Starting phenix.real_space_refine on Thu Mar 13 23:19:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vui_32129/03_2025/7vui_32129.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vui_32129/03_2025/7vui_32129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2025/7vui_32129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2025/7vui_32129.map" model { file = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2025/7vui_32129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vui_32129/03_2025/7vui_32129.cif" } resolution = 3.3 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 Cl 1 4.86 5 C 5274 2.51 5 N 1433 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8287 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1940 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2295 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.66 Number of scatterers: 8287 At special positions: 0 Unit cell: (76.96, 98.8, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 49 16.00 P 3 15.00 Mg 1 11.99 O 1526 8.00 N 1433 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 2.37 Conformation dependent library (CDL) restraints added in 912.7 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.795A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.669A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.147A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.797A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.875A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.595A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 53 removed outlier: 3.973A pdb=" N SER R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) Proline residue: R 42 - end of helix removed outlier: 3.706A pdb=" N GLN R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 58 removed outlier: 3.887A pdb=" N ARG R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 82 removed outlier: 3.574A pdb=" N TYR R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 removed outlier: 5.342A pdb=" N ASP R 89 " --> pdb=" O PHE R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.861A pdb=" N VAL R 106 " --> pdb=" O LYS R 102 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 135 through 140 Processing helix chain 'R' and resid 141 through 160 removed outlier: 3.560A pdb=" N LYS R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR R 153 " --> pdb=" O ILE R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 removed outlier: 3.655A pdb=" N TRP R 165 " --> pdb=" O PRO R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.873A pdb=" N HIS R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 213 Processing helix chain 'R' and resid 222 through 253 Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 259 through 286 removed outlier: 4.087A pdb=" N MET R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 273 " --> pdb=" O ILE R 269 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA R 274 " --> pdb=" O ALA R 270 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU R 275 " --> pdb=" O ASN R 271 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 301 removed outlier: 3.740A pdb=" N MET R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS R 301 " --> pdb=" O ALA R 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.517A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.035A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.540A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.537A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.597A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.702A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.656A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.532A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.803A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.680A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 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: 2.29 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1328 1.31 - 1.44: 2379 1.44 - 1.56: 4686 1.56 - 1.69: 5 1.69 - 1.81: 70 Bond restraints: 8468 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.450 -0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C2 