Starting phenix.real_space_refine on Sun Sep 29 10:51:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/09_2024/7mxy_24076_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/09_2024/7mxy_24076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/09_2024/7mxy_24076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/09_2024/7mxy_24076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/09_2024/7mxy_24076_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/09_2024/7mxy_24076_trim.cif" } resolution = 2.18 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.432 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 70 5.16 5 C 7416 2.51 5 N 1714 2.21 5 O 1911 1.98 5 F 25 1.80 5 H 11129 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22265 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4457 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 4, 'TRANS': 278} Chain: "B" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4433 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain: "C" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4400 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 3, 'TRANS': 275} Chain: "D" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4446 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 4, 'TRANS': 277} Chain: "E" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4422 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.40, per 1000 atoms: 0.47 Number of scatterers: 22265 At special positions: 0 Unit cell: (87.74, 99.51, 98.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 F 25 9.00 O 1911 8.00 N 1714 7.00 C 7416 6.00 H 11129 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: 5.39 Conformation dependent library (CDL) restraints added in 1.6 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 1 sheets defined 85.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 removed outlier: 3.801A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N HIS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.916A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 91 through 100 removed outlier: 4.231A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.167A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 181 through 206 Processing helix chain 'A' and resid 209 through 227 removed outlier: 4.369A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 274 through 291 removed outlier: 5.481A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 36 removed outlier: 3.605A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 68 Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.835A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 91 through 99 removed outlier: 4.222A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.821A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 152 Processing helix chain 'B' and resid 164 through 179 Processing helix chain 'B' and resid 181 through 206 Processing helix chain 'B' and resid 208 through 227 removed outlier: 4.042A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 249 through 271 removed outlier: 3.843A pdb=" N LYS B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 273 through 291 removed outlier: 5.487A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 removed outlier: 3.602A pdb=" N LYS C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 68 Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.820A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 101 removed outlier: 4.228A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.970A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.545A pdb=" N GLY C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 179 Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.951A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 273 through 289 removed outlier: 6.026A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 36 removed outlier: 3.716A pdb=" N LYS D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 68 Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.664A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 91 through 101 removed outlier: 4.244A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.971A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 164 through 179 removed outlier: 3.544A pdb=" N GLN D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 206 Processing helix chain 'D' and resid 208 through 226 removed outlier: 3.871A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 249 through 255 removed outlier: 3.721A pdb=" N TYR D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 273 through 289 removed