Starting phenix.real_space_refine on Tue Sep 24 19:36:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/09_2024/6so5_10266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/09_2024/6so5_10266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/09_2024/6so5_10266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/09_2024/6so5_10266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/09_2024/6so5_10266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6so5_10266/09_2024/6so5_10266.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 73 5.16 5 C 5673 2.51 5 N 1425 2.21 5 O 1565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8737 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2464 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 1 Chain: "B" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2301 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 17, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain breaks: 1 Chain: "D" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1160 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain breaks: 1 Chain: "E" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 835 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 816 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4310 SG CYS B 289 46.170 112.721 80.191 1.00101.14 S ATOM 4333 SG CYS B 292 44.838 111.737 77.378 1.00 91.48 S Time building chain proxies: 4.74, per 1000 atoms: 0.54 Number of scatterers: 8737 At special positions: 0 Unit cell: (87.48, 129.6, 106.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 73 16.00 O 1565 8.00 N 1425 7.00 C 5673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 284 " distance=1.75 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 289 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 292 " 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 3 sheets defined 71.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 4.006A pdb=" N ILE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.970A pdb=" N ASP A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 4.177A pdb=" N LEU A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 125 through 139 removed outlier: 3.517A pdb=" N LYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 159 removed outlier: 4.043A pdb=" N VAL A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 203 removed outlier: 3.838A pdb=" N THR A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 215 through 238 removed outlier: 4.053A pdb=" N ALA A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.543A pdb=" N ASP A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 289 through 310 removed outlier: 3.558A pdb=" N ASP A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 4.087A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 49 through 64 Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.586A pdb=" N ASP B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.765A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 128 through 134 removed outlier: 4.476A pdb=" N GLU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 157 Processing helix chain 'B' and resid 175 through 182 Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.597A pdb=" N LEU B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.661A pdb=" N THR B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 289 through 308 removed outlier: 3.610A pdb=" N ASP B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 4.217A pdb=" N VAL B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 27 removed outlier: 3.740A pdb=" N ASN C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 61 removed outlier: 3.519A pdb=" N PHE C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 124 Processing helix chain 'C' and resid 150 through 171 removed outlier: 4.457A pdb=" N CYS C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS C 162 " --> pdb=" O TRP C 158 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 28 removed outlier: 3.999A pdb=" N TRP D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU D 15 " --> pdb=" O TRP D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 62 Processing helix chain 'D' and resid 64 through 124 removed outlier: 8.319A pdb=" N ALA D 70 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ARG