Starting phenix.real_space_refine on Thu Feb 13 13:04:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzv_26919/02_2025/7uzv_26919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzv_26919/02_2025/7uzv_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_26919/02_2025/7uzv_26919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzv_26919/02_2025/7uzv_26919.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzv_26919/02_2025/7uzv_26919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzv_26919/02_2025/7uzv_26919.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP: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: 4.68, per 1000 atoms: 0.50 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: 2.27 Conformation dependent library (CDL) restraints added in 732.0 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: 0.79 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: 3.18 Time building geometry restraints manager: 2.73 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: 0.850 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: 0.160 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.150 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.980 ------------------------------------------------------------------------------- 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= 0.178 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP E 81 HIS 0.003 0.001 HIS C 101 PHE 0.011 0.001 PHE E 314 TYR 0.008 0.001 TYR E 278 ARG 0.012 0.001 ARG E 112 *********************** 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 : 0.748 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: 0.7399 (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: 2.9432 time to fit residues: 316.5370 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 : 0.750 ------------------------------------------------------------------------------- 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 48 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.162002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.128304 restraints weight = 12500.705| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.62 r_work: 0.3086 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0700 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= 0.252 Angle : 0.581 4.668 6405 Z= 0.298 Chirality : 0.040 0.137 733 Planarity : 0.004 0.031 840 Dihedral : 8.247 56.436 653 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.26 % Allowed : 20.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.35), residues: 574 helix: 1.72 (0.36), residues: 221 sheet: 1.54 (0.53), residues: 99 loop : 0.12 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 81 HIS 0.003 0.001 HIS C 101 PHE 0.017 0.002 PHE E 314 TYR 0.011 0.002 TYR E 278 ARG 0.006 0.001 ARG E 112 *********************** 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 109 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6727 (tm-30) REVERT: E 239 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7364 (pp30) REVERT: E 302 GLN cc_start: 0.7270 (mm110) cc_final: 0.7038 (mm110) REVERT: E 308 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8192 (tp) REVERT: C 202 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.5125 (mp0) outliers start: 21 outliers final: 13 residues processed: 101 average time/residue: 2.8696 time to fit residues: 300.0683 Evaluate side-chains 102 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 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 300 MET 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 46 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.162009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.127114 restraints weight = 12592.566| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.74 r_work: 0.3094 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4713 Z= 0.234 Angle : 0.561 4.562 6405 Z= 0.289 Chirality : 0.039 0.145 733 Planarity : 0.004 0.030 840 Dihedral : 7.615 57.783 649 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.35), residues: 574 helix: 1.54 (0.36), residues: 221 sheet: 1.17 (0.51), residues: 100 loop : 0.09 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 PHE 0.017 0.002 PHE E 314 TYR 0.011 0.002 TYR E 278 ARG 0.006 0.000 ARG E 112 *********************** 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 116 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6615 (tm-30) REVERT: E 239 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7286 (pp30) REVERT: E 308 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (tp) REVERT: C 202 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.5103 (mp0) outliers start: 23 outliers final: 15 residues processed: 108 average time/residue: 2.8915 time to fit residues: 323.0646 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 : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 VAL 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 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 49 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.161528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.126797 restraints weight = 12510.704| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.73 r_work: 0.3081 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4713 Z= 0.248 Angle : 0.569 4.583 6405 Z= 0.293 Chirality : 0.039 0.143 733 Planarity : 0.004 0.033 840 Dihedral : 7.428 58.442 649 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.87 % Allowed : 19.27 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.35), residues: 574 helix: 1.47 (0.36), residues: 221 sheet: 1.02 (0.52), residues: 96 loop : -0.00 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 PHE 0.017 0.002 PHE E 314 TYR 0.011 0.002 TYR E 278 ARG 0.008 0.001 ARG E 112 *********************** 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 117 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6556 (tm-30) REVERT: E 219 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5735 (pttt) REVERT: E 239 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7266 (pp30) REVERT: E 308 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8202 (tp) REVERT: C 202 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.5107 (mp0) outliers start: 24 outliers final: 15 residues processed: 109 average time/residue: 2.9773 time to fit residues: 335.1792 Evaluate side-chains 111 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 VAL 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 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 40 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.162105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127158 restraints weight = 12522.463| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.73 r_work: 0.3118 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4713 Z= 0.226 Angle : 0.556 4.555 6405 Z= 0.286 Chirality : 0.039 0.146 733 Planarity : 0.004 0.035 840 Dihedral : 7.029 58.800 647 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.46 % Allowed : 20.