 300 " ideal model delta sigma weight residual 120.51 117.39 3.12 1.43e+00 4.89e-01 4.77e+00 angle pdb=" CA LYS B 300 " pdb=" C LYS B 300 " pdb=" N ASP B 301 " ideal model delta sigma weight residual 116.84 120.58 -3.74 1.71e+00 3.42e-01 4.77e+00 angle pdb=" C GLU B 56 " pdb=" N TRP B 57 " pdb=" CA TRP B 57 " ideal model delta sigma weight residual 120.29 122.98 -2.69 1.42e+00 4.96e-01 3.58e+00 angle pdb=" C SER A 92 " pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 120.55 123.26 -2.71 1.60e+00 3.91e-01 2.86e+00 ... (remaining 15274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 3642 16.88 - 33.75: 257 33.75 - 50.63: 65 50.63 - 67.50: 63 67.50 - 84.38: 3 Dihedral angle restraints: 4030 sinusoidal: 2039 harmonic: 1991 Sorted by residual: dihedral pdb=" CB GLU B 56 " pdb=" CG GLU B 56 " pdb=" CD GLU B 56 " pdb=" OE1 GLU B 56 " ideal model delta sinusoidal sigma weight residual 0.00 -84.38 84.38 1 3.00e+01 1.11e-03 9.62e+00 dihedral pdb=" CA LEU A 88 " pdb=" C LEU A 88 " pdb=" N GLY A 89 " pdb=" CA GLY A 89 " ideal model delta harmonic sigma weight residual 180.00 165.34 14.66 0 5.00e+00 4.00e-02 8.60e+00 dihedral pdb=" CA LEU A 139 " pdb=" CB LEU A 139 " pdb=" CG LEU A 139 " pdb=" CD1 LEU A 139 " ideal model delta sinusoidal sigma weight residual 60.00 104.50 -44.50 3 1.50e+01 4.44e-03 8.00e+00 ... (remaining 4027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 427 0.022 - 0.045: 161 0.045 - 0.067: 91 0.067 - 0.089: 43 0.089 - 0.112: 10 Chirality restraints: 732 Sorted by residual: chirality pdb=" CA PRO A 87 " pdb=" N PRO A 87 " pdb=" C PRO A 87 " pdb=" CB PRO A 87 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.12e-01 chirality pdb=" CA ILE A 136 " pdb=" N ILE A 136 " pdb=" C ILE A 136 " pdb=" CB ILE A 136 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA PRO B 149 " pdb=" N PRO B 149 " pdb=" C PRO B 149 " pdb=" CB PRO B 149 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.54e-01 ... (remaining 729 not shown) Planarity restraints: 1287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 86 " -0.013 5.00e-02 4.00e+02 2.01e-02 6.44e-01 pdb=" N PRO A 87 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 210 " -0.013 5.00e-02 4.00e+02 1.96e-02 6.14e-01 pdb=" N PRO B 211 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 60 " 0.006 2.00e-02 2.50e+03 3.76e-03 5.64e-01 pdb=" CG TRP B 60 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP B 60 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP B 60 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 60 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 60 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 60 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 60 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 60 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 60 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 60 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP B 60 " -0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP B 60 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 60 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 60 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP B 60 " 0.000 2.00e-02 2.50e+03 ... (remaining 1284 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1013 2.26 - 2.85: 18743 2.85 - 3.43: 21772 3.43 - 4.02: 27895 4.02 - 4.60: 43817 Nonbonded interactions: 113240 Sorted by model distance: nonbonded pdb=" HZ3 LYS B 32 " pdb=" O LEU B 240 " model vdw 1.676 2.450 nonbonded pdb=" HE1 TRP B 59 " pdb=" OD1 ASN B 237 " model vdw 1.763 2.450 nonbonded pdb=" O LEU B 179 " pdb=" HG1 THR B 183 " model vdw 1.793 2.450 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 501 " model vdw 1.817 2.050 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 503 " model vdw 1.829 2.050 ... (remaining 113235 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 8 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 71 through 78 or (resid 7 \ 9 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 80 through 128 or (resid 129 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or res \ id 130 through 133 or (resid 134 through 138 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 139 through 153 or (resid 15 \ 4 and (name N or name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) or resid 1 \ 55 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 173 through 196 or (resid 197 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 198 thr \ ough 200 or (resid 201 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 202 through 203 or (resid 204 through 207 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 08 through 215 or (resid 216 and (name N or name CA or name C or name O or name \ CB or name HA )) or resid 217 through 218 or (resid 219 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name NE1 or \ name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2 or name H or name HA )) \ or resid 220 through 268 or (resid 269 through 270 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 271 through 301)) selection = (chain 'B' and (resid 8 or (resid 9 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name OD2 or name H or name HA )) or resid 10 \ through 30 or (resid 31 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name H or name HA )) or (resid 32 \ through 33 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or (resid 34 and (name N or name CA or name C or name O or name H )) or \ (resid 35 through 39 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or (resid 46 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or (resid 47 and (name N or name CA or name C or \ name O or name H )) or (resid 48 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or (resid 49 and (name N or name CA or name C or \ name O or name H )) or resid 50 through 74 or (resid 75 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA )) or \ resid 76 through 101 or (resid 102 through 103 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 104 or (resid 105 through \ 107 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 108 