outlier: 5.953A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 36 removed outlier: 3.550A pdb=" N TYR E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 68 Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.590A pdb=" N GLU E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.942A pdb=" N VAL E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 100 removed outlier: 4.232A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.114A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 153 removed outlier: 4.267A pdb=" N LEU E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 181 through 206 Processing helix chain 'E' and resid 208 through 227 removed outlier: 4.090A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 273 through 289 removed outlier: 5.628A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.678A pdb=" N VAL D 13 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL B 13 " --> pdb=" O LYS C 16 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2559 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: 7.87 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 11089 1.00 - 1.20: 49 1.20 - 1.40: 4971 1.40 - 1.61: 6344 1.61 - 1.81: 100 Bond restraints: 22553 Sorted by residual: bond pdb=" SG CYS D 96 " pdb=" HG CYS D 96 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" SG CYS D 192 " pdb=" HG CYS D 192 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" ND2 ASN E 108 " pdb="HD21 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" ND2 ASN E 108 " pdb="HD22 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" ND2 ASN D 193 " pdb="HD21 ASN D 193 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.40e+01 ... (remaining 22548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 40014 1.89 - 3.78: 497 3.78 - 5.66: 65 5.66 - 7.55: 9 7.55 - 9.44: 6 Bond angle restraints: 40591 Sorted by residual: angle pdb=" N ILE D 194 " pdb=" CA ILE D 194 " pdb=" C ILE D 194 " ideal model delta sigma weight residual 110.62 102.71 7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" N LEU E 262 " pdb=" CA LEU E 262 " pdb=" C LEU E 262 " ideal model delta sigma weight residual 111.28 106.27 5.01 1.09e+00 8.42e-01 2.12e+01 angle pdb=" N THR D 109 " pdb=" CA THR D 109 " pdb=" CB THR D 109 " ideal model delta sigma weight residual 110.32 116.71 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N GLY E 264 " pdb=" CA GLY E 264 " pdb=" C GLY E 264 " ideal model delta sigma weight residual 112.77 108.12 4.65 1.28e+00 6.10e-01 1.32e+01 angle pdb=" N PHE D 94 " pdb=" CA PHE D 94 " pdb=" C PHE D 94 " ideal model delta sigma weight residual 111.28 107.38 3.90 1.09e+00 8.42e-01 1.28e+01 ... (remaining 40586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9308 18.00 - 36.00: 883 36.00 - 54.00: 370 54.00 - 71.99: 103 71.99 - 89.99: 12 Dihedral angle restraints: 10676 sinusoidal: 5398 harmonic: 5278 Sorted by residual: dihedral pdb=" CA PHE C 90 " pdb=" C PHE C 90 " pdb=" N PRO C 91 " pdb=" CA PRO C 91 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL C 158 " pdb=" C VAL C 158 " pdb=" N HIS C 159 " pdb=" CA HIS C 159 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA VAL E 213 " pdb=" C VAL E 213 " pdb=" N PHE E 214 " pdb=" CA PHE E 214 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 10673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1665 0.078 - 0.155: 81 0.155 - 0.233: 6 0.233 - 0.311: 3 0.311 - 0.388: 2 Chirality restraints: 1757 Sorted by residual: chirality pdb=" CA ASN D 193 " pdb=" N ASN D 193 " pdb=" C ASN D 193 " pdb=" CB ASN D 193 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA THR E 261 " pdb=" N THR E 261 " pdb=" C THR E 261 " pdb=" CB THR E 261 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA THR D 109 " pdb=" N THR D 109 " pdb=" C THR D 109 " pdb=" CB THR D 109 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1754 not shown) Planarity restraints: 3269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 108 " 0.192 2.00e-02 2.50e+03 1.92e-01 5.51e+02 pdb=" CG ASN E 108 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 108 " -0.180 2.00e-02 2.50e+03 pdb=" ND2 ASN E 108 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 108 " -0.272 2.00e-02 2.50e+03 pdb="HD22 ASN E 108 " 0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 193 " 0.180 2.00e-02 2.50e+03 1.79e-01 4.79e+02 pdb=" CG ASN D 193 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN D 193 " -0.169 2.00e-02 2.50e+03 pdb=" ND2 ASN D 193 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN D 193 " 0.261 2.00e-02 2.50e+03 pdb="HD22 ASN D 193 " -0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 