D 71 " --> pdb=" O ASP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 171 Processing helix chain 'E' and resid 190 through 208 removed outlier: 5.063A pdb=" N ALA E 205 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE E 206 " --> pdb=" O GLY E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 231 removed outlier: 3.951A pdb=" N THR E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR E 228 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 251 Processing helix chain 'E' and resid 253 through 291 removed outlier: 4.029A pdb=" N MET E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 209 removed outlier: 3.562A pdb=" N LEU F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA F 205 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 229 removed outlier: 3.568A pdb=" N THR F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 Processing helix chain 'F' and resid 252 through 291 removed outlier: 3.575A pdb=" N VAL F 256 " --> pdb=" O ILE F 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 257 " --> pdb=" O PRO F 253 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.859A pdb=" N LEU A 69 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 242 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N ASN A 274 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 244 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE A 276 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A 246 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 70 removed outlier: 6.227A pdb=" N LEU B 69 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 43 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR B 272 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE B 244 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN B 274 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS B 246 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N HIS B 273 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B 316 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2719 1.34 - 1.46: 2033 1.46 - 1.58: 4049 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 8918 Sorted by residual: bond pdb=" N CYS F 208 " pdb=" CA CYS F 208 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.31e-02 5.83e+03 7.41e+00 bond pdb=" N LYS F 209 " pdb=" CA LYS F 209 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.70e+00 bond pdb=" N TYR F 210 " pdb=" CA TYR F 210 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.28e-02 6.10e+03 5.44e+00 bond pdb=" CA LEU B 28 " pdb=" C LEU B 28 " ideal model delta sigma weight residual 1.522 1.491 0.031 1.72e-02 3.38e+03 3.15e+00 bond pdb=" C ASP B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 1.337 1.322 0.014 9.80e-03 1.04e+04 2.11e+00 ... (remaining 8913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 11668 1.98 - 3.96: 306 3.96 - 5.94: 62 5.94 - 7.92: 7 7.92 - 9.89: 2 Bond angle restraints: 12045 Sorted by residual: angle pdb=" C LEU E 274 " pdb=" N CYS E 275 " pdb=" CA CYS E 275 " ideal model delta sigma weight residual 122.38 112.49 9.89 1.81e+00 3.05e-01 2.99e+01 angle pdb=" N ILE E 190 " pdb=" CA ILE E 190 " pdb=" C ILE E 190 " ideal model delta sigma weight residual 111.91 107.69 4.22 8.90e-01 1.26e+00 2.25e+01 angle pdb=" CA CYS E 275 " pdb=" CB CYS E 275 " pdb=" SG CYS E 275 " ideal model delta sigma weight residual 114.40 123.08 -8.68 2.30e+00 1.89e-01 1.42e+01 angle pdb=" N CYS F 208 " pdb=" CA CYS F 208 " pdb=" C CYS F 208 " ideal model delta sigma weight residual 113.18 108.71 4.47 1.21e+00 6.83e-01 1.36e+01 angle pdb=" N ALA C 6 " pdb=" CA ALA C 6 " pdb=" C ALA C 6 " ideal model delta sigma weight residual 111.82 107.62 4.20 1.16e+00 7.43e-01 1.31e+01 ... (remaining 12040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4663 16.21 - 32.42: 596 32.42 - 48.62: 124 48.62 - 64.83: 21 64.83 - 81.04: 8 Dihedral angle restraints: 5412 sinusoidal: 2193 harmonic: 3219 Sorted by residual: dihedral pdb=" CB CYS F 208 " pdb=" SG CYS F 208 " pdb=" SG CYS F 284 " pdb=" CB CYS F 284 " ideal model delta sinusoidal sigma weight residual -86.00 -155.23 69.23 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CA SER F 212 " pdb=" C SER F 212 " pdb=" N ILE F 213 " pdb=" CA ILE F 213 