through 138 or (resid 139 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name H or name HA )) or re \ sid 140 through 155 or (resid 156 through 161 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 162 or (resid 163 through 1 \ 66 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 167 or (resid 168 through 169 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 170 through 206 or (resid 207 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 208 through 211 or (resid 212 through 214 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or (resid 215 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 \ or name HE2)) or resid 216 or (resid 217 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 218 through 222 or (resid 223 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 224 through 242 or (resid 243 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ o \ r name H or name HA )) or (resid 244 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 245 through 277 or (resid 278 and (n \ ame N or name CA or name C or name O or name CB or name CG or name OD1 or name O \ D2 or name H or name HA )) or resid 279 through 301)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 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 : 0.002 0.030 4353 Z= 0.115 Angle : 0.467 5.113 5946 Z= 0.277 Chirality : 0.034 0.112 732 Planarity : 0.002 0.020 724 Dihedral : 11.877 84.379 1413 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.95 (0.37), residues: 578 helix: 2.53 (0.25), residues: 435 sheet: None (None), residues: 0 loop : 0.15 (0.59), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.010 0.001 TYR A 77 PHE 0.007 0.001 PHE B 243 TRP 0.013 0.001 TRP B 60 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 ( 4353) covalent geometry : angle 0.46661 / 0.28 ( 5946) hydrogen bonds : bond 0.12940 / 7.86 ( 357) hydrogen bonds : angle 5.61413 / 4.06 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 ILE cc_start: 0.8484 (mm) cc_final: 0.7896 (mt) REVERT: A 59 TRP cc_start: 0.8008 (t60) cc_final: 0.7723 (t60) REVERT: A 113 LYS cc_start: 0.8647 (mttt) cc_final: 0.8269 (mmtt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1220 time to fit residues: 25.7745 Evaluate side-chains 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.0000 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 272 GLN A 140 ASN A 232 GLN A 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.168425 restraints weight = 16822.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174176 restraints weight = 7206.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.177432 restraints weight = 3784.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.179766 restraints weight = 2319.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.181052 restraints weight = 1508.339| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4353 Z= 0.114 Angle : 0.481 4.986 5946 Z= 0.256 Chirality : 0.036 0.120 732 Planarity : 0.004 0.044 724 Dihedral : 3.365 16.459 604 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.94 % Allowed : 12.74 % Favored : 86.32 % 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: 3.02 (0.37), residues: 578 helix: 2.56 (0.25), residues: 442 sheet: None (None), residues: 0 loop : 0.10 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.008 0.001 TYR B 235 PHE 0.009 0.001 PHE B 299 TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 4353) covalent geometry : angle 0.48058 / 0.26 ( 5946) hydrogen bonds : bond 0.03795 / 2.55 ( 357) hydrogen bonds : angle 4.26182 / 3.15 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 111 average time/residue: 0.0942 time to fit residues: 14.3754 Evaluate side-chains 102 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 263 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 38 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.3332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.183901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167357 restraints weight = 17094.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.172946 restraints weight = 7439.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.176407 restraints weight = 3984.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.178541 restraints weight = 2410.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.179761 restraints weight = 1602.529| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4353 Z= 0.110 Angle : 0.466 4.981 5946 Z= 0.248 Chirality : 0.035 0.116 732 Planarity : 0.004 0.046 724 Dihedral : 3.351 16.344 604 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.94 % Allowed : 12.26 % Favored : 86.79 % 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: 2.95 (0.36), residues: 578 helix: 2.54 (0.24), residues: 443 sheet: None (None), residues: 0 loop : -0.09 (0.60), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.007 0.001 TYR B 235 PHE 0.016 0.001 PHE A 154 TRP 0.013 0.001 TRP B 59 HIS 0.002 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 4353) covalent geometry : angle 0.46572 / 0.25 ( 5946) hydrogen bonds : bond 0.03526 / 2.39 ( 357) hydrogen bonds : angle 4.11824 / 3.05 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 268 PHE cc_start: 0.7379 (m-10) cc_final: 0.7175 (m-80) outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.0845 time to fit residues: 12.5315 Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.178259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.161660 restraints weight = 17279.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.167285 restraints weight = 7466.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170735 restraints weight = 3978.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.172655 restraints weight = 2421.