Starting phenix.real_space_refine on Wed Sep 25 18:22:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqq_21354/09_2024/6vqq_21354.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqq_21354/09_2024/6vqq_21354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqq_21354/09_2024/6vqq_21354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqq_21354/09_2024/6vqq_21354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqq_21354/09_2024/6vqq_21354.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqq_21354/09_2024/6vqq_21354.cif" } resolution = 2.56 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= 0.298 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 7324 2.51 5 N 1715 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10987 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2190 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 3, 'TRANS': 275} Chain: "B" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2216 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 3, 'TRANS': 278} Chain: "C" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2183 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 3, 'TRANS': 274} Chain: "D" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2221 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 4, 'TRANS': 278} Chain: "E" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2177 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 3, 'TRANS': 273} Time building chain proxies: 6.76, per 1000 atoms: 0.62 Number of scatterers: 10987 At special positions: 0 Unit cell: (87.48, 100.44, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1878 8.00 N 1715 7.00 C 7324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.5 seconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 20 through 36 removed outlier: 3.573A pdb=" N SER A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 68 Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.696A pdb=" N GLU A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.988A pdb=" N VAL A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.030A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.066A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 removed outlier: 3.516A pdb=" N TYR A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 removed outlier: 4.135A pdb=" N LEU A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.627A pdb=" N CYS A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 4.111A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.541A pdb=" N ILE A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.506A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.767A pdb=" N ARG A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.683A pdb=" N CYS B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 69 Processing helix chain 'B' and resid 70 through 78 removed outlier: 4.028A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.081A 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 92 through 101 Processing helix chain 'B' and resid 104 through 118 removed outlier: 4.592A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 178 removed outlier: 4.122A pdb=" N LEU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 207 removed outlier: 3.762A pdb=" N LEU B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 227 removed outlier: 3.561A pdb=" N VAL B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 274 through 290 removed outlier: 3.552A pdb=" N TYR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 41 through 68 removed outlier: 3.886A pdb=" N ALA C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 4.065A pdb=" N GLU C 75 " --> pdb=" O HIS C 71 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.994A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.945A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 166 through 178 removed outlier: 3.864A pdb=" N LEU C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 210 through 227 removed outlier: 4.864A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.614A pdb=" N TYR C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 273 through 289 removed outlier: 5.576A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE C 288 " --> pdb=" O HIS C 284 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU C 289 " --> pdb=" O TYR C 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 35 Processing helix chain 'D' and resid 39 through 69 Processing helix chain 'D' and resid 70 