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA HIS E 285 " pdb=" C HIS E 285 " pdb=" N GLU E 286 " pdb=" CA GLU E 286 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 933 0.039 - 0.078: 330 0.078 - 0.117: 104 0.117 - 0.156: 15 0.156 - 0.195: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA CYS E 275 " pdb=" N CYS E 275 " pdb=" C CYS E 275 " pdb=" CB CYS E 275 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA PRO D 29 " pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CB PRO D 29 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CB ILE F 252 " pdb=" CA ILE F 252 " pdb=" CG1 ILE F 252 " pdb=" CG2 ILE F 252 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 1383 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 168 " 0.047 5.00e-02 4.00e+02 7.14e-02 8.17e+00 pdb=" N PRO B 169 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 207 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C VAL F 207 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL F 207 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS F 208 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 159 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ILE D 159 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE D 159 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU D 160 " -0.012 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 130 2.56 - 3.14: 8344 3.14 - 3.73: 14458 3.73 - 4.31: 18665 4.31 - 4.90: 28255 Nonbonded interactions: 69852 Sorted by model distance: nonbonded pdb=" CG2 THR E 219 " pdb=" CE2 TYR E 277 " model vdw 1.973 3.760 nonbonded pdb=" OE1 GLU A 259 " pdb=" OH TYR A 310 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR A 256 " pdb=" NH2 ARG A 260 " model vdw 2.196 3.120 nonbonded pdb=" OE2 GLU A 251 " pdb=" N SER A 254 " model vdw 2.220 3.120 nonbonded pdb=" OE2 GLU C 46 " pdb=" NE ARG C 50 " model vdw 2.223 3.120 ... (remaining 69847 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 24 through 190 or resid 220 through 344)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 191 through 291) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.020 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.005 0.046 8918 Z= 0.340 Angle : 0.816 9.894 12045 Z= 0.466 Chirality : 0.044 0.195 1386 Planarity : 0.005 0.071 1497 Dihedral : 14.990 81.038 3308 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % 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: -4.60 (0.21), residues: 1077 helix: -2.53 (0.15), residues: 684 sheet: -4.50 (0.37), residues: 97 loop : -3.21 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 9 HIS 0.012 0.002 HIS A 296 PHE 0.016 0.002 PHE F 283 TYR 0.014 0.002 TYR E 224 ARG 0.005 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9192 (mm) cc_final: 0.8870 (tp) REVERT: A 124 MET cc_start: 0.2545 (ttp) cc_final: 0.2177 (tpp) REVERT: A 185 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8448 (tpm170) REVERT: A 189 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7755 (mmm160) REVERT: A 221 LYS cc_start: 0.9224 (mttt) cc_final: 0.8955 (mmmt) REVERT: A 241 GLN cc_start: 0.8011 (pt0) cc_final: 0.7765 (pt0) REVERT: A 257 GLU cc_start: 0.8290 (tp30) cc_final: 0.8023 (tm-30) REVERT: B 153 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8712 (mmm-85) REVERT: B 249 ILE cc_start: 0.9427 (mt) cc_final: 0.9149 (tt) REVERT: B 288 PRO cc_start: 0.7272 (Cg_endo) cc_final: 0.7041 (Cg_exo) REVERT: C 76 GLU cc_start: 0.8268 (tp30) cc_final: 0.8045 (tp30) REVERT: C 81 LYS cc_start: 0.9294 (tttt) cc_final: 0.9070 (ttmm) REVERT: C 155 ILE cc_start: 0.7736 (mt) cc_final: 0.7486 (mt) REVERT: D 13 LEU cc_start: 0.9003 (tp) cc_final: 0.8549 (tp) REVERT: D 17 PHE cc_start: 0.8789 (m-80) cc_final: 0.8561 (m-80) REVERT: D 19 PHE cc_start: 0.8746 (m-80) cc_final: 0.8175 (m-80) REVERT: D 31 PHE cc_start: 0.6747 (m-80) cc_final: 0.6474 (m-80) REVERT: D 49 MET cc_start: 0.8686 (mmm) cc_final: 0.8388 (mmm) REVERT: D 52 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8651 (mt-10) REVERT: D 53 ILE cc_start: 0.9635 (mt) cc_final: 0.9356 (mt) REVERT: D 56 MET cc_start: 0.8797 (ptp) cc_final: 0.8494 (mtm) REVERT: D 57 LYS cc_start: 0.9647 (mttt) cc_final: 0.9290 (mttp) REVERT: D 101 LYS cc_start: 0.9307 (tmtt) cc_final: 0.9029 (tmtt) REVERT: D 108 PHE cc_start: 0.8381 (t80) cc_final: 0.8142 (t80) REVERT: D 123 TYR cc_start: 0.7861 (p90) cc_final: 0.7619 (t80) REVERT: D 155 ILE cc_start: 0.9369 (mt) cc_final: 0.8812 (mt) REVERT: E 266 LYS cc_start: 0.8690 (mttt) cc_final: 0.8202 (mtmt) REVERT: E 273 ASP cc_start: 0.9214 (m-30) cc_final: 0.8807 (m-30) REVERT: E 274 LEU cc_start: 0.9001 (mm) cc_final: 0.8667 (mm) REVERT: F 225 MET cc_start: 0.8809 (mmt) cc_final: 0.8543 (mmt) REVERT: F 227 LEU cc_start: 0.9264 (mt) cc_final: 0.8924 (mm) REVERT: F 248 LEU cc_start: 0.7080 (pp) cc_final: 0.6838 (pp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2510 time to fit residues: 108.4828 Evaluate side-chains 261 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 235 GLN B 332 ASN C 45 GLN C 89 HIS D 22 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8918 Z= 0.214 Angle : 0.693 8.460 12045 Z= 0.359 Chirality : 0.045 0.280 1386 Planarity : 0.005 0.063 1497 Dihedral : 5.140 20.391 1162 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.31 % Allowed : 6.19 % Favored : 93.50 % 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: -2.27 (0.24), residues: 1077 helix: -0.63 (0.18), residues: 714 sheet: -3.52 (0.45), residues: 92 loop : -2.77 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 158 HIS 0.005 0.001 HIS B 314 PHE 0.016 0.002 PHE F 278 TYR 0.030 0.002 TYR E 277 ARG 0.008 0.001 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 350 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9117 (mm) cc_final: 0.8848 (tp) REVERT: A 131 MET cc_start: 0.6923 (mmt) cc_final: 0.6644 (mmm) REVERT: A 189 ARG cc_start: 0.8170 (mtt180) cc_final: 0.7478 (mmm160) REVERT: A 257 GLU cc_start: 0.8170 (tp30) cc_final: 0.7900 (tm-30) REVERT: B 99 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8516 (t0) REVERT: B 101 PHE cc_start: 0.7612 (m-10) cc_final: 0.6789 (m-10) REVERT: B 136 MET cc_start: 0.0897 (mmp) cc_final: 0.0688 (mmm) REVERT: B 152 MET cc_start: 0.8724 (mmm) cc_final: 0.8427 (mmm) REVERT: B 153 ARG cc_start: 0.8858 (mtt180) cc_final: 0.8534 (mmm-85) REVERT: C 49 MET cc_start: 0.8675 (mpp) cc_final: 0.8365 (mmm) REVERT: C 60 LEU cc_start: 0.9049 (tt) cc_final: 0.8325 (tt) REVERT: C 157 CYS cc_start: 0.9299 (m) cc_final: 0.9066 (p) REVERT: D 13 LEU cc_start: 0.8877 (tp) cc_final: 0.8371 (tp) REVERT: D 17 PHE cc_start: 0.8696 (m-10) cc_final: 0.8486 (m-80) REVERT: D 47 SER cc_start: 0.9205 (p) cc_final: 0.8889 (p) REVERT: D 49 MET cc_start: 0.8602 (mmm) cc_final: 0.8179 (mmm) REVERT: D 55 ASP cc_start: 0.8276 (t70) cc_final: 0.8017 (t70) REVERT: D 72 TYR cc_start: 0.8276 (t80) cc_final: 0.7992 (t80) REVERT: D 101 LYS cc_start: 0.9280 (tmtt) cc_final: 0.8989 (tmtt) REVERT: D 163 ASN cc_start: 0.8709 (m110) cc_final: 0.8297 (m110) REVERT: E 273 ASP cc_start: 0.9134 (m-30) cc_final: 0.8845 (m-30) REVERT: F 225 MET cc_start: 0.8844 (mmt) cc_final: 0.8635 (mmm) REVERT: F 227 LEU cc_start: 0.8648 (mt) cc_final: 0.8394 (tp) outliers start: 3 outliers final: 0 residues processed: 353 average time/residue: 0.2190 time to fit residues: 102.6494 Evaluate side-chains 284 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN D 8 HIS D 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8918 Z= 0.309 Angle : 0.736 9.085 12045 Z= 0.385 Chirality : 0.046 0.244 1386 Planarity : 0.005 0.054 1497 Dihedral : 5.186 19.664 1162 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.21 % Allowed : 4.95 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1077 helix: -0.26 (0.18), residues: 712 sheet: -3.38 (0.46), residues: 92 loop : -2.37 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 158 HIS 0.007 0.001 HIS A 296 PHE 0.041 0.002 PHE D 19 TYR 0.021 0.002 TYR B 302 ARG 0.007 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.9139 (mm) cc_final: 0.8856 (tp) REVERT: A 221 LYS cc_start: 0.9409 (mmtm) cc_final: 0.9198 (mmmt) REVERT: A 257 GLU cc_start: 0.8200 (tp30) cc_final: 0.7926 (tm-30) REVERT: B 60 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7749 (mm110) REVERT: B 69 LEU cc_start: 0.8767 (tp) cc_final: 0.8523 (tp) REVERT: B 101 PHE cc_start: 0.7706 (m-10) cc_final: 0.7392 (m-10) REVERT: B 152 MET cc_start: 0.8772 (mmm) cc_final: 0.8452 (mmm) REVERT: B 153 ARG cc_start: 0.8905 (mtt180) cc_final: 0.8485 (ttm170) REVERT: B 241 GLN cc_start: 0.7570 (pt0) cc_final: 0.7263 (pt0) REVERT: B 315 ILE cc_start: 0.8727 (mp) cc_final: 0.8439 (mp) REVERT: C 72 TYR cc_start: 0.8281 (t80) cc_final: 0.7922 (t80) REVERT: C 157 CYS cc_start: 0.9304 (m) cc_final: 0.9047 (p) REVERT: D 13 LEU cc_start: 0.8902 (tp) cc_final: 0.8369 (tp) REVERT: D 17 PHE cc_start: 0.8676 (m-10) cc_final: 0.8457 (m-80) REVERT: D 19 PHE cc_start: 0.8558 (m-80) cc_final: 0.8219 (m-80) REVERT: D 49 MET cc_start: 0.8880 (mmm) cc_final: 0.8198 (mmm) REVERT: D 68 GLU cc_start: 0.7446 (tp30) cc_final: 0.6761 (tp30) REVERT: D 91 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8772 (mtpp) REVERT: D 155 ILE cc_start: 0.9382 (mt) cc_final: 0.8907 (mt) REVERT: D 163 ASN cc_start: 0.8772 (m110) cc_final: 0.8216 (m110) REVERT: E 266 LYS cc_start: 0.8529 (mttt) cc_final: 0.8211 (mtmt) REVERT: E 273 ASP cc_start: 0.9306 (m-30) cc_final: 0.8908 (m-30) REVERT: E 274 LEU cc_start: 0.8971 (mm) cc_final: 0.8745 (mm) REVERT: E 277 TYR cc_start: 0.8316 (m-80) cc_final: 0.7956 (m-80) REVERT: F 221 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8622 (tp-100) REVERT: F 225 MET cc_start: 0.9067 (mmt) cc_final: 0.8341 (mmm) REVERT: F 227 LEU cc_start: 0.8817 (mt) cc_final: 0.8387 (tp) outliers start: 2 outliers final: 1 residues processed: 323 average time/residue: 0.2074 time to fit residues: 90.8375 Evaluate side-chains 269 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 10 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN B 296 HIS C 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8918 Z= 0.227 Angle : 0.684 9.279 12045 Z= 0.358 Chirality : 0.045 0.253 1386 Planarity : 0.005 0.059 1497 Dihedral : 4.940 19.102 1162 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.10 % Allowed : 4.13 % Favored : 95.77 % 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: -1.27 (0.25), residues: 1077 helix: 0.04 (0.18), residues: 722 sheet: -2.99 (0.49), residues: 91 loop : -2.21 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP D 158 HIS 0.004 0.001 HIS B 314 PHE 0.030 0.002 PHE D 19 TYR 0.016 0.001 TYR D 123 ARG 0.005 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8891 (tmm) cc_final: 0.8616 (tmm) REVERT: B 60 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7790 (mm110) REVERT: B 69 LEU cc_start: 0.8625 (tp) cc_final: 0.8414 (tp) REVERT: B 101 PHE cc_start: 0.7679 (m-10) cc_final: 0.7340 (m-10) REVERT: B 152 MET cc_start: 0.8771 (mmm) cc_final: 0.8435 (mmm) REVERT: B 162 VAL cc_start: 0.8466 (t) cc_final: 0.8258 (m) REVERT: C 49 MET cc_start: 0.8625 (mmp) cc_final: 0.7981 (mmm) REVERT: C 159 ILE cc_start: 0.9357 (pt) cc_final: 0.9135 (pt) REVERT: D 19 PHE cc_start: 0.8516 (m-80) cc_final: 0.8213 (m-80) REVERT: D 49 MET cc_start: 0.8771 (mmm) cc_final: 0.8373 (mmm) REVERT: D 55 ASP cc_start: 0.8378 (t70) cc_final: 0.8072 (t70) REVERT: D 72 TYR cc_start: 0.8257 (t80) cc_final: 0.7519 (t80) REVERT: D 76 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 155 ILE cc_start: 0.9448 (mt) cc_final: 0.9079 (mt) REVERT: D 163 ASN cc_start: 0.8723 (m110) cc_final: 0.8144 (m110) REVERT: E 266 LYS cc_start: 0.8542 (mttt) cc_final: 0.8177 (mtmt) REVERT: E 277 TYR cc_start: 0.8359 (m-80) cc_final: 0.8126 (m-80) REVERT: F 221 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8498 (tp-100) REVERT: F 225 MET cc_start: 0.9067 (mmt) cc_final: 0.8222 (mmm) REVERT: F 227 LEU cc_start: 0.8734 (mt) cc_final: 0.8366 (tp) REVERT: F 229 LYS cc_start: 0.8580 (mppt) cc_final: 0.8320 (tptt) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.2074 time to fit residues: 89.7280 Evaluate side-chains 252 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN D 45 GLN F 285 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8918 Z= 0.202 Angle : 0.682 9.477 12045 Z= 0.357 Chirality : 0.046 0.330 1386 Planarity : 0.005 0.066 1497 Dihedral : 4.768 19.127 1162 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.21 % Allowed : 1.96 % Favored : 97.83 % 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: -0.86 (0.26), residues: 1077 helix: 0.38 (0.19), residues: 720 sheet: -2.77 (0.51), residues: 89 loop : -2.19 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 158 HIS 0.009 0.001 HIS F 285 PHE 0.022 0.002 PHE D 19 TYR 0.015 