Starting phenix.real_space_refine on Tue Mar 3 22:24:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzv_26919/03_2026/7uzv_26919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzv_26919/03_2026/7uzv_26919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzv_26919/03_2026/7uzv_26919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzv_26919/03_2026/7uzv_26919.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzv_26919/03_2026/7uzv_26919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzv_26919/03_2026/7uzv_26919.cif" } resolution = 2.5 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= 0.002 sd= 0.354 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 2941 2.51 5 N 805 2.21 5 O 924 1.98 5 H 4592 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9274 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4557 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 19, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4654 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Time building chain proxies: 1.70, per 1000 atoms: 0.18 Number of scatterers: 9274 At special positions: 0 Unit cell: (90.47, 83, 75.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 924 8.00 N 805 7.00 C 2941 6.00 H 4592 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: 0.71 Conformation dependent library (CDL) restraints added in 220.1 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 41.3% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.684A pdb=" N LYS E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 146 through 158 removed outlier: 3.699A pdb=" N ARG E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU E 151 " --> pdb=" O PRO E 147 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU E 152 " --> pdb=" O GLN E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 194 through 201 Processing helix chain 'E' and resid 277 through 291 Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.689A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 335 through 350 removed outlier: 4.138A pdb=" N SER E 349 " --> pdb=" O ARG E 345 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER E 350 " --> pdb=" O ARG E 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.654A pdb=" N LYS C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.598A pdb=" N LEU C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 168' Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 277 through 291 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.368A pdb=" N VAL C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 85 through 87 removed outlier: 6.945A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 123 removed outlier: 6.089A pdb=" N THR E 118 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ARG E 246 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU E 120 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN E 248 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP E 122 " --> pdb=" O GLN E 248 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N ALA E 250 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 11.964A pdb=" N GLY E 243 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N GLY E 270 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 12.545A pdb=" N VAL E 245 " --> pdb=" O LEU E 268 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N LEU E 268 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 11.819A pdb=" N LEU E 247 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N PHE E 266 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N GLU E 249 " --> pdb=" O PHE E 264 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA E 226 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE E 264 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG E 233 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N MET E 66 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 87 removed outlier: 5.273A pdb=" N TRP C 75 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 65 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLU C 77 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU C 63 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS C 56 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 227 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR C 58 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 229 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU C 60 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL C 231 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN C 62 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ARG C 233 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU C 64 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE C 262 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA C 226 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 270 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG C 263 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 119 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ARG C 246 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 121 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN C 248 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 123 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA C 250 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 87 removed outlier: 5.273A pdb=" N TRP C 75 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 65 