through 78 removed outlier: 4.255A pdb=" N GLU D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.674A 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 100 removed outlier: 3.958A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.811A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 147 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 164 through 178 removed outlier: 4.090A pdb=" N PHE D 169 " --> pdb=" O HIS D 165 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 204 Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.696A pdb=" N VAL D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.793A pdb=" N TYR D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.726A pdb=" N LEU D 277 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.801A pdb=" N TYR E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 68 removed outlier: 3.586A pdb=" N LEU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 4.122A pdb=" N GLU E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.565A pdb=" N CYS E 96 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY E 101 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.706A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 removed outlier: 3.537A pdb=" N TYR E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 3.786A pdb=" N PHE E 169 " --> pdb=" O HIS E 165 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 170 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU E 175 " --> pdb=" O ASN E 171 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 206 Processing helix chain 'E' and resid 208 through 226 removed outlier: 4.186A pdb=" N PHE E 218 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 273 through 281 removed outlier: 3.770A pdb=" N LEU E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 292 removed outlier: 3.929A pdb=" N TYR E 285 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS E 292 " --> pdb=" O PHE E 288 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1848 1.33 - 1.45: 3240 1.45 - 1.57: 6087 1.57 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 11275 Sorted by residual: bond pdb=" CA THR A 113 " pdb=" C THR A 113 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.35e-02 5.49e+03 7.55e+00 bond pdb=" CA GLU D 229 " pdb=" C GLU D 229 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.18e-02 7.18e+03 6.99e+00 bond pdb=" C HIS D 230 " pdb=" O HIS D 230 " ideal model delta sigma weight residual 1.235 1.205 0.030 1.14e-02 7.69e+03 6.99e+00 bond pdb=" N HIS D 230 " pdb=" CA HIS D 230 " ideal model delta sigma weight residual 1.457 1.489 -0.033 1.24e-02 6.50e+03 6.95e+00 bond pdb=" N ASP B 208 " pdb=" CA ASP B 208 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.76e+00 ... (remaining 11270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 14981 2.28 - 4.57: 267 4.57 - 6.85: 22 6.85 - 9.14: 3 9.14 - 11.42: 5 Bond angle restraints: 15278 Sorted by residual: angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 113.57 124.99 -11.42 1.38e+00 5.25e-01 6.85e+01 angle pdb=" N ILE A 231 " pdb=" CA ILE A 231 " pdb=" C ILE A 231 " ideal model delta sigma weight residual 110.62 117.36 -6.74 1.02e+00 9.61e-01 4.37e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 110.62 118.10 -7.48 1.14e+00 7.69e-01 4.31e+01 angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 111.17 118.89 -7.72 1.38e+00 5.25e-01 3.13e+01 angle pdb=" N PHE E 105 " pdb=" CA PHE E 105 " pdb=" C PHE E 105 " ideal model delta sigma weight residual 111.11 117.65 -6.54 1.20e+00 6.94e-01 2.97e+01 ... (remaining 15273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 5637 16.31 - 32.63: 611 32.63 - 48.94: 135 48.94 - 65.25: 18 65.25 - 81.57: 5 Dihedral angle restraints: 6406 sinusoidal: 2324 harmonic: 4082 Sorted by residual: dihedral pdb=" CA HIS D 37 " pdb=" C HIS D 37 " pdb=" N TYR D 38 " pdb=" CA TYR D 38 " ideal model delta harmonic sigma weight residual 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA SER C 39 " pdb=" C SER C 39 " pdb=" N ASN C 40 " pdb=" CA ASN C 40 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE A 280 " pdb=" C ILE A 280 " pdb=" N TYR A 281 " pdb=" CA TYR A 281 " ideal model delta harmonic sigma weight residual 180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.357: 1741 0.357 - 0.714: 0 0.714 - 1.070: 0 1.070 - 1.427: 0 1.427 - 1.784: 2 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CG LEU B 73 " pdb=" CB LEU B 73 " pdb=" CD1 LEU B 73 " pdb=" CD2 