Starting phenix.real_space_refine (version: dev) on Sun Feb 19 03:52:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzv_26919/02_2023/7uzv_26919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzv_26919/02_2023/7uzv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzv_26919/02_2023/7uzv_26919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzv_26919/02_2023/7uzv_26919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzv_26919/02_2023/7uzv_26919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzv_26919/02_2023/7uzv_26919.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "E GLU 63": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E ASP 297": "OD1" <-> "OD2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E ASP 316": "OD1" <-> "OD2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C GLU 238": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.64, 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 - 3.50 Amino acid : False - 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: 8.11 Conformation dependent library (CDL) restraints added in 926.6 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: 0.29 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: 3.63 Time building geometry restraints manager: 8.23 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: 100.46 - 107.17: 332 107.17 - 113.88: 11127 113.88 - 120.58: 2950 120.58 - 127.29: 2403 127.29 - 134.00: 66 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: 3227 17.80 - 35.60: 341 35.60 - 53.40: 97 53.40 - 71.21: 31 71.21 - 89.01: 17 Dihedral angle restraints: 3713 sinusoidal: 1770 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 3710 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 1.850 nonbonded pdb="HH12 ARG E 246 " pdb=" O ALA E 301 " model vdw 1.647 1.850 nonbonded pdb=" OE1 GLU C 225 " pdb=" HH TYR C 299 " model vdw 1.679 1.850 nonbonded pdb=" OE1 GLN E 339 " pdb=" HG SER C 328 " model vdw 1.689 1.850 nonbonded pdb="HH12 ARG C 246 " pdb=" O ALA C 301 " model vdw 1.693 1.850 ... (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 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 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. 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: 0.650 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: 0.150 Extract box with map and model: 4.160 Check model and map are aligned: 0.130 Process input model: 32.570 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 % 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 *********************** 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 fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 2.8094 time to fit residues: 302.2943 Evaluate side-chains 99 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 0.8852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.0030 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.0170 overall best weight: 2.7832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0708 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= 0.220 Angle : 0.558 4.511 6405 Z= 0.283 Chirality : 0.039 0.145 733 Planarity : 0.004 0.032 840 Dihedral : 4.359 26.825 630 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 5.27 % 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: 1.59 (0.35), residues: 574 helix: 1.77 (0.36), residues: 221 sheet: 1.75 (0.52), residues: 101 loop : 0.18 (0.38), residues: 252 *********************** 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 113 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 102 average time/residue: 2.6788 time to fit residues: 283.5970 Evaluate side-chains 102 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.7704 time to fit residues: 4.4547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 4713 Z= 0.342 Angle : 0.631 4.993 6405 Z= 0.327 Chirality : 0.042 0.144 733 Planarity : 0.005 0.047 840 Dihedral : 4.861 27.504 630 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 5.68 % 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 (0.34), residues: 574 helix: 1.32 (0.36), residues: 221 sheet: 1.63 (0.55), residues: 85 loop : -0.07 (0.36), residues: 268 *********************** 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 119 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 107 average time/residue: 2.8481 time to fit residues: 315.2056 Evaluate side-chains 109 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 1.2671 time to fit residues: 9.0908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1099 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= 0.277 Angle : 0.589 4.694 6405 Z= 0.302 Chirality : 0.040 0.146 733 Planarity : 0.005 0.036 840 Dihedral : 4.773 28.167 630 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 5.07 % 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: 1.02 (0.34), residues: 574 helix: 1.30 (0.36), residues: 221 sheet: 1.54 (0.54), residues: 87 loop : -0.09 (0.36), residues: 266 *********************** 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 113 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 103 average time/residue: 2.8253 time to fit residues: 301.4413 Evaluate side-chains 107 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.9667 time to fit residues: 6.2895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 GLN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1089 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= 0.201 Angle : 0.548 