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLU C 77 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N GLU C 63 " --> pdb=" O GLU C 77 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 579 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: 1.99 Time building geometry restraints manager: 1.02 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: 4588 1.03 - 1.23: 4 1.23 - 1.42: 1927 1.42 - 1.62: 2766 1.62 - 1.81: 20 Bond restraints: 9305 Sorted by residual: bond pdb=" C VAL C 173 " pdb=" N LYS C 174 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.59e-02 3.96e+03 2.73e+00 bond pdb=" CA VAL E 82 " pdb=" C VAL E 82 " ideal model delta sigma weight residual 1.527 1.519 0.008 8.50e-03 1.38e+04 8.80e-01 bond pdb=" CB ASN E 133 " pdb=" CG ASN E 133 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.29e-01 bond pdb=" CB ILE C 276 " pdb=" CG2 ILE C 276 " ideal model delta sigma weight residual 1.521 1.545 -0.024 3.30e-02 9.18e+02 5.25e-01 bond pdb=" CA VAL E 82 " pdb=" CB VAL E 82 " ideal model delta sigma weight residual 1.532 1.540 -0.008 1.08e-02 8.57e+03 5.20e-01 ... (remaining 9300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 15715 1.08 - 2.15: 1039 2.15 - 3.23: 85 3.23 - 4.31: 30 4.31 - 5.39: 9 Bond angle restraints: 16878 Sorted by residual: angle pdb=" CG ARG E 112 " pdb=" CD ARG E 112 " pdb=" NE ARG E 112 " ideal model delta sigma weight residual 112.00 117.39 -5.39 2.20e+00 2.07e-01 5.99e+00 angle pdb=" CA GLU C 329 " pdb=" CB GLU C 329 " pdb=" CG GLU C 329 " ideal model delta sigma weight residual 114.10 117.98 -3.88 2.00e+00 2.50e-01 3.77e+00 angle pdb=" N GLN C 83 " pdb=" CA GLN C 83 " pdb=" C GLN C 83 " ideal model delta sigma weight residual 113.55 111.19 2.36 1.26e+00 6.30e-01 3.52e+00 angle pdb=" CD ARG E 112 " pdb=" NE ARG E 112 " pdb=" CZ ARG E 112 " ideal model delta sigma weight residual 124.40 126.93 -2.53 1.40e+00 5.10e-01 3.28e+00 angle pdb=" CA PRO C 175 " pdb=" C PRO C 175 " pdb=" N ALA C 176 " ideal model delta sigma weight residual 115.33 117.46 -2.13 1.28e+00 6.10e-01 2.77e+00 ... (remaining 16873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3756 17.80 - 35.60: 387 35.60 - 53.40: 145 53.40 - 71.21: 46 71.21 - 89.01: 17 Dihedral angle restraints: 4351 sinusoidal: 2408 harmonic: 1943 Sorted by residual: dihedral pdb=" CA TRP E 81 " pdb=" C TRP E 81 " pdb=" N VAL E 82 " pdb=" CA VAL E 82 " ideal model delta harmonic sigma weight residual 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LEU E 84 " pdb=" C LEU E 84 " pdb=" N GLU E 85 " pdb=" CA GLU E 85 " ideal model delta harmonic sigma weight residual -180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CG ARG E 112 " pdb=" CD ARG E 112 " pdb=" NE ARG E 112 " pdb=" CZ ARG E 112 " ideal model delta sinusoidal sigma weight residual -90.00 -40.21 -49.79 2 1.50e+01 4.44e-03 1.24e+01 ... (remaining 4348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 452 0.028 - 0.055: 197 0.055 - 0.083: 46 0.083 - 0.111: 28 0.111 - 0.138: 10 Chirality restraints: 733 Sorted by residual: chirality pdb=" CB VAL C 113 " pdb=" CA VAL C 113 " pdb=" CG1 VAL C 113 " pdb=" CG2 VAL C 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL E 260 " pdb=" N VAL E 260 " pdb=" C VAL E 260 " pdb=" CB VAL E 260 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 730 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 112 " -0.178 9.50e-02 1.11e+02 5.96e-02 4.47e+00 pdb=" NE ARG C 112 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 112 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 112 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 112 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG C 112 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 112 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG C 112 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG C 112 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 112 " -0.116 9.50e-02 1.11e+02 3.92e-02 2.25e+00 pdb=" NE ARG E 112 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 112 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 112 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 112 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 112 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG E 112 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 112 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 112 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 174 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO E 175 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO E 175 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 175 " 0.015 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 466 2.18 - 2.78: 18485 2.78 - 3.39: 27034 3.39 - 3.99: 36090 3.99 - 4.60: 54218 Nonbonded interactions: 136293 Sorted by model distance: nonbonded pdb=" OD1 ASP E 316 " pdb=" HE1 TRP C 105 " model vdw 1.573 2.450 nonbonded pdb="HH12 ARG E 246 " pdb=" O ALA E 301 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLU C 225 " pdb=" HH TYR C 299 " model vdw 1.679 2.450 nonbonded pdb=" OE1 GLN E 339 " pdb=" HG SER C 328 " model vdw 1.689 2.450 nonbonded pdb="HH12 ARG C 246 " pdb=" O ALA C 301 " model vdw 1.693 2.450 ... (remaining 136288 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 'C' and ((resid 56 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 57 through 160 or (resid 161 and (name N or name CA or na \ me 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 