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.35), residues: 574 helix: 1.48 (0.36), residues: 221 sheet: 0.78 (0.51), residues: 103 loop : 0.08 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 PHE 0.016 0.002 PHE E 314 TYR 0.011 0.002 TYR E 278 ARG 0.010 0.001 ARG C 112 *********************** 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 116 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 186 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6526 (tm-30) REVERT: E 219 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5744 (pttt) REVERT: E 239 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7223 (pp30) REVERT: E 304 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: E 308 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8197 (tp) REVERT: C 202 GLU cc_start: 0.5490 (OUTLIER) cc_final: 0.5130 (mp0) outliers start: 22 outliers final: 14 residues processed: 107 average time/residue: 2.9966 time to fit residues: 331.3784 Evaluate side-chains 111 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.163353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129444 restraints weight = 12453.578| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.69 r_work: 0.3082 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4713 Z= 0.258 Angle : 0.578 4.601 6405 Z= 0.298 Chirality : 0.040 0.145 733 Planarity : 0.005 0.037 840 Dihedral : 7.060 59.550 647 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.87 % Allowed : 19.47 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.35), residues: 574 helix: 1.42 (0.36), residues: 221 sheet: 0.81 (0.52), residues: 97 loop : -0.02 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.005 0.001 HIS C 101 PHE 0.018 0.002 PHE E 314 TYR 0.011 0.002 TYR C 278 ARG 0.009 0.001 ARG C 112 *********************** 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 117 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 219 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5746 (pttt) REVERT: E 239 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7226 (pp30) REVERT: E 304 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8007 (ttm170) REVERT: E 308 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8191 (tp) outliers start: 24 outliers final: 15 residues processed: 107 average time/residue: 2.9716 time to fit residues: 328.4072 Evaluate side-chains 111 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 VAL 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 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 276 ILE 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 55 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.160733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.126102 restraints weight = 12635.604| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.67 r_work: 0.3076 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1361 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= 0.323 Angle : 0.620 4.796 6405 Z= 0.322 Chirality : 0.041 0.145 733 Planarity : 0.005 0.048 840 Dihedral : 6.955 59.735 644 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.46 % Allowed : 20.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.34), residues: 574 helix: 1.26 (0.36), residues: 221 sheet: 0.79 (0.52), residues: 97 loop : -0.08 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 81 HIS 0.005 0.001 HIS C 101 PHE 0.021 0.003 PHE E 314 TYR 0.013 0.003 TYR E 278 ARG 0.010 0.001 ARG E 112 *********************** 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 : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 239 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: E 304 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8060 (ttm170) REVERT: E 308 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8203 (tp) outliers start: 22 outliers final: 14 residues processed: 109 average time/residue: 2.9383 time to fit residues: 331.0428 Evaluate side-chains 109 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.161600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.124094 restraints weight = 12676.325| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.71 r_work: 0.3081 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1370 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= 0.264 Angle : 0.588 4.738 6405 Z= 0.304 Chirality : 0.040 0.145 733 Planarity : 0.005 0.041 840 Dihedral : 6.834 59.136 644 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.45 % Allowed : 21.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.34), residues: 574 helix: 1.29 (0.36), residues: 221 sheet: 0.74 (0.52), residues: 97 loop : -0.07 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 81 HIS 0.005 0.001 HIS C 101 PHE 0.018 0.002 PHE E 314 TYR 0.012 0.002 TYR E 278 ARG 0.010 0.001 ARG C 112 *********************** 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 112 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 239 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7217 (pp30) REVERT: E 304 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8021 (ttm170) REVERT: E 308 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8174 (tp) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 3.0448 time to fit residues: 337.0355 Evaluate side-chains 110 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.162413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.125007 restraints weight = 12530.464| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.72 r_work: 0.3098 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4713 Z= 0.220 Angle : 0.559 4.937 6405 Z= 0.288 Chirality : 0.039 0.145 733 Planarity : 0.005 0.045 840 Dihedral : 6.651 59.098 644 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.09 % Favored : 97.74 % Rotamer: Outliers : 3.45 % Allowed : 21.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.35), residues: 574 helix: 1.38 (0.36), residues: 221 sheet: 0.65 (0.50), residues: 103 loop : 0.03 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 PHE 0.016 0.002 PHE E 314 TYR 0.011 0.002 TYR E 278 ARG 0.010 0.001 ARG C 112 *********************** 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 113 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 239 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7064 (pp30) REVERT: E 249 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6903 (mm-30) REVERT: E 304 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8000 (ttm170) REVERT: E 308 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8184 (tp) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 3.0016 time to fit residues: 334.8934 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 : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 46 optimal weight: 0.1980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.163433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129531 restraints weight = 12739.896| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.63 r_work: 0.3134 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4713 Z= 0.176 Angle : 0.537 4.982 6405 Z= 0.276 Chirality : 0.038 0.146 733 Planarity : 0.005 0.060 840 Dihedral : 6.453 58.685 644 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.09 % Favored : 97.74 % Rotamer: Outliers : 2.64 % Allowed : 22.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.35), residues: 574 helix: 1.47 (0.36), residues: 221 sheet: 0.72 (0.50), residues: 102 loop : 0.09 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 PHE 0.013 0.002 PHE E 314 TYR 0.012 0.002 TYR E 278 ARG 0.011 0.001 ARG C 112 ********************** 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 108 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6938 (mm-30) REVERT: C 332 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8245 (mm) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 2.9043 time to fit residues: 318.3740 Evaluate side-chains 103 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 308 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 4 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.163922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.126880 restraints weight = 12546.706| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.71 r_work: 0.3104 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1394 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= 0.202 Angle : 0.551 4.904 6405 Z= 0.283 Chirality : 0.039 0.161 733 Planarity : 0.005 0.050 840 Dihedral : 5.829 49.306 640 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.26 % Favored : 97.56 % Rotamer: Outliers : 2.43 % Allowed : 22.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.35), residues: 574 helix: 1.49 (0.36), residues: 221 sheet: 0.64 (0.50), residues: 103 loop : 0.13 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 81 HIS 0.004 0.001 HIS C 101 PHE 0.015 0.002 PHE E 314 TYR 0.010 0.002 TYR E 278 ARG 0.012 0.001 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9049.40 seconds wall clock time: 159 minutes 0.19 seconds (9540.19 seconds total)