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.174220 restraints weight = 1690.271| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4353 Z= 0.153 Angle : 0.485 4.754 5946 Z= 0.266 Chirality : 0.035 0.121 732 Planarity : 0.004 0.051 724 Dihedral : 3.545 16.509 604 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.65 % Allowed : 12.50 % Favored : 85.85 % 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: 2.70 (0.35), residues: 578 helix: 2.34 (0.24), residues: 443 sheet: None (None), residues: 0 loop : -0.06 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.011 0.001 TYR B 235 PHE 0.018 0.001 PHE A 154 TRP 0.016 0.002 TRP B 59 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4353) covalent geometry : angle 0.48459 / 0.27 ( 5946) hydrogen bonds : bond 0.03815 / 2.64 ( 357) hydrogen bonds : angle 4.13789 / 3.10 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 0.1032 time to fit residues: 15.3389 Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain A residue 234 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.0370 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 ASN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.181066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.165553 restraints weight = 17022.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.171029 restraints weight = 7385.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174328 restraints weight = 3921.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.176244 restraints weight = 2348.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177600 restraints weight = 1587.745| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4353 Z= 0.105 Angle : 0.439 4.603 5946 Z= 0.238 Chirality : 0.035 0.115 732 Planarity : 0.004 0.060 724 Dihedral : 3.385 16.336 604 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.18 % Allowed : 14.86 % Favored : 83.96 % 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: 3.00 (0.36), residues: 578 helix: 2.57 (0.24), residues: 443 sheet: None (None), residues: 0 loop : -0.05 (0.59), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 37 TYR 0.007 0.001 TYR A 235 PHE 0.019 0.001 PHE A 154 TRP 0.016 0.001 TRP B 59 HIS 0.003 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 4353) covalent geometry : angle 0.43942 / 0.24 ( 5946) hydrogen bonds : bond 0.03445 / 2.36 ( 357) hydrogen bonds : angle 3.95780 / 2.97 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.8242 (t60) cc_final: 0.7714 (t60) outliers start: 5 outliers final: 3 residues processed: 100 average time/residue: 0.1012 time to fit residues: 14.2862 Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.178005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162517 restraints weight = 16899.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167906 restraints weight = 7378.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171135 restraints weight = 3940.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.173174 restraints weight = 2392.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.174568 restraints weight = 1585.842| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4353 Z= 0.145 Angle : 0.463 4.692 5946 Z= 0.255 Chirality : 0.035 0.122 732 Planarity : 0.004 0.055 724 Dihedral : 3.451 16.324 604 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.42 % Allowed : 16.04 % Favored : 82.55 % 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: 2.91 (0.36), residues: 578 helix: 2.47 (0.24), residues: 449 sheet: None (None), residues: 0 loop : -0.06 (0.60), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.009 0.001 TYR B 235 PHE 0.020 0.001 PHE A 154 TRP 0.016 0.001 TRP B 59 HIS 0.002 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 4353) covalent geometry : angle 0.46326 / 0.25 ( 5946) hydrogen bonds : bond 0.03634 / 2.49 ( 357) hydrogen bonds : angle 4.02800 / 3.03 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.8484 (tp) cc_final: 0.7988 (mm) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.1037 time to fit residues: 14.1414 Evaluate side-chains 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 258 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 ASN ** 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 = 0.4032 r_free = 0.4032 target = 0.177397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161829 restraints weight = 17039.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167050 restraints weight = 7472.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170255 restraints weight = 4047.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172266 restraints weight = 2493.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.173700 restraints weight = 1696.968| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4353 Z= 0.134 Angle : 0.460 4.612 5946 Z= 0.252 Chirality : 0.035 0.122 732 Planarity : 0.004 0.059 724 Dihedral : 3.459 16.504 604 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.94 % Allowed : 16.51 % Favored : 82.55 % 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: 2.99 (0.35), residues: 578 helix: 2.56 (0.24), residues: 443 sheet: None (None), residues: 0 loop : 0.00 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 37 TYR 0.008 0.001 TYR B 235 PHE 0.022 0.001 PHE A 154 TRP 0.020 0.001 TRP B 59 HIS 0.002 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4353) covalent geometry : angle 0.45953 / 0.25 ( 5946) hydrogen bonds : bond 0.03657 / 2.51 ( 357) hydrogen bonds : angle 4.02280 / 3.03 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.8533 (tp) cc_final: 0.8055 (mm) outliers start: 4 outliers final: 4 residues processed: 96 average time/residue: 0.1026 time to fit residues: 13.8139 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain A residue 234 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 ASN ** 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 = 0.4037 r_free = 0.4037 target = 0.177844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162374 restraints weight = 16773.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.167622 restraints weight = 7435.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170887 restraints weight = 4000.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172816 restraints weight = 2433.