LEU B 73 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.95e+01 chirality pdb=" CG LEU D 275 " pdb=" CB LEU D 275 " pdb=" CD1 LEU D 275 " pdb=" CD2 LEU D 275 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.78e+01 chirality pdb=" CA PHE D 90 " pdb=" N PHE D 90 " pdb=" C PHE D 90 " pdb=" CB PHE D 90 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1740 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 229 " -0.022 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C GLU D 229 " 0.079 2.00e-02 2.50e+03 pdb=" O GLU D 229 " -0.031 2.00e-02 2.50e+03 pdb=" N HIS D 230 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 196 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C VAL D 196 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL D 196 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS D 197 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 171 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C ASN A 171 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 171 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 172 " -0.015 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 74 2.51 - 3.11: 9057 3.11 - 3.71: 16858 3.71 - 4.30: 25630 4.30 - 4.90: 42328 Nonbonded interactions: 93947 Sorted by model distance: nonbonded pdb=" O CYS C 19 " pdb=" OG1 THR C 205 " model vdw 1.916 3.040 nonbonded pdb=" O ASN B 257 " pdb=" OG1 THR B 261 " model vdw 1.950 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O LYS E 207 " model vdw 1.974 3.040 nonbonded pdb=" O VAL C 148 " pdb=" OG SER C 152 " model vdw 1.981 3.040 nonbonded pdb=" O VAL A 148 " pdb=" OG SER A 152 " model vdw 2.014 3.040 ... (remaining 93942 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 16 through 290) selection = (chain 'B' and resid 16 through 290) selection = (chain 'C' and resid 16 through 290) selection = (chain 'D' and resid 16 through 290) selection = (chain 'E' and resid 16 through 290) } 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: 0.020 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.900 Find NCS groups from input model: 0.540 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: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.063 11275 Z= 0.360 Angle : 0.767 11.422 15278 Z= 0.490 Chirality : 0.076 1.784 1743 Planarity : 0.005 0.054 1862 Dihedral : 13.928 81.568 3828 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.60 % 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: -3.82 (0.18), residues: 1389 helix: -2.01 (0.13), residues: 1052 sheet: None (None), residues: 0 loop : -3.68 (0.26), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 37 PHE 0.014 0.002 PHE A 223 TYR 0.027 0.002 TYR B 201 ARG 0.003 0.000 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.100 Fit side-chains REVERT: A 251 TYR cc_start: 0.8275 (t80) cc_final: 0.7903 (t80) REVERT: B 119 LYS cc_start: 0.6811 (mttp) cc_final: 0.6454 (mmmt) REVERT: B 279 PHE cc_start: 0.6214 (t80) cc_final: 0.5950 (t80) REVERT: C 35 LYS cc_start: 0.7905 (mmtp) cc_final: 0.7164 (mtpm) REVERT: C 72 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7370 (mmtm) REVERT: D 33 LYS cc_start: 0.7294 (tttm) cc_final: 0.7076 (tptt) REVERT: D 200 VAL cc_start: 0.8632 (t) cc_final: 0.8093 (m) REVERT: E 202 PHE cc_start: 0.7404 (m-10) cc_final: 0.7197 (m-10) REVERT: E 282 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7499 (tmmt) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.8349 time to fit residues: 205.5573 Evaluate side-chains 187 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 265 ASN B 37 HIS B 239 ASN B 257 ASN D 193 ASN D 245 ASN D 257 ASN E 265 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11275 Z= 0.235 Angle : 0.584 7.871 15278 Z= 0.330 Chirality : 0.044 0.155 1743 Planarity : 0.004 0.050 1862 Dihedral : 4.771 21.537 1525 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.74 % Allowed : 14.19 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1389 helix: 0.11 (0.15), residues: 1080 sheet: None (None), residues: 0 loop : -2.90 (0.28), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 37 PHE 0.033 0.002 PHE A 223 TYR 0.028 0.002 TYR C 69 ARG 0.002 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 0.984 Fit side-chains REVERT: A 163 LYS cc_start: 0.7422 (tttm) cc_final: 0.6975 (mptt) REVERT: A 251 TYR cc_start: 0.8177 (t80) cc_final: 0.7875 (t80) REVERT: B 130 MET cc_start: 0.7786 (mmt) cc_final: 0.7574 (mmt) REVERT: B 149 SER