nam \ e HE1)) or resid 162 through 203 or resid 217 through 348)) selection = (chain 'E' and ((resid 56 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 57 through 162 or (resid 163 and (name N or name CA or na \ me 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 HD2 or name HE1 or nam \ e HE2)) or resid 164 through 181 or (resid 192 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 HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resi \ d 193 through 348)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.650 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4713 Z= 0.118 Angle : 0.578 5.386 6405 Z= 0.289 Chirality : 0.038 0.138 733 Planarity : 0.004 0.080 840 Dihedral : 19.054 89.007 1763 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 1.39 % Favored : 98.26 % Rotamer: Outliers : 2.84 % Allowed : 22.92 % Favored : 74.24 % 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: 1.78 (0.36), residues: 574 helix: 2.00 (0.36), residues: 217 sheet: 1.81 (0.55), residues: 100 loop : 0.28 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 112 TYR 0.008 0.001 TYR E 278 PHE 0.011 0.001 PHE E 314 TRP 0.009 0.001 TRP E 81 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4713) covalent geometry : angle 0.57776 ( 6405) hydrogen bonds : bond 0.15193 ( 194) hydrogen bonds : angle 5.93866 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6830 (tm-30) REVERT: C 112 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7398 (ttm170) REVERT: C 202 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.5058 (mp0) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 1.4134 time to fit residues: 151.4349 Evaluate side-chains 100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.162765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.128977 restraints weight = 12584.352| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.64 r_work: 0.3102 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4713 Z= 0.147 Angle : 0.562 4.523 6405 Z= 0.287 Chirality : 0.039 0.140 733 Planarity : 0.004 0.031 840 Dihedral : 8.150 56.322 653 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.25 % Allowed : 21.50 % Favored : 75.25 % 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: 1.52 (0.35), residues: 574 helix: 1.78 (0.36), residues: 221 sheet: 1.53 (0.52), residues: 101 loop : 0.17 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 112 TYR 0.011 0.002 TYR E 278 PHE 0.016 0.002 PHE E 314 TRP 0.010 0.001 TRP E 81 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4713) covalent geometry : angle 0.56164 ( 6405) hydrogen bonds : bond 0.04928 ( 194) hydrogen bonds : angle 4.72199 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6731 (tm-30) REVERT: E 302 GLN cc_start: 0.7261 (mm110) cc_final: 0.7036 (mm110) REVERT: C 202 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5085 (mp0) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 1.3409 time to fit residues: 138.5676 Evaluate side-chains 101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.160816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.126685 restraints weight = 12580.460| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.65 r_work: 0.3063 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4713 Z= 0.211 Angle : 0.617 4.839 6405 Z= 0.320 Chirality : 0.041 0.146 733 Planarity : 0.005 0.045 840 Dihedral : 7.240 55.966 645 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.67 % Allowed : 20.08 % Favored : 75.25 % 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: 1.05 (0.35), residues: 574 helix: 1.40 (0.36), residues: 221 sheet: 1.09 (0.52), residues: 98 loop : 0.01 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 112 TYR 0.013 0.003 TYR C 278 PHE 0.021 0.003 PHE E 314 TRP 0.011 0.002 TRP E 81 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4713) covalent geometry : angle 0.61693 ( 6405) hydrogen bonds : bond 0.05477 ( 194) hydrogen bonds : angle 4.68463 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7459 (ptp90) REVERT: E 186 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6556 (tm-30) REVERT: E 239 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7373 (pp30) REVERT: E 308 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8147 (tp) REVERT: C 71 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5735 (tp40) REVERT: C 202 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.5202 (mp0) outliers start: 23 outliers final: 13 residues processed: 104 average time/residue: 1.3615 time to fit residues: 146.2318 Evaluate side-chains 107 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.162285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.128421 restraints weight = 12551.469| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.62 r_work: 0.3095 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4713 Z= 0.137 Angle : 0.547 4.527 6405 Z= 0.281 Chirality : 0.039 0.148 733 Planarity : 0.004 0.031 840 Dihedral : 6.830 49.090 645 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.87 % Allowed : 19.68 % Favored : 75.46 % 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: 1.10 (0.35), residues: 574 helix: 1.48 (0.36), residues: 221 sheet: 0.91 (0.50), residues: 100 loop : 0.08 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 112 TYR 0.010 0.002 TYR E 278 PHE 0.015 0.002 PHE E 314 TRP 0.011 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4713) covalent geometry : angle 