265 " -0.068 2.00e-02 2.50e+03 6.66e-02 6.65e+01 pdb=" CG ASN E 265 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN E 265 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN E 265 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN E 265 " 0.094 2.00e-02 2.50e+03 pdb="HD22 ASN E 265 " -0.094 2.00e-02 2.50e+03 ... (remaining 3266 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1845 2.21 - 2.81: 47808 2.81 - 3.40: 67237 3.40 - 4.00: 89789 4.00 - 4.60: 137785 Nonbonded interactions: 344464 Sorted by model distance: nonbonded pdb=" O ASN B 257 " pdb=" HG1 THR B 261 " model vdw 1.611 2.450 nonbonded pdb=" O THR C 106 " pdb=" HG1 THR C 109 " model vdw 1.628 2.450 nonbonded pdb=" OE1 GLU C 229 " pdb="HD21 ASN C 234 " model vdw 1.634 2.450 nonbonded pdb=" OD1 ASN B 157 " pdb="HD22 ASN B 164 " model vdw 1.638 2.450 nonbonded pdb=" O CYS C 96 " pdb=" HG1 THR C 100 " model vdw 1.659 2.450 ... (remaining 344459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 289 or resid 1001)) selection = (chain 'B' and (resid 12 through 289 or resid 401)) selection = (chain 'C' and (resid 12 through 289 or resid 401)) selection = (chain 'D' and (resid 12 through 289 or resid 401)) selection = (chain 'E' and (resid 12 through 289 or resid 401)) } 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: 0.030 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: 0.360 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 44.800 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.050 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:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 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 : 0.006 0.090 11424 Z= 0.396 Angle : 0.655 8.012 15507 Z= 0.369 Chirality : 0.042 0.388 1757 Planarity : 0.004 0.042 1886 Dihedral : 18.004 89.992 3862 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.20 % Allowed : 30.88 % Favored : 65.92 % 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: 1.25 (0.22), residues: 1396 helix: 1.49 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 230 PHE 0.019 0.001 PHE E 223 TYR 0.018 0.001 TYR B 228 ARG 0.005 0.001 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 373 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8332 (t) REVERT: A 83 VAL cc_start: 0.7988 (t) cc_final: 0.7713 (t) REVERT: B 279 PHE cc_start: 0.7429 (m-80) cc_final: 0.6323 (t80) REVERT: C 258 LEU cc_start: 0.7748 (mt) cc_final: 0.7344 (mt) REVERT: D 261 THR cc_start: 0.7959 (m) cc_final: 0.7748 (m) REVERT: E 158 VAL cc_start: 0.7326 (t) cc_final: 0.7108 (m) REVERT: E 283 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4410 (mt-10) outliers start: 37 outliers final: 27 residues processed: 405 average time/residue: 1.1929 time to fit residues: 569.2798 Evaluate side-chains 383 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11424 Z= 0.326 Angle : 0.578 5.787 15507 Z= 0.330 Chirality : 0.039 0.165 1757 Planarity : 0.004 0.051 1886 Dihedral : 8.483 88.246 1596 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.62 % Allowed : 27.94 % Favored : 66.44 % 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 (0.22), residues: 1396 helix: 1.32 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.016 0.002 TYR C 38 ARG 0.002 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 357 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6102 (mt-10) REVERT: B 279 PHE cc_start: 0.7471 (m-80) cc_final: 0.6355 (t80) REVERT: C 23 GLU cc_start: 0.6964 (mp0) cc_final: 0.6624 (mp0) REVERT: D 261 THR cc_start: 0.7722 (m) cc_final: 0.7504 (m) REVERT: E 158 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.7189 (m) REVERT: E 173 ILE cc_start: 0.8420 (mm) cc_final: 0.7955 (mt) outliers start: 65 outliers final: 42 residues processed: 397 average time/residue: 1.3159 time to fit residues: 613.1234 Evaluate side-chains 393 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 349 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN D 157 ASN D 284 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11424 Z= 0.336 Angle : 0.577 5.383 15507 Z= 0.331 Chirality : 0.040 0.173 1757 Planarity : 0.004 0.048 1886 Dihedral : 7.972 83.285 1585 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.06 % Allowed : 27.68 % Favored : 66.26 % 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: 0.87 (0.22), residues: 1396 helix: 1.22 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -2.04 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.018 0.002 TYR B 212 ARG 0.002 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 358 