GTP A 401 " pdb=" N3 GTP A 401 " ideal model delta sigma weight residual 1.380 1.321 0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C8 GTP A 401 " pdb=" N7 GTP A 401 " ideal model delta sigma weight residual 1.350 1.300 0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 8463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11264 1.81 - 3.62: 177 3.62 - 5.43: 32 5.43 - 7.25: 12 7.25 - 9.06: 7 Bond angle restraints: 11492 Sorted by residual: angle pdb=" C4 GTP A 401 " pdb=" N9 GTP A 401 " pdb=" C8 GTP A 401 " ideal model delta sigma weight residual 108.00 117.06 -9.06 3.00e+00 1.11e-01 9.11e+00 angle pdb=" CB ARG A 270 " pdb=" CG ARG A 270 " pdb=" CD ARG A 270 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.88e+00 angle pdb=" C5 GTP A 401 " pdb=" C4 GTP A 401 " pdb=" N9 GTP A 401 " ideal model delta sigma weight residual 108.00 99.48 8.52 3.00e+00 1.11e-01 8.07e+00 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 101.13 8.37 3.00e+00 1.11e-01 7.78e+00 angle pdb=" O1A GTP A 401 " pdb=" PA GTP A 401 " pdb=" O2A GTP A 401 " ideal model delta sigma weight residual 109.50 101.18 8.32 3.00e+00 1.11e-01 7.69e+00 ... (remaining 11487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 4927 33.60 - 67.20: 89 67.20 - 100.81: 13 100.81 - 134.41: 2 134.41 - 168.01: 3 Dihedral angle restraints: 5034 sinusoidal: 2005 harmonic: 3029 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -6.48 -79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 -14.69 -168.01 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -49.86 154.45 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 893 0.038 - 0.076: 297 0.076 - 0.114: 88 0.114 - 0.152: 13 0.152 - 0.190: 4 Chirality restraints: 1295 Sorted by residual: chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.66 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" C10 7ZQ R 401 " pdb=" C11 7ZQ R 401 " pdb=" C12 7ZQ R 401 " pdb=" N2 7ZQ R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.62 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" C4' GTP A 401 " pdb=" C3' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O4' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.63 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1292 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 80 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ILE R 80 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE R 80 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL R 81 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 82 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C PHE R 82 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE R 82 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL R 83 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 322 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.026 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 257 2.71 - 3.26: 8379 3.26 - 3.81: 13443 3.81 - 4.35: 16385 4.35 - 4.90: 27938 Nonbonded interactions: 66402 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.165 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.176 3.040 nonbonded pdb=" O2G GTP A 401 " pdb="MG MG A 402 " model vdw 2.179 2.170 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.181 3.040 ... (remaining 66397 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.590 Find NCS groups from input model: 0.080 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8468 Z= 0.192 Angle : 0.628 9.057 11492 Z= 0.306 Chirality : 0.042 0.190 1295 Planarity : 0.004 0.047 1452 Dihedral : 14.880 168.009 3068 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -0.34 (0.27), residues: 1022 helix: 1.06 (0.27), residues: 400 sheet: -0.97 (0.36), residues: 215 loop : -1.00 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 170 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.001 PHE R 287 TYR 0.010 0.001 TYR B 59 ARG 0.007 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6845 (tmm160) cc_final: 0.5875 (tmm160) REVERT: A 270 ARG cc_start: 0.6386 (ppt170) cc_final: 0.6171 (ppt170) REVERT: A 289 GLU cc_start: 0.7270 (tp30) cc_final: 0.6706 (tp30) REVERT: A 309 THR cc_start: 