0.54745 ( 6405) hydrogen bonds : bond 0.04477 ( 194) hydrogen bonds : angle 4.49152 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6538 (tm-30) REVERT: E 219 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5729 (pttt) REVERT: E 239 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: E 308 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 66 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7307 (ttm) REVERT: C 71 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5619 (tp40) REVERT: C 202 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.5187 (mp0) outliers start: 24 outliers final: 13 residues processed: 108 average time/residue: 1.4472 time to fit residues: 160.8580 Evaluate side-chains 110 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 219 LYS Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.160913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125871 restraints weight = 12461.439| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.73 r_work: 0.3063 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4713 Z= 0.193 Angle : 0.599 4.779 6405 Z= 0.310 Chirality : 0.040 0.147 733 Planarity : 0.005 0.044 840 Dihedral : 6.646 48.252 643 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.07 % Allowed : 19.47 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.34), residues: 574 helix: 1.32 (0.36), residues: 221 sheet: 0.81 (0.52), residues: 98 loop : 0.00 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 112 TYR 0.013 0.003 TYR C 278 PHE 0.020 0.003 PHE E 314 TRP 0.012 0.002 TRP E 81 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 4713) covalent geometry : angle 0.59943 ( 6405) hydrogen bonds : bond 0.05044 ( 194) hydrogen bonds : angle 4.55624 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7077 (tm-30) cc_final: 0.6543 (tm-30) REVERT: E 239 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7276 (pp30) REVERT: E 308 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8157 (tp) REVERT: C 66 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7357 (ttm) REVERT: C 71 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5644 (tp40) outliers start: 25 outliers final: 14 residues processed: 106 average time/residue: 1.5069 time to fit residues: 164.4420 Evaluate side-chains 110 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 0.0070 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.163730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.128781 restraints weight = 12576.871| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.75 r_work: 0.3130 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4713 Z= 0.114 Angle : 0.528 4.512 6405 Z= 0.270 Chirality : 0.038 0.147 733 Planarity : 0.004 0.037 840 Dihedral : 5.991 49.544 640 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.65 % Allowed : 20.89 % Favored : 75.46 % 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: 1.10 (0.35), residues: 574 helix: 1.50 (0.36), residues: 221 sheet: 0.73 (0.50), residues: 101 loop : 0.16 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 112 TYR 0.011 0.002 TYR E 278 PHE 0.013 0.002 PHE E 314 TRP 0.012 0.001 TRP E 81 HIS 0.003 0.000 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4713) covalent geometry : angle 0.52762 ( 6405) hydrogen bonds : bond 0.04026 ( 194) hydrogen bonds : angle 4.37234 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 308 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8153 (tp) REVERT: C 66 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7301 (ttm) REVERT: C 71 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5603 (tp40) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 1.4835 time to fit residues: 163.4745 Evaluate side-chains 110 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.161838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126680 restraints weight = 12672.370| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.74 r_work: 0.3103 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4713 Z= 0.163 Angle : 0.572 4.657 6405 Z= 0.295 Chirality : 0.039 0.147 733 Planarity : 0.005 0.039 840 Dihedral : 6.088 48.801 640 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.46 % Allowed : 20.69 % Favored : 74.85 % 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: 1.03 (0.35), residues: 574 helix: 1.42 (0.36), residues: 221 sheet: 0.76 (0.50), residues: 101 loop : 0.10 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 112 TYR 0.011 0.002 TYR C 278 PHE 0.018 0.002 PHE E 314 TRP 0.011 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4713) covalent geometry : angle 0.57219 ( 6405) hydrogen bonds : bond 0.04649 ( 194) hydrogen bonds : angle 4.43487 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 239 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7202 (pp30) REVERT: E 308 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8164 (tp) REVERT: C 66 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7345 (ttm) REVERT: C 71 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.5645 (tp40) outliers start: 22 outliers final: 11 residues processed: 107 average time/residue: 1.4275 time to fit residues: 157.4114 Evaluate side-chains 110 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.163434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128518 restraints weight = 12541.167| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.73 r_work: 0.3096 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4713 