0.001 TYR A 148 ARG 0.006 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 328 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8870 (tmm) cc_final: 0.8335 (tmm) REVERT: A 221 LYS cc_start: 0.9398 (mmtm) cc_final: 0.9045 (mmmt) REVERT: B 60 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7702 (mm110) REVERT: B 152 MET cc_start: 0.8736 (mmm) cc_final: 0.8400 (mmm) REVERT: C 48 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8519 (tm-30) REVERT: C 49 MET cc_start: 0.8541 (mmp) cc_final: 0.8244 (mmm) REVERT: C 58 GLN cc_start: 0.8414 (pp30) cc_final: 0.7858 (tm-30) REVERT: C 61 SER cc_start: 0.9318 (m) cc_final: 0.9028 (t) REVERT: D 19 PHE cc_start: 0.8503 (m-80) cc_final: 0.8156 (m-80) REVERT: D 49 MET cc_start: 0.8850 (mmm) cc_final: 0.8377 (mmm) REVERT: D 55 ASP cc_start: 0.8353 (t70) cc_final: 0.7986 (t70) REVERT: D 72 TYR cc_start: 0.8301 (t80) cc_final: 0.6634 (t80) REVERT: D 76 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8195 (mm-30) REVERT: D 91 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8797 (ptpp) REVERT: D 155 ILE cc_start: 0.9369 (mt) cc_final: 0.9150 (mt) REVERT: D 163 ASN cc_start: 0.8714 (m110) cc_final: 0.7999 (m110) REVERT: E 273 ASP cc_start: 0.9280 (m-30) cc_final: 0.8912 (m-30) REVERT: E 277 TYR cc_start: 0.8307 (m-80) cc_final: 0.7984 (m-80) REVERT: F 221 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8446 (tp-100) REVERT: F 225 MET cc_start: 0.9068 (mmt) cc_final: 0.8447 (mmm) REVERT: F 258 ASN cc_start: 0.8424 (p0) cc_final: 0.7922 (m-40) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.1959 time to fit residues: 88.0000 Evaluate side-chains 259 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0040 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 HIS D 22 ASN D 45 GLN F 285 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8918 Z= 0.217 Angle : 0.699 9.414 12045 Z= 0.365 Chirality : 0.045 0.316 1386 Planarity : 0.005 0.067 1497 Dihedral : 4.707 16.338 1162 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1077 helix: 0.44 (0.19), residues: 714 sheet: -2.66 (0.51), residues: 90 loop : -2.26 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP D 158 HIS 0.008 0.001 HIS F 285 PHE 0.019 0.002 PHE D 19 TYR 0.016 0.002 TYR A 148 ARG 0.006 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.9288 (mmtm) cc_final: 0.9081 (mmmt) REVERT: A 318 LEU cc_start: 0.9412 (tt) cc_final: 0.9035 (tt) REVERT: B 152 MET cc_start: 0.8705 (mmm) cc_final: 0.8350 (mmm) REVERT: B 241 GLN cc_start: 0.7509 (pt0) cc_final: 0.7258 (pt0) REVERT: B 295 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8083 (mmm160) REVERT: C 48 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8520 (tm-30) REVERT: C 58 GLN cc_start: 0.8458 (pp30) cc_final: 0.7870 (tm-30) REVERT: C 123 TYR cc_start: 0.4205 (t80) cc_final: 0.3920 (t80) REVERT: D 49 MET cc_start: 0.8803 (mmm) cc_final: 0.8481 (mmm) REVERT: D 55 ASP cc_start: 0.8382 (t70) cc_final: 0.8036 (t70) REVERT: D 63 VAL cc_start: 0.8967 (t) cc_final: 0.8673 (p) REVERT: D 91 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8820 (ptpp) REVERT: D 155 ILE cc_start: 0.9363 (mt) cc_final: 0.9139 (mt) REVERT: D 163 ASN cc_start: 0.8617 (m110) cc_final: 0.8195 (m110) REVERT: E 273 ASP cc_start: 0.9294 (m-30) cc_final: 0.8916 (m-30) REVERT: E 277 TYR cc_start: 0.8259 (m-80) cc_final: 0.7884 (m-80) REVERT: F 221 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8385 (tp-100) REVERT: F 225 MET cc_start: 0.9028 (mmt) cc_final: 0.8202 (mmm) REVERT: F 258 ASN cc_start: 0.8433 (p0) cc_final: 0.7883 (m-40) REVERT: F 286 GLU cc_start: 0.8012 (mp0) cc_final: 0.7747 (tp30) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.2037 time to fit residues: 85.6861 Evaluate side-chains 253 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN D 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8918 Z= 0.201 Angle : 0.712 10.007 12045 Z= 0.369 Chirality : 0.045 0.322 1386 Planarity : 0.005 0.070 1497 Dihedral : 4.669 16.659 1162 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -0.76 (0.26), residues: 1077 helix: 0.45 (0.19), residues: 715 sheet: -2.60 (0.53), residues: 92 loop : -2.12 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP D 158 HIS 0.004 0.001 HIS A 172 PHE 0.017 0.001 PHE