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7375 (mmt) cc_final: 0.7036 (mmm) REVERT: A 95 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6739 (mpp) REVERT: A 163 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6971 (mtpt) REVERT: B 175 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6108 (mt-10) REVERT: B 223 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7081 (t80) REVERT: B 279 PHE cc_start: 0.7520 (m-80) cc_final: 0.6327 (t80) REVERT: C 23 GLU cc_start: 0.6917 (mp0) cc_final: 0.6584 (mp0) REVERT: C 86 TYR cc_start: 0.7896 (t80) cc_final: 0.7335 (t80) REVERT: D 104 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7486 (mp) REVERT: D 261 THR cc_start: 0.7756 (m) cc_final: 0.7526 (m) REVERT: E 86 TYR cc_start: 0.7758 (t80) cc_final: 0.7248 (t80) REVERT: E 283 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.4520 (mt-10) outliers start: 70 outliers final: 45 residues processed: 396 average time/residue: 1.2845 time to fit residues: 593.4812 Evaluate side-chains 390 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 339 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN D 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11424 Z= 0.343 Angle : 0.575 5.519 15507 Z= 0.331 Chirality : 0.040 0.174 1757 Planarity : 0.004 0.050 1886 Dihedral : 7.776 81.795 1583 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.14 % Allowed : 28.20 % Favored : 65.66 % 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: 0.79 (0.22), residues: 1396 helix: 1.17 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -2.11 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.016 0.002 TYR D 236 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 354 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7414 (mmt) cc_final: 0.7104 (mmm) REVERT: A 163 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6949 (mtpt) REVERT: B 175 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6092 (mt-10) REVERT: B 223 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7098 (t80) REVERT: B 279 PHE cc_start: 0.7554 (m-80) cc_final: 0.6340 (t80) REVERT: C 23 GLU cc_start: 0.7016 (mp0) cc_final: 0.6643 (mp0) REVERT: C 86 TYR cc_start: 0.7989 (t80) cc_final: 0.7435 (t80) REVERT: D 261 THR cc_start: 0.7776 (m) cc_final: 0.7568 (m) REVERT: E 86 TYR cc_start: 0.7810 (t80) cc_final: 0.7284 (t80) REVERT: E 158 VAL cc_start: 0.7385 (OUTLIER) cc_final: 0.7119 (m) REVERT: E 283 GLU cc_start: 0.5240 (OUTLIER) cc_final: 0.4403 (mt-10) outliers start: 71 outliers final: 44 residues processed: 388 average time/residue: 1.2293 time to fit residues: 560.4685 Evaluate side-chains 393 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 344 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 283 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN D 157 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 11424 Z= 0.451 Angle : 0.638 5.551 15507 Z= 0.369 Chirality : 0.043 0.177 1757 Planarity : 0.005 0.064 1886 Dihedral : 7.926 81.420 1581 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.83 % Allowed : 27.68 % Favored : 65.48 % 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: 0.37 (0.22), residues: 1396 helix: 0.86 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -2.20 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS D 284 PHE 0.022 0.002 PHE E 223 TYR 0.021 0.002 TYR B 212 ARG 0.005 0.001 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 356 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7432 (mmt) cc_final: 0.7068 (mmm) REVERT: A 163 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.6960 (mtpt) REVERT: B 23 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6739 (mp0) REVERT: B 175 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.6044 (mt-10) REVERT: B 223 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7236 (t80) REVERT: B 279 PHE cc_start: 0.7648 (m-80) cc_final: 0.6375 (t80) REVERT: C 23 GLU cc_start: 0.7021 (mp0) cc_final: 0.6692 (mp0) REVERT: C 86 TYR cc_start: 0.8158 (t80) cc_final: 0.7520 (t80) REVERT: D 221 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7359 (t80) REVERT: D 261 THR cc_start: 0.7787 (m) cc_final: 0.7575 (m) REVERT: E 86 TYR cc_start: 0.7944 (t80) cc_final: 0.7377 (t80) REVERT: E 158 VAL cc_start: 0.7401 (OUTLIER) cc_final: 0.7097 (m) REVERT: E 173 ILE cc_start: 0.8417 (mm) cc_final: 0.7983 (mt) REVERT: E 283 GLU cc_start: 0.5446 (OUTLIER) cc_final: 0.4384 (mm-30) outliers start: 79 outliers final: 53 residues processed: 398 average time/residue: 1.2442 time to fit residues: 583.3422 Evaluate side-chains 406 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 