4.501 6405 Z= 0.278 Chirality : 0.038 0.146 733 Planarity : 0.004 0.033 840 Dihedral : 4.548 27.403 630 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.44 % Favored : 97.39 % Rotamer Outliers : 4.06 % 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: 1.18 (0.35), residues: 574 helix: 1.44 (0.36), residues: 221 sheet: 1.45 (0.50), residues: 99 loop : 0.01 (0.37), residues: 254 *********************** 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 111 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 2.7480 time to fit residues: 304.5489 Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.0368 time to fit residues: 3.2109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1161 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= 0.251 Angle : 0.575 4.691 6405 Z= 0.293 Chirality : 0.039 0.147 733 Planarity : 0.004 0.037 840 Dihedral : 4.668 28.521 630 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 4.87 % 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: 1.37 (0.36), residues: 221 sheet: 1.49 (0.54), residues: 87 loop : -0.05 (0.36), residues: 266 *********************** 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 fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 2.7366 time to fit residues: 297.5735 Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.5618 time to fit residues: 2.7891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 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 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4713 Z= 0.205 Angle : 0.551 4.542 6405 Z= 0.279 Chirality : 0.038 0.149 733 Planarity : 0.004 0.051 840 Dihedral : 4.546 28.172 630 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 4.46 % 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: 1.14 (0.35), residues: 574 helix: 1.43 (0.36), residues: 221 sheet: 1.41 (0.50), residues: 99 loop : -0.04 (0.37), residues: 254 *********************** 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 111 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 104 average time/residue: 2.8316 time to fit residues: 304.8982 Evaluate side-chains 103 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 2.1248 time to fit residues: 5.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1206 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= 0.248 Angle : 0.576 4.694 6405 Z= 0.293 Chirality : 0.039 0.147 733 Planarity : 0.004 0.042 840 Dihedral : 4.648 28.448 630 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 4.87 % 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: 1.04 (0.34), residues: 574 helix: 1.37 (0.36), residues: 221 sheet: 1.47 (0.54), residues: 87 loop : -0.10 (0.36), residues: 266 *********************** 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 111 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 102 average time/residue: 2.7795 time to fit residues: 293.5959 Evaluate side-chains 104 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 1.7138 time to fit residues: 6.3428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 48 optimal weight: 0.0010 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 4713 Z= 0.161 Angle : 0.529 4.660 6405 Z= 0.266 Chirality : 0.038 0.151 733 Planarity : 0.005 0.081 840 Dihedral : 4.375 27.661 630 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 3.25 % 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: 1.23 (0.35), residues: 574 helix: 1.56 (0.36), residues: 221 sheet: 1.38 (0.51), residues: 100 loop : -0.01 (0.37), residues: 253 *********************** 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 106 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 104 average time/residue: 2.7406 time to fit residues: 295.2722 Evaluate side-chains 101 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 0.0050 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 4713 Z= 0.156 Angle : 0.520 4.635 6405 Z= 0.260 Chirality : 0.037 0.150 733 Planarity : 0.004 0.044 840 Dihedral : 4.236 27.688 630 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.74 % Favored : 98.08 % Rotamer Outliers : 3.25 % 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: 1.30 (0.35), residues: 574 helix: 1.64 (0.36), residues: 221 sheet: 1.38 (0.51), residues: 100 loop : 0.02 (0.37), residues: 253 ********************** 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 106 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 103 average time/residue: 2.8856 time to fit residues: 308.1848 Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.8164 time to fit residues: 2.7881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.164889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.131746 restraints weight = 12458.872| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.59 r_work: 0.3111 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 4713 Z= 0.150 Angle : 0.515 4.677 6405 Z= 0.256 Chirality : 0.037 0.149 733 Planarity : 0.004 0.044 840 Dihedral : 4.154 27.401 630 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.57 % Favored : 98.26 % Rotamer Outliers : 2.84 % 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: 1.37 (0.35), residues: 574 helix: 1.72 (0.36), residues: 221 sheet: 1.40 (0.51), residues: 100 loop : 0.05 (0.37), residues: 253 =============================================================================== Job complete usr+sys time: 5492.76 seconds wall clock time: 96 minutes 27.17 seconds (5787.17 seconds total)