C 19 TYR 0.013 0.001 TYR F 277 ARG 0.010 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.9244 (mmmt) cc_final: 0.8964 (mtpp) REVERT: A 103 MET cc_start: 0.8754 (tmm) cc_final: 0.7915 (tmm) REVERT: A 189 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7400 (mmm160) REVERT: A 318 LEU cc_start: 0.9412 (tt) cc_final: 0.9127 (tt) REVERT: B 152 MET cc_start: 0.8659 (mmm) cc_final: 0.8314 (mmm) REVERT: B 295 ARG cc_start: 0.8344 (mmm160) cc_final: 0.8080 (mmm160) REVERT: C 58 GLN cc_start: 0.8450 (pp30) cc_final: 0.7852 (tm-30) REVERT: C 66 MET cc_start: 0.7909 (tpp) cc_final: 0.7446 (tpt) REVERT: C 123 TYR cc_start: 0.4224 (t80) cc_final: 0.3945 (t80) REVERT: D 17 PHE cc_start: 0.8700 (m-80) cc_final: 0.8262 (m-80) REVERT: D 63 VAL cc_start: 0.8958 (t) cc_final: 0.8649 (p) REVERT: D 91 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8786 (ptpp) REVERT: D 112 GLN cc_start: 0.8166 (tt0) cc_final: 0.7960 (tt0) REVERT: D 163 ASN cc_start: 0.8343 (m110) cc_final: 0.8137 (m110) REVERT: E 273 ASP cc_start: 0.9276 (m-30) cc_final: 0.8903 (m-30) REVERT: E 277 TYR cc_start: 0.8193 (m-80) cc_final: 0.7881 (m-80) REVERT: F 221 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8238 (tp-100) REVERT: F 225 MET cc_start: 0.8923 (mmt) cc_final: 0.8122 (mmm) REVERT: F 258 ASN cc_start: 0.8380 (p0) cc_final: 0.7808 (m-40) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1993 time to fit residues: 85.4871 Evaluate side-chains 250 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 30.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8918 Z= 0.246 Angle : 0.741 9.697 12045 Z= 0.391 Chirality : 0.046 0.318 1386 Planarity : 0.006 0.063 1497 Dihedral : 4.759 19.818 1162 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -0.68 (0.26), residues: 1077 helix: 0.45 (0.19), residues: 700 sheet: -2.66 (0.51), residues: 92 loop : -1.74 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP D 158 HIS 0.005 0.001 HIS A 172 PHE 0.034 0.002 PHE E 278 TYR 0.017 0.002 TYR A 148 ARG 0.006 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8822 (tmm) cc_final: 0.7980 (tmm) REVERT: A 105 ILE cc_start: 0.9229 (tp) cc_final: 0.9028 (tp) REVERT: A 318 LEU cc_start: 0.9469 (tt) cc_final: 0.8856 (tt) REVERT: B 152 MET cc_start: 0.8689 (mmm) cc_final: 0.8316 (mmm) REVERT: B 153 ARG cc_start: 0.8736 (ttm170) cc_final: 0.8423 (ptp-170) REVERT: B 295 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8079 (mmm160) REVERT: C 58 GLN cc_start: 0.8494 (pp30) cc_final: 0.7946 (tm-30) REVERT: D 17 PHE cc_start: 0.8497 (m-80) cc_final: 0.8208 (m-80) REVERT: D 49 MET cc_start: 0.8905 (mmp) cc_final: 0.8621 (mmm) REVERT: D 56 MET cc_start: 0.8767 (ptm) cc_final: 0.8565 (ptt) REVERT: D 163 ASN cc_start: 0.8620 (m110) cc_final: 0.8140 (m110) REVERT: E 273 ASP cc_start: 0.9332 (m-30) cc_final: 0.8869 (m-30) REVERT: E 277 TYR cc_start: 0.8330 (m-80) cc_final: 0.8001 (m-80) REVERT: F 221 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8072 (tp-100) REVERT: F 225 MET cc_start: 0.8970 (mmt) cc_final: 0.8153 (mmm) REVERT: F 258 ASN cc_start: 0.8378 (p0) cc_final: 0.7807 (m-40) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2141 time to fit residues: 90.7961 Evaluate side-chains 248 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8918 Z= 0.244 Angle : 0.759 8.533 12045 Z= 0.396 Chirality : 0.047 0.320 1386 Planarity : 0.005 0.060 1497 Dihedral : 4.842 19.260 1162 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -0.75 (0.26), residues: 1077 helix: 0.40 (0.19), residues: 708 sheet: -2.54 (0.51), residues: 90 loop : -1.91 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.003 TRP D 158 HIS 0.004 0.001 HIS A 172 PHE 0.028 0.002 PHE A 165 TYR 0.023 0.002 TYR D 72 ARG 0.012 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8810 (tmm) cc_final: 0.8051 (tmm) REVERT: A 189 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7646 (mmm160) REVERT: A 318 LEU cc_start: 0.9474 (tt) cc_final: 0.8729 (tt) REVERT: A 326 ARG cc_start: 0.7483 (mmm160) cc_final: 0.7211 (mmm-85) REVERT: B 152 MET cc_start: 0.8724 (mmm) cc_final: 0.8348 (mmm) REVERT: B 153 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8443 (ptp-170) REVERT: B 295 ARG cc_start: 0.8373 (mmm160) cc_final: 0.8048 (mmm160) REVERT: C 21 CYS