347 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11424 Z= 0.371 Angle : 0.598 5.412 15507 Z= 0.344 Chirality : 0.040 0.172 1757 Planarity : 0.004 0.051 1886 Dihedral : 7.806 79.126 1581 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 6.66 % Allowed : 28.37 % Favored : 64.97 % 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: 0.50 (0.22), residues: 1396 helix: 0.96 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -2.19 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.018 0.002 TYR D 236 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 354 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7452 (mmt) cc_final: 0.7094 (mmm) REVERT: A 163 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6906 (mtpt) REVERT: B 23 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6735 (mp0) REVERT: B 175 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6054 (mt-10) REVERT: B 223 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7187 (t80) REVERT: B 279 PHE cc_start: 0.7613 (m-80) cc_final: 0.6370 (t80) REVERT: C 23 GLU cc_start: 0.6982 (mp0) cc_final: 0.6607 (mp0) REVERT: C 86 TYR cc_start: 0.8168 (t80) cc_final: 0.7544 (t80) REVERT: D 261 THR cc_start: 0.7777 (m) cc_final: 0.7565 (m) REVERT: E 86 TYR cc_start: 0.7983 (t80) cc_final: 0.7410 (t80) REVERT: E 158 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.7066 (m) REVERT: E 283 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.4338 (mm-30) outliers start: 77 outliers final: 53 residues processed: 400 average time/residue: 1.2205 time to fit residues: 573.9186 Evaluate side-chains 407 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 349 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11424 Z= 0.357 Angle : 0.596 5.372 15507 Z= 0.342 Chirality : 0.040 0.170 1757 Planarity : 0.004 0.051 1886 Dihedral : 7.685 77.575 1580 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.14 % Allowed : 28.63 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.22), residues: 1396 helix: 1.03 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -2.14 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS D 284 PHE 0.021 0.002 PHE E 223 TYR 0.022 0.002 TYR B 212 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 348 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7459 (mmt) cc_final: 0.7103 (mmm) REVERT: A 163 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6907 (mtpt) REVERT: B 175 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6048 (mt-10) REVERT: B 223 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7081 (t80) REVERT: B 279 PHE cc_start: 0.7503 (m-80) cc_final: 0.6340 (t80) REVERT: C 23 GLU cc_start: 0.6906 (mp0) cc_final: 0.6532 (mp0) REVERT: C 86 TYR cc_start: 0.8242 (t80) cc_final: 0.7642 (t80) REVERT: D 261 THR cc_start: 0.7771 (m) cc_final: 0.7560 (m) REVERT: E 30 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7247 (mm-30) REVERT: E 86 TYR cc_start: 0.8010 (t80) cc_final: 0.7397 (t80) REVERT: E 158 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.7045 (m) REVERT: E 283 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4333 (mm-30) outliers start: 71 outliers final: 52 residues processed: 387 average time/residue: 1.2434 time to fit residues: 564.4420 Evaluate side-chains 401 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 344 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.0470 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11424 Z= 0.252 Angle : 0.545 5.062 15507 Z= 0.310 Chirality : 0.038 0.162 1757 Planarity : 0.004 0.041 1886 Dihedral : 7.328 76.571 1579 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.62 % Allowed : 29.76 % Favored : 64.62 % 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 (0.22), residues: 1396 helix: 1.37 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 284 PHE 0.025 0.002 PHE A 202 TYR 0.021 0.002 TYR B 286 ARG 0.001 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 348 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7431 (mmt) cc_final: 0.7171 (mmm) REVERT: A 163 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6980 (mtpt) REVERT: B 175 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6006 (mt-10) REVERT: B 223 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 279 PHE cc_start: 0.7428 (m-80) cc_final: 0.6293 (t80) REVERT: C 23 GLU cc_start: 0.6763 (mp0) cc_final: 0.6379 (mp0) REVERT: C 86 TYR cc_start: 0.8210 (t80) cc_final: 0.7570 (t80) REVERT: D 261 THR cc_start: 0.7770 (m) cc_final: 0.7555 (m) REVERT: E 22 GLU cc_start: 0.6912 (pt0) cc_final: 0.6620 (pt0) REVERT: E 30 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7207 (mm-30) REVERT: E 86 TYR cc_start: 0.7993 (t80) cc_final: 0.7400 (t80) outliers start: 65 outliers final: 41 residues processed: 387 average time/residue: 1.2821 time to fit residues: 584.4171 Evaluate side-chains 382 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 338 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11424 Z= 0.359 Angle : 0.602 5.988 15507 Z= 0.345 Chirality : 0.040 0.168 1757 Planarity : 0.004 0.040 1886 Dihedral : 7.142 76.954 1576 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.71 % Allowed : 30.02 % Favored : 64.27 % 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: 0.78 (0.22), residues: 1396 helix: 1.17 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.11 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS D 284 PHE 0.031 0.002 PHE A 202 TYR 0.021 0.002 TYR B 212 ARG 0.005 0.001 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 345 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7465 (mmt) cc_final: 0.7109 (mmm) REVERT: A 163 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.6994 (mtpt) REVERT: B 175 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6029 (mt-10) REVERT: B 223 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7065 (t80) REVERT: B 258 LEU cc_start: 0.7626 (mt) cc_final: 0.7415 (mt) REVERT: B 279 PHE cc_start: 0.7513 (m-80) cc_final: 0.6336 (t80) REVERT: C 23 GLU cc_start: 0.6926 (mp0) cc_final: 0.6628 (mp0) REVERT: C 86 TYR cc_start: 0.8292 (t80) cc_final: 0.7646 (t80) REVERT: D 261 THR cc_start: 0.7779 (m) cc_final: 0.7568 (m) REVERT: E 22 GLU cc_start: 0.6975 (pt0) cc_final: 0.6664 (pt0) REVERT: E 30 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7259 (mm-30) outliers start: 66 outliers final: 48 residues processed: 381 average time/residue: 1.2296 time to fit residues: 549.9741 Evaluate side-chains 394 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 343 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11424 Z= 0.293 Angle : 0.578 9.487 15507 Z= 0.328 Chirality : 0.039 0.163 1757 Planarity : 0.004 0.041 1886 Dihedral : 7.002 77.836 1576 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.67 % Allowed : 31.23 % Favored : 64.10 % 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 (0.22), residues: 1396 helix: 1.29 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -2.16 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 284 PHE 0.034 0.002 PHE A 202 TYR 0.023 0.002 TYR B 286 ARG 0.003 0.000 ARG C 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 353 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7450 (mmt) cc_final: 0.7092 (mmm) REVERT: A 163 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7049 (mtpt) REVERT: B 175 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5994 (mt-10) REVERT: B 223 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 258 LEU cc_start: 0.7621 (mt) cc_final: 0.7414 (mt) REVERT: B 279 PHE cc_start: 0.7462 (m-80) cc_final: 0.6306 (t80) REVERT: C 23 GLU cc_start: 0.6820 (mp0) cc_final: 0.6449 (mp0) REVERT: C 86 TYR cc_start: 0.8284 (t80) cc_final: 0.7597 (t80) REVERT: D 261 THR cc_start: 0.7780 (m) cc_final: 0.7569 (m) REVERT: E 22 GLU cc_start: 0.6931 (pt0) cc_final: 0.6630 (pt0) REVERT: E 30 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7211 (mm-30) outliers start: 54 outliers final: 44 residues processed: 384 average time/residue: 1.2390 time to fit residues: 558.8956 Evaluate side-chains 392 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 345 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 284 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.233587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.226480 restraints weight = 31543.725| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 0.86 r_work: 0.4604 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4535 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11424 Z= 0.407 Angle : 0.632 6.957 15507 Z= 0.362 Chirality : 0.042 0.170 1757 Planarity : 0.004 0.043 1886 Dihedral : 7.223 78.429 1576 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.67 % Allowed : 31.49 % Favored : 63.84 % 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: 0.54 (0.22), residues: 1396 helix: 1.01 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -2.25 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS D 284 PHE 0.041 0.002 PHE A 202 TYR 0.021 0.002 TYR B 212 ARG 0.004 0.001 ARG C 128 =============================================================================== Job complete usr+sys time: 9137.38 seconds wall clock time: 158 minutes 43.51 seconds (9523.51 seconds total)