cc_start: 0.8855 (t) cc_final: 0.8483 (m) REVERT: B 229 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5893 (mt-10) REVERT: C 119 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7859 (mttp) REVERT: C 267 ILE cc_start: 0.7291 (mt) cc_final: 0.7060 (mt) REVERT: D 200 VAL cc_start: 0.8611 (t) cc_final: 0.8411 (t) REVERT: E 81 MET cc_start: 0.7054 (mmm) cc_final: 0.6841 (mmm) REVERT: E 120 LYS cc_start: 0.7758 (mmmt) cc_final: 0.7502 (mmmt) REVERT: E 163 LYS cc_start: 0.7048 (mttm) cc_final: 0.6665 (mtmt) REVERT: E 234 ASN cc_start: 0.8500 (m-40) cc_final: 0.8060 (m-40) REVERT: E 282 LYS cc_start: 0.7574 (tmtt) cc_final: 0.7323 (tmmt) outliers start: 20 outliers final: 9 residues processed: 234 average time/residue: 0.7609 time to fit residues: 200.0141 Evaluate side-chains 221 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 134 optimal weight: 0.0570 chunk 110 optimal weight: 30.0000 chunk 123 optimal weight: 0.0870 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 HIS ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN E 193 ASN E 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11275 Z= 0.130 Angle : 0.457 5.994 15278 Z= 0.259 Chirality : 0.038 0.137 1743 Planarity : 0.003 0.044 1862 Dihedral : 4.158 19.680 1525 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.65 % Allowed : 17.32 % Favored : 81.03 % 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 (0.22), residues: 1389 helix: 1.27 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 59 PHE 0.026 0.001 PHE A 223 TYR 0.022 0.001 TYR C 69 ARG 0.001 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 225 time to evaluate : 1.045 Fit side-chains REVERT: A 163 LYS cc_start: 0.7348 (tttm) cc_final: 0.6986 (mptt) REVERT: B 130 MET cc_start: 0.7808 (mmt) cc_final: 0.7511 (mmm) REVERT: B 149 SER cc_start: 0.8752 (t) cc_final: 0.8414 (m) REVERT: C 156 THR cc_start: 0.8686 (p) cc_final: 0.8284 (t) REVERT: C 179 HIS cc_start: 0.6787 (m-70) cc_final: 0.6567 (t70) REVERT: C 245 ASN cc_start: 0.8203 (t0) cc_final: 0.7984 (t0) REVERT: D 195 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: D 200 VAL cc_start: 0.8548 (t) cc_final: 0.8302 (t) REVERT: D 251 TYR cc_start: 0.6571 (t80) cc_final: 0.6300 (t80) REVERT: E 282 LYS cc_start: 0.7581 (tmtt) cc_final: 0.7273 (tmmt) outliers start: 19 outliers final: 10 residues processed: 231 average time/residue: 0.7177 time to fit residues: 187.2801 Evaluate side-chains 215 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 273 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 118 optimal weight: 30.0000 chunk 35 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11275 Z= 0.320 Angle : 0.609 6.144 15278 Z= 0.342 Chirality : 0.045 0.163 1743 Planarity : 0.004 0.040 1862 Dihedral : 4.663 21.225 1525 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.39 % Allowed : 18.45 % Favored : 78.15 % 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: 0.29 (0.22), residues: 1389 helix: 0.88 (0.15), residues: 1097 sheet: None (None), residues: 0 loop : -2.35 (0.30), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 165 PHE 0.031 0.002 PHE A 223 TYR 0.027 0.002 TYR C 69 ARG 0.004 0.001 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 1.171 Fit side-chains REVERT: A 163 LYS cc_start: 0.7441 (tttm) cc_final: 0.7162 (mptt) REVERT: B 149 SER cc_start: 0.9031 (t) cc_final: 0.8597 (m) REVERT: B 164 ASN cc_start: 0.8711 (t0) cc_final: 0.8489 (t0) REVERT: B 195 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: C 56 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7588 (tp) REVERT: C 67 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7517 (tt) REVERT: C 69 TYR cc_start: 0.8259 (t80) cc_final: 0.7558 (t80) REVERT: C 72 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7726 (mptm) REVERT: C 119 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7898 (mttp) REVERT: D 195 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: D 200 VAL cc_start: 0.8666 (t) cc_final: 0.8462 (t) REVERT: D 223 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.6769 (t80) REVERT: D 251 TYR cc_start: 0.6700 (t80) cc_final: 0.6467 (t80) REVERT: E 223 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.6829 (t80) REVERT: E 282 LYS cc_start: 0.7530 (tmtt) cc_final: 0.7269 (tmmt) outliers start: 39 outliers final: 14 residues processed: 250 average time/residue: 0.7572 time to fit residues: 211.8879 Evaluate side-chains 238 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 