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.174233 restraints weight = 1666.186| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4353 Z= 0.119 Angle : 0.445 4.559 5946 Z= 0.243 Chirality : 0.035 0.115 732 Planarity : 0.004 0.063 724 Dihedral : 3.410 16.394 604 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.24 % Allowed : 17.45 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.36), residues: 578 helix: 2.66 (0.24), residues: 443 sheet: None (None), residues: 0 loop : 0.01 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.007 0.001 TYR A 235 PHE 0.019 0.001 PHE B 154 TRP 0.015 0.001 TRP B 59 HIS 0.003 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4353) covalent geometry : angle 0.44496 / 0.24 ( 5946) hydrogen bonds : bond 0.03555 / 2.42 ( 357) hydrogen bonds : angle 3.92061 / 2.95 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.1019 time to fit residues: 12.7190 Evaluate side-chains 91 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.177957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162626 restraints weight = 16926.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167861 restraints weight = 7420.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171134 restraints weight = 3991.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.173073 restraints weight = 2420.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174451 restraints weight = 1637.252| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4353 Z= 0.116 Angle : 0.445 4.530 5946 Z= 0.243 Chirality : 0.035 0.119 732 Planarity : 0.004 0.058 724 Dihedral : 3.380 16.223 604 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.94 % Allowed : 16.75 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.36), residues: 578 helix: 2.68 (0.24), residues: 444 sheet: None (None), residues: 0 loop : -0.01 (0.58), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 37 TYR 0.007 0.001 TYR A 235 PHE 0.019 0.001 PHE B 154 TRP 0.026 0.001 TRP B 59 HIS 0.003 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 4353) covalent geometry : angle 0.44531 / 0.24 ( 5946) hydrogen bonds : bond 0.03499 / 2.39 ( 357) hydrogen bonds : angle 3.90621 / 2.94 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 96 average time/residue: 0.1040 time to fit residues: 14.0974 Evaluate side-chains 95 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 234 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 ASN ** 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 = 0.4026 r_free = 0.4026 target = 0.176748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160657 restraints weight = 17013.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166120 restraints weight = 7447.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169468 restraints weight = 4026.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.171442 restraints weight = 2461.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172893 restraints weight = 1691.126| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4353 Z= 0.141 Angle : 0.472 4.477 5946 Z= 0.259 Chirality : 0.035 0.125 732 Planarity : 0.004 0.059 724 Dihedral : 3.477 16.529 604 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.94 % Allowed : 16.75 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.36), residues: 578 helix: 2.58 (0.24), residues: 440 sheet: None (None), residues: 0 loop : 0.12 (0.59), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 37 TYR 0.009 0.001 TYR B 253 PHE 0.021 0.001 PHE B 154 TRP 0.019 0.001 TRP B 59 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 4353) covalent geometry : angle 0.47172 / 0.26 ( 5946) hydrogen bonds : bond 0.03733 / 2.56 ( 357) hydrogen bonds : angle 4.01583 / 3.03 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue SER 43 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue ILE 136 is missing expected H atoms. Skipping. Residue THR 138 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue ILE 201 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue VAL 158 is missing expected H atoms. Skipping. Residue VAL 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue VAL 161 is missing expected H atoms. Skipping. Residue LEU 163 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 169 is missing expected H atoms. Skipping. Residue LYS 204 is missing expected H atoms. Skipping. Residue LEU 206 is missing expected H atoms. Skipping. Residue LYS 210 is missing expected H atoms. Skipping. Residue VAL 212 is missing expected H atoms. Skipping. Residue LEU 213 is missing expected H atoms. Skipping. Residue LEU 217 is missing expected H atoms. Skipping. Residue LEU 223 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 ILE cc_start: 0.8553 (tp) cc_final: 0.8076 (mm) outliers start: 4 outliers final: 4 residues processed: 96 average time/residue: 0.1015 time to fit residues: 13.6605 Evaluate side-chains 94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 234 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.177888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162391 restraints weight = 16759.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167644 restraints weight = 7399.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.170886 restraints weight = 4016.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173003 restraints weight = 2458.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.174375 restraints weight = 1620.365| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4353 Z= 0.122 Angle : 0.462 4.494 5946 Z= 0.252 Chirality : 0.035 0.121 732 Planarity : 0.004 0.058 724 Dihedral : 3.411 16.175 604 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.94 % Allowed : 16.75 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.36), residues: 578 helix: 2.61 (0.24), residues: 444 sheet: None (None), residues: 0 loop : 0.10 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 37 TYR 0.007 0.001 TYR B 235 PHE 0.018 0.001 PHE B 154 TRP 0.029 0.002 TRP A 59 HIS 0.003 0.000 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4353) covalent geometry : angle 0.46232 / 0.25 ( 5946) hydrogen bonds : bond 0.03624 / 2.49 ( 357) hydrogen bonds : angle 3.95463 / 2.98 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1594.30 seconds wall clock time: 27 minutes 49.17 seconds (1669.17 seconds total)