Z= 0.123 Angle : 0.539 4.924 6405 Z= 0.276 Chirality : 0.038 0.147 733 Planarity : 0.004 0.042 840 Dihedral : 5.891 49.337 640 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.65 % Allowed : 21.30 % Favored : 75.05 % 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: 1.11 (0.35), residues: 574 helix: 1.49 (0.36), residues: 221 sheet: 0.73 (0.50), residues: 101 loop : 0.18 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 112 TYR 0.012 0.002 TYR E 278 PHE 0.014 0.002 PHE E 314 TRP 0.012 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4713) covalent geometry : angle 0.53878 ( 6405) hydrogen bonds : bond 0.04126 ( 194) hydrogen bonds : angle 4.34073 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 308 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8159 (tp) REVERT: C 66 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7310 (ttm) REVERT: C 71 GLN cc_start: 0.6207 (OUTLIER) cc_final: 0.5598 (tp40) REVERT: C 332 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8185 (mm) outliers start: 18 outliers final: 11 residues processed: 106 average time/residue: 1.4823 time to fit residues: 161.7211 Evaluate side-chains 109 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.162575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.128440 restraints weight = 12425.458| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.64 r_work: 0.3093 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4713 Z= 0.131 Angle : 0.547 4.975 6405 Z= 0.281 Chirality : 0.038 0.148 733 Planarity : 0.004 0.044 840 Dihedral : 5.858 49.379 640 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.25 % Allowed : 21.91 % Favored : 74.85 % 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: 1.12 (0.35), residues: 574 helix: 1.50 (0.36), residues: 221 sheet: 0.73 (0.50), residues: 101 loop : 0.18 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 112 TYR 0.011 0.002 TYR E 278 PHE 0.015 0.002 PHE E 314 TRP 0.011 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4713) covalent geometry : angle 0.54736 ( 6405) hydrogen bonds : bond 0.04217 ( 194) hydrogen bonds : angle 4.33771 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 308 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8165 (tp) REVERT: C 71 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5761 (tp40) REVERT: C 332 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8278 (mm) outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 1.5216 time to fit residues: 163.0714 Evaluate side-chains 106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 1 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.162962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.129208 restraints weight = 12559.688| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.64 r_work: 0.3100 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4713 Z= 0.179 Angle : 0.592 4.943 6405 Z= 0.305 Chirality : 0.040 0.147 733 Planarity : 0.005 0.044 840 Dihedral : 6.017 48.511 640 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.04 % Allowed : 22.31 % Favored : 74.65 % 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: 1.01 (0.35), residues: 574 helix: 1.38 (0.36), residues: 221 sheet: 0.73 (0.50), residues: 101 loop : 0.12 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 112 TYR 0.012 0.003 TYR C 278 PHE 0.018 0.002 PHE E 314 TRP 0.011 0.002 TRP E 81 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4713) covalent geometry : angle 0.59178 ( 6405) hydrogen bonds : bond 0.04758 ( 194) hydrogen bonds : angle 4.41844 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 349 is missing expected H atoms. Skipping. Residue SER 350 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue THR 39 is missing expected H atoms. Skipping. Residue THR 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 239 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7074 (pp30) REVERT: E 308 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8172 (tp) REVERT: C 71 GLN cc_start: 0.6235 (OUTLIER) cc_final: 0.5753 (tp40) REVERT: C 332 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8296 (mm) outliers start: 15 outliers final: 10 residues processed: 105 average time/residue: 1.4837 time to fit residues: 160.4505 Evaluate side-chains 107 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 300 MET Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.162458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127606 restraints weight = 12547.173| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.73 r_work: 0.3111 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4713 Z= 0.141 Angle : 0.560 4.905 6405 Z= 0.288 Chirality : 0.039 0.147 733 Planarity : 0.005 0.045 840 Dihedral : 5.899 48.867 640 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.64 % Allowed : 22.72 % Favored : 74.65 % 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: 1.04 (0.35), residues: 574 helix: 1.43 (0.36), residues: 221 sheet: 0.71 (0.50), residues: 101 loop : 0.13 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 112 TYR 0.011 0.002 TYR E 278 PHE 0.016 0.002 PHE E 314 TRP 0.011 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4713) covalent geometry : angle 0.56021 ( 6405) hydrogen bonds : bond 0.04367 ( 194) hydrogen bonds : angle 4.35866 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4661.50 seconds wall clock time: 79 minutes 9.55 seconds (4749.55 seconds total)