218 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 113 optimal weight: 0.1980 chunk 91 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11275 Z= 0.194 Angle : 0.510 6.275 15278 Z= 0.288 Chirality : 0.041 0.142 1743 Planarity : 0.003 0.040 1862 Dihedral : 4.404 20.558 1525 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.57 % Allowed : 19.93 % Favored : 76.50 % 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: 0.67 (0.22), residues: 1389 helix: 1.16 (0.16), residues: 1094 sheet: None (None), residues: 0 loop : -2.22 (0.30), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 165 PHE 0.028 0.001 PHE A 223 TYR 0.020 0.001 TYR C 69 ARG 0.003 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7506 (tttm) cc_final: 0.7220 (mptt) REVERT: B 149 SER cc_start: 0.8990 (t) cc_final: 0.8558 (m) REVERT: B 164 ASN cc_start: 0.8663 (t0) cc_final: 0.8447 (t0) REVERT: B 195 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: C 56 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7491 (tp) REVERT: C 69 TYR cc_start: 0.8150 (t80) cc_final: 0.7180 (t80) REVERT: C 119 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7841 (mttp) REVERT: C 267 ILE cc_start: 0.7128 (mt) cc_final: 0.6924 (mt) REVERT: D 195 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.5769 (m-80) REVERT: D 200 VAL cc_start: 0.8671 (t) cc_final: 0.8452 (t) REVERT: D 223 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.6857 (t80) REVERT: E 122 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6938 (mmtp) REVERT: E 223 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6740 (t80) REVERT: E 234 ASN cc_start: 0.8518 (m-40) cc_final: 0.8062 (m-40) REVERT: E 282 LYS cc_start: 0.7577 (tmtt) cc_final: 0.7279 (tmmt) outliers start: 41 outliers final: 23 residues processed: 234 average time/residue: 0.7719 time to fit residues: 202.7084 Evaluate side-chains 238 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 110 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11275 Z= 0.205 Angle : 0.519 6.224 15278 Z= 0.291 Chirality : 0.041 0.159 1743 Planarity : 0.003 0.040 1862 Dihedral : 4.357 20.375 1525 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.74 % Allowed : 20.10 % Favored : 76.15 % 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: 0.81 (0.22), residues: 1389 helix: 1.26 (0.15), residues: 1093 sheet: None (None), residues: 0 loop : -2.17 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.028 0.001 PHE A 288 TYR 0.019 0.001 TYR C 69 ARG 0.003 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 218 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7500 (tttm) cc_final: 0.7257 (mptt) REVERT: A 263 LEU cc_start: 0.8376 (tp) cc_final: 0.8063 (tp) REVERT: B 149 SER cc_start: 0.9016 (t) cc_final: 0.8548 (m) REVERT: B 195 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: C 56 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7512 (tp) REVERT: C 69 TYR cc_start: 0.8105 (t80) cc_final: 0.7159 (t80) REVERT: C 119 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7844 (mttp) REVERT: C 267 ILE cc_start: 0.7059 (mt) cc_final: 0.6814 (mt) REVERT: D 195 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: D 200 VAL cc_start: 0.8642 (t) cc_final: 0.8421 (t) REVERT: D 223 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.6993 (t80) REVERT: D 243 MET cc_start: 0.7930 (mtt) cc_final: 0.7532 (mtt) REVERT: D 283 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: E 114 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7018 (mtt) REVERT: E 122 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6929 (mmtp) REVERT: E 223 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.6765 (t80) REVERT: E 234 ASN cc_start: 0.8499 (m-40) cc_final: 0.8036 (m-40) REVERT: E 282 LYS cc_start: 0.7564 (tmtt) cc_final: 0.7287 (tmmt) outliers start: 43 outliers final: 24 residues processed: 239 average time/residue: 0.7181 time to fit residues: 194.0007 Evaluate side-chains 248 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11275 Z= 0.232 Angle : 0.543 7.923 15278 Z= 0.304 Chirality : 0.042 0.211 1743 Planarity : 0.003 0.038 1862 Dihedral : 4.436 20.532 1525 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.92 % Allowed : 20.63 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1389 helix: 1.19 (0.15), residues: 1096 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 165 PHE 0.028 0.001 PHE A 288 TYR 0.019 0.002 TYR C 69 ARG 0.002 