0.7900 (p) cc_final: 0.7698 (t) REVERT: A 317 GLU cc_start: 0.6478 (mp0) cc_final: 0.6091 (mp0) REVERT: A 371 ASP cc_start: 0.7313 (t70) cc_final: 0.6717 (t0) REVERT: B 66 ASP cc_start: 0.7062 (p0) cc_final: 0.6724 (p0) REVERT: B 67 SER cc_start: 0.8411 (m) cc_final: 0.7872 (t) REVERT: B 103 CYS cc_start: 0.7243 (m) cc_final: 0.6817 (m) REVERT: B 121 CYS cc_start: 0.7334 (t) cc_final: 0.6838 (t) REVERT: B 155 ASN cc_start: 0.7740 (t0) cc_final: 0.7237 (t0) REVERT: B 169 TRP cc_start: 0.8099 (m100) cc_final: 0.7657 (m100) REVERT: B 212 ASP cc_start: 0.7515 (t0) cc_final: 0.7287 (t70) REVERT: B 256 ARG cc_start: 0.7847 (ptp-110) cc_final: 0.7632 (ptp-110) REVERT: B 258 ASP cc_start: 0.7495 (t70) cc_final: 0.6832 (t0) REVERT: B 273 ILE cc_start: 0.8184 (mp) cc_final: 0.7878 (mp) REVERT: G 28 ILE cc_start: 0.8119 (mp) cc_final: 0.7864 (mp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2726 time to fit residues: 76.7294 Evaluate side-chains 195 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.0000 chunk 78 optimal weight: 0.0030 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 377 ASN B 119 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.151408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133058 restraints weight = 11796.228| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.19 r_work: 0.3589 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8468 Z= 0.193 Angle : 0.593 7.734 11492 Z= 0.303 Chirality : 0.043 0.185 1295 Planarity : 0.004 0.053 1452 Dihedral : 10.166 150.855 1161 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.01 % Favored : 95.79 % Rotamer: Outliers : 1.67 % Allowed : 10.38 % Favored : 87.95 % 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: -0.10 (0.27), residues: 1022 helix: 1.20 (0.27), residues: 399 sheet: -0.73 (0.36), residues: 219 loop : -0.86 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 170 HIS 0.006 0.001 HIS R 113 PHE 0.021 0.001 PHE R 82 TYR 0.011 0.001 TYR B 59 ARG 0.004 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7949 (ttmm) REVERT: A 289 GLU cc_start: 0.7990 (tp30) cc_final: 0.7335 (tp30) REVERT: A 317 GLU cc_start: 0.6635 (mp0) cc_final: 0.6072 (mp0) REVERT: A 366 PHE cc_start: 0.7885 (t80) cc_final: 0.7636 (t80) REVERT: A 371 ASP cc_start: 0.8131 (t70) cc_final: 0.7667 (t0) REVERT: B 67 SER cc_start: 0.8696 (m) cc_final: 0.8321 (t) REVERT: B 103 CYS cc_start: 0.7805 (m) cc_final: 0.7377 (m) REVERT: B 169 TRP cc_start: 0.8462 (m100) cc_final: 0.8021 (m100) REVERT: B 212 ASP cc_start: 0.8192 (t0) cc_final: 0.7944 (t0) REVERT: B 220 GLN cc_start: 0.8058 (pt0) cc_final: 0.7747 (pt0) REVERT: B 258 ASP cc_start: 0.8087 (t70) cc_final: 0.7613 (t0) REVERT: B 263 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8421 (m) REVERT: B 273 ILE cc_start: 0.8501 (mp) cc_final: 0.8223 (mp) outliers start: 15 outliers final: 8 residues processed: 210 average time/residue: 0.2718 time to fit residues: 72.8741 Evaluate side-chains 214 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.0050 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 99 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 282 ASN A 377 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN R 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132811 restraints weight = 11972.787| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.20 r_work: 0.3585 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8468 Z= 0.185 Angle : 0.557 7.181 11492 Z= 0.287 Chirality : 0.042 0.153 1295 Planarity : 0.004 0.055 1452 Dihedral : 9.748 148.432 1161 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 2.23 % Allowed : 14.40 % Favored : 83.37 % 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: -0.04 (0.27), residues: 1022 helix: 1.29 (0.27), residues: 400 sheet: -0.51 (0.36), residues: 216 loop : -1.03 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 170 HIS 0.004 0.001 HIS R 113 PHE 0.018 0.001 PHE R 82 TYR 0.014 0.001 TYR R 32 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7890 (ttmm) REVERT: A 289 GLU cc_start: 0.7980 (tp30) cc_final: 0.7365 (tp30) REVERT: A 317 GLU cc_start: 0.6673 (mp0) cc_final: 0.6127 (mp0) REVERT: A 346 