cc_start: 0.8128 (m) cc_final: 0.7902 (t) REVERT: C 49 MET cc_start: 0.9441 (ttm) cc_final: 0.8956 (mmm) REVERT: C 58 GLN cc_start: 0.8475 (pp30) cc_final: 0.7933 (tm-30) REVERT: D 17 PHE cc_start: 0.8485 (m-80) cc_final: 0.8229 (m-80) REVERT: D 49 MET cc_start: 0.8871 (mmp) cc_final: 0.8596 (mmm) REVERT: D 55 ASP cc_start: 0.8408 (t70) cc_final: 0.8057 (t70) REVERT: D 59 GLU cc_start: 0.8571 (pt0) cc_final: 0.8046 (pt0) REVERT: D 91 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8809 (ptpp) REVERT: D 163 ASN cc_start: 0.8537 (m110) cc_final: 0.8077 (m110) REVERT: E 204 ARG cc_start: 0.8322 (ppt170) cc_final: 0.8003 (ppt170) REVERT: E 273 ASP cc_start: 0.9323 (m-30) cc_final: 0.8951 (m-30) REVERT: E 277 TYR cc_start: 0.8324 (m-80) cc_final: 0.8009 (m-80) REVERT: F 221 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8027 (tp-100) REVERT: F 225 MET cc_start: 0.8995 (mmt) cc_final: 0.8083 (mmm) REVERT: F 258 ASN cc_start: 0.8379 (p0) cc_final: 0.7810 (m-40) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1967 time to fit residues: 82.8424 Evaluate side-chains 246 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8918 Z= 0.275 Angle : 0.789 9.028 12045 Z= 0.410 Chirality : 0.048 0.319 1386 Planarity : 0.005 0.058 1497 Dihedral : 4.909 20.455 1162 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 (0.26), residues: 1077 helix: 0.29 (0.19), residues: 712 sheet: -2.80 (0.48), residues: 93 loop : -1.81 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.003 TRP D 158 HIS 0.007 0.001 HIS A 172 PHE 0.027 0.002 PHE D 19 TYR 0.031 0.002 TYR D 72 ARG 0.011 0.001 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.8773 (tmm) cc_final: 0.8137 (tmm) REVERT: A 105 ILE cc_start: 0.9238 (tp) cc_final: 0.9023 (tp) REVERT: A 185 ARG cc_start: 0.8426 (tpt90) cc_final: 0.8118 (tpm170) REVERT: A 318 LEU cc_start: 0.9475 (tt) cc_final: 0.9137 (tt) REVERT: A 326 ARG cc_start: 0.7506 (mmm160) cc_final: 0.7159 (mmm-85) REVERT: B 152 MET cc_start: 0.8750 (mmm) cc_final: 0.8374 (mmm) REVERT: B 153 ARG cc_start: 0.8724 (ttm170) cc_final: 0.8492 (ptp-170) REVERT: B 293 GLU cc_start: 0.8098 (pp20) cc_final: 0.7583 (tm-30) REVERT: C 21 CYS cc_start: 0.8124 (m) cc_final: 0.7866 (t) REVERT: C 49 MET cc_start: 0.9453 (ttm) cc_final: 0.9252 (ttm) REVERT: C 58 GLN cc_start: 0.8516 (pp30) cc_final: 0.7937 (tm-30) REVERT: D 17 PHE cc_start: 0.8502 (m-80) cc_final: 0.8232 (m-80) REVERT: D 49 MET cc_start: 0.8876 (mmp) cc_final: 0.8584 (mmm) REVERT: D 55 ASP cc_start: 0.8382 (t70) cc_final: 0.8028 (t70) REVERT: D 59 GLU cc_start: 0.8581 (pt0) cc_final: 0.7990 (pt0) REVERT: D 91 LYS cc_start: 0.9132 (mtpp) cc_final: 0.8799 (ptpp) REVERT: D 163 ASN cc_start: 0.8568 (m110) cc_final: 0.8077 (m110) REVERT: E 204 ARG cc_start: 0.8422 (ppt170) cc_final: 0.8061 (ppt170) REVERT: E 255 GLU cc_start: 0.8548 (pm20) cc_final: 0.8306 (pm20) REVERT: E 273 ASP cc_start: 0.9343 (m-30) cc_final: 0.8884 (m-30) REVERT: E 277 TYR cc_start: 0.8440 (m-80) cc_final: 0.8085 (m-80) REVERT: F 221 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8007 (tp-100) REVERT: F 225 MET cc_start: 0.9000 (mmt) cc_final: 0.8109 (mmm) REVERT: F 258 ASN cc_start: 0.8400 (p0) cc_final: 0.7825 (m-40) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1915 time to fit residues: 80.7046 Evaluate side-chains 250 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS B 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086714 restraints weight = 27862.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089066 restraints weight = 17362.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090609 restraints weight = 12839.185| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8918 Z= 0.236 Angle : 0.786 9.807 12045 Z= 0.408 Chirality : 0.047 0.319 1386 Planarity : 0.005 0.058 1497 Dihedral : 4.879 19.892 1162 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 1077 helix: 0.34 (0.19), residues: 712 sheet: -2.54 (0.51), residues: 90 loop : -1.84 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.003 TRP D 158 HIS 0.007 0.001 HIS A 172 PHE 0.029 0.002 PHE F 279 TYR 0.026 0.002 TYR E 264 ARG 0.011 0.001 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.77 seconds wall clock time: 43 minutes 40.29 seconds (2620.29 seconds total)