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.7540 (tttm) cc_final: 0.7300 (mptt) REVERT: A 263 LEU cc_start: 0.8391 (tp) cc_final: 0.8068 (tp) REVERT: B 134 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7656 (mt) REVERT: B 149 SER cc_start: 0.9023 (t) cc_final: 0.8544 (m) REVERT: B 195 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: B 234 ASN cc_start: 0.7830 (m110) cc_final: 0.7574 (m110) REVERT: C 56 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7520 (tp) REVERT: C 69 TYR cc_start: 0.8133 (t80) cc_final: 0.7301 (t80) REVERT: C 119 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7840 (mttp) REVERT: C 267 ILE cc_start: 0.7083 (mt) cc_final: 0.6807 (mt) REVERT: D 163 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7220 (mttp) REVERT: D 195 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: D 200 VAL cc_start: 0.8638 (t) cc_final: 0.8416 (t) REVERT: D 223 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.6954 (t80) REVERT: D 283 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5506 (pm20) REVERT: E 34 LYS cc_start: 0.6219 (mmmt) cc_final: 0.4598 (ptpt) REVERT: E 114 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7044 (mtt) REVERT: E 122 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6958 (mmtp) REVERT: E 223 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.6764 (t80) REVERT: E 234 ASN cc_start: 0.8521 (m-40) cc_final: 0.8036 (m-40) REVERT: E 282 LYS cc_start: 0.7605 (tmtt) cc_final: 0.7334 (tmmt) outliers start: 45 outliers final: 24 residues processed: 238 average time/residue: 0.7305 time to fit residues: 195.9239 Evaluate side-chains 246 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 212 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11275 Z= 0.269 Angle : 0.576 8.646 15278 Z= 0.320 Chirality : 0.044 0.240 1743 Planarity : 0.003 0.038 1862 Dihedral : 4.563 20.794 1525 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.92 % Allowed : 21.41 % Favored : 74.67 % 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: 0.53 (0.22), residues: 1389 helix: 1.04 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -2.22 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 165 PHE 0.031 0.002 PHE A 288 TYR 0.019 0.002 TYR C 69 ARG 0.002 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: B 134 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7688 (mt) REVERT: B 149 SER cc_start: 0.9058 (t) cc_final: 0.8549 (m) REVERT: B 195 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: C 56 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7517 (tp) REVERT: C 69 TYR cc_start: 0.8151 (t80) cc_final: 0.7456 (t80) REVERT: C 119 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7838 (mttp) REVERT: C 179 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6471 (t70) REVERT: C 267 ILE cc_start: 0.7236 (mt) cc_final: 0.6948 (mt) REVERT: D 195 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.5924 (m-80) REVERT: D 200 VAL cc_start: 0.8639 (t) cc_final: 0.8416 (t) REVERT: D 223 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6928 (t80) REVERT: D 247 LYS cc_start: 0.5939 (ttpm) cc_final: 0.5714 (ttpm) REVERT: D 283 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5455 (pm20) REVERT: E 34 LYS cc_start: 0.6270 (mmmt) cc_final: 0.4574 (ptpt) REVERT: E 108 ASN cc_start: 0.7741 (p0) cc_final: 0.7411 (p0) REVERT: E 122 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6973 (mmtp) REVERT: E 163 LYS cc_start: 0.7221 (pttm) cc_final: 0.6804 (pttp) REVERT: E 223 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6745 (t80) REVERT: E 282 LYS cc_start: 0.7611 (tmtt) cc_final: 0.7320 (tmmt) outliers start: 45 outliers final: 26 residues processed: 244 average time/residue: 0.7838 time to fit residues: 214.9871 Evaluate side-chains 254 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN D 108 ASN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11275 Z= 0.270 Angle : 0.583 10.463 15278 Z= 0.323 Chirality : 0.044 0.249 1743 Planarity : 0.003 0.038 1862 Dihedral : 4.591 20.836 1525 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.22 % Allowed : 22.63 % Favored : 74.15 % 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: 0.49 (0.22), residues: 1389 helix: 1.02 (0.15), residues: 1094 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.033 0.002 PHE A 288 TYR 0.018 0.002 TYR C 69 ARG 0.002 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: B 195 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: C 35 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7422 (mtpp) REVERT: C 56 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7517 (tp) REVERT: C 69 TYR cc_start: 0.8048 (t80) cc_final: 0.7290 (t80) REVERT: C 119 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7856 (mttp) REVERT: C 179 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6534 (t70) REVERT: C 267 ILE cc_start: 0.7231 (mt) cc_final: 0.6947 (mt) REVERT: D 195 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: D 200 VAL cc_start: 0.8628 (t) cc_final: 0.8400 (t) REVERT: D 223 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6970 (t80) REVERT: D 247 LYS cc_start: 0.5952 (ttpm) cc_final: 0.5748 (ttpm) REVERT: D 283 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5488 (pm20) REVERT: E 34 LYS cc_start: 0.6283 (mmmt) cc_final: 0.4572 (ptpt) REVERT: E 108 ASN cc_start: 0.7802 (p0) cc_final: 0.7436 (p0) REVERT: E 122 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6948 (mmtp) REVERT: E 223 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.6791 (t80) REVERT: E 282 LYS cc_start: 0.7610 (tmtt) cc_final: 0.7306 (tmmt) outliers start: 37 outliers final: 23 residues processed: 234 average time/residue: 0.7775 time to fit residues: 204.6852 Evaluate side-chains 247 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11275 Z= 0.231 Angle : 0.559 12.810 15278 Z= 0.309 Chirality : 0.042 0.258 1743 Planarity : 0.003 0.038 1862 Dihedral : 4.499 20.817 1525 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.13 % Allowed : 23.15 % Favored : 73.72 % 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: 0.63 (0.22), residues: 1389 helix: 1.12 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -2.28 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.033 0.002 PHE A 288 TYR 0.018 0.002 TYR A 286 ARG 0.002 0.000 ARG D 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 214 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: B 149 SER cc_start: 0.8932 (t) cc_final: 0.8442 (m) REVERT: C 35 LYS cc_start: 0.7961 (mmtp) cc_final: 0.7453 (mtpp) REVERT: C 56 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7506 (tp) REVERT: C 69 TYR cc_start: 0.8056 (t80) cc_final: 0.7295 (t80) REVERT: C 119 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7838 (mttp) REVERT: C 179 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6464 (t70) REVERT: C 267 ILE cc_start: 0.7058 (mt) cc_final: 0.6804 (mt) REVERT: D 195 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: D 200 VAL cc_start: 0.8598 (t) cc_final: 0.8365 (t) REVERT: D 223 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7016 (t80) REVERT: D 243 MET cc_start: 0.7951 (mtt) cc_final: 0.7490 (mtt) REVERT: D 247 LYS cc_start: 0.5991 (ttpm) cc_final: 0.5790 (ttpm) REVERT: D 283 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5452 (pm20) REVERT: E 34 LYS cc_start: 0.6240 (mmmt) cc_final: 0.4575 (ptpt) REVERT: E 108 ASN cc_start: 0.7806 (p0) cc_final: 0.7429 (p0) REVERT: E 122 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6954 (mmtp) REVERT: E 223 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.6800 (t80) REVERT: E 282 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7291 (tmmt) outliers start: 36 outliers final: 25 residues processed: 229 average time/residue: 0.7760 time to fit residues: 199.8547 Evaluate side-chains 246 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 195 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN E 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.183724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168176 restraints weight = 13261.341| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.66 r_work: 0.3907 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11275 Z= 0.231 Angle : 0.562 12.171 15278 Z= 0.310 Chirality : 0.043 0.256 1743 Planarity : 0.003 0.038 1862 Dihedral : 4.497 20.650 1525 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.31 % Allowed : 22.98 % Favored : 73.72 % 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: 0.65 (0.22), residues: 1389 helix: 1.13 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -2.26 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 165 PHE 0.034 0.002 PHE A 288 TYR 0.018 0.002 TYR B 117 ARG 0.002 0.000 ARG D 290 =============================================================================== Job complete usr+sys time: 3688.59 seconds wall clock time: 69 minutes 6.67 seconds (4146.67 seconds total)