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.8032 (mtt-85) REVERT: A 363 ARG cc_start: 0.8048 (tpp-160) cc_final: 0.7716 (mmm160) REVERT: A 366 PHE cc_start: 0.8005 (t80) cc_final: 0.7618 (t80) REVERT: A 371 ASP cc_start: 0.8194 (t70) cc_final: 0.7720 (t0) REVERT: B 49 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7525 (mtt90) REVERT: B 67 SER cc_start: 0.8757 (m) cc_final: 0.8367 (t) REVERT: B 103 CYS cc_start: 0.7757 (m) cc_final: 0.7384 (m) REVERT: B 169 TRP cc_start: 0.8468 (m100) cc_final: 0.8074 (m100) REVERT: B 220 GLN cc_start: 0.7985 (pt0) cc_final: 0.7703 (pt0) REVERT: B 258 ASP cc_start: 0.8103 (t70) cc_final: 0.7587 (t0) REVERT: B 259 GLN cc_start: 0.8434 (tt0) cc_final: 0.8219 (tt0) REVERT: B 273 ILE cc_start: 0.8481 (mp) cc_final: 0.8200 (mp) REVERT: B 304 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7834 (ttm-80) outliers start: 20 outliers final: 17 residues processed: 220 average time/residue: 0.2702 time to fit residues: 76.2381 Evaluate side-chains 213 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.128974 restraints weight = 11860.318| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.18 r_work: 0.3551 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8468 Z= 0.265 Angle : 0.587 7.387 11492 Z= 0.303 Chirality : 0.044 0.148 1295 Planarity : 0.004 0.045 1452 Dihedral : 9.650 145.826 1161 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 2.46 % Allowed : 18.30 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 1022 helix: 1.18 (0.27), residues: 400 sheet: -0.42 (0.36), residues: 228 loop : -1.14 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 170 HIS 0.004 0.001 HIS R 113 PHE 0.021 0.002 PHE R 82 TYR 0.017 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7885 (ttmm) REVERT: A 289 GLU cc_start: 0.7976 (tp30) cc_final: 0.7379 (tp30) REVERT: A 317 GLU cc_start: 0.6741 (mp0) cc_final: 0.6199 (mp0) REVERT: A 371 ASP cc_start: 0.8188 (t70) cc_final: 0.7704 (t70) REVERT: B 49 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7621 (mtt90) REVERT: B 67 SER cc_start: 0.8821 (m) cc_final: 0.8407 (t) REVERT: B 103 CYS cc_start: 0.7817 (m) cc_final: 0.7406 (m) REVERT: B 169 TRP cc_start: 0.8507 (m100) cc_final: 0.8070 (m100) REVERT: B 220 GLN cc_start: 0.8006 (pt0) cc_final: 0.7695 (pt0) REVERT: B 223 THR cc_start: 0.7867 (m) cc_final: 0.7592 (p) REVERT: B 258 ASP cc_start: 0.8114 (t70) cc_final: 0.7502 (t0) REVERT: B 304 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7929 (ttm-80) REVERT: G 28 ILE cc_start: 0.8089 (mp) cc_final: 0.7826 (mp) REVERT: R 199 PHE cc_start: 0.6812 (m-10) cc_final: 0.6610 (m-80) REVERT: R 239 THR cc_start: 0.8192 (p) cc_final: 0.7943 (p) outliers start: 22 outliers final: 13 residues processed: 214 average time/residue: 0.2727 time to fit residues: 74.0037 Evaluate side-chains 212 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 40 optimal weight: 0.1980 chunk 34 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130236 restraints weight = 11915.813| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.25 r_work: 0.3550 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8468 Z= 0.156 Angle : 0.542 6.691 11492 Z= 0.278 Chirality : 0.042 0.155 1295 Planarity : 0.003 0.041 1452 Dihedral : 9.404 145.548 1161 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.42 % Favored : 96.38 % Rotamer: Outliers : 2.12 % Allowed : 20.54 % Favored : 77.34 % 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: 0.14 (0.27), residues: 1022 helix: 1.47 (0.27), residues: 392 sheet: -0.20 (0.36), residues: 225 loop : -1.07 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 170 HIS 0.007 0.001 HIS A 352 PHE 0.024 0.001 PHE R 82 TYR 0.018 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7777 (ttmm) REVERT: A 289 GLU cc_start: 0.8016 (tp30) cc_final: 0.7378 (tp30) REVERT: A 309 THR cc_start: 0.8162 (t) cc_final: 0.7891 (p) REVERT: A 317 GLU cc_start: 0.6716 (mp0) cc_final: 0.6168 (mp0) REVERT: A 346 ARG cc_start: 0.8184 (mtt-85) cc_final: 0.7662 (mtt-85) REVERT: A 363 ARG cc_start: 0.7936 (tpp-160) cc_final: 0.7725 (tpp-160) REVERT: A 366 PHE cc_start: 0.7928 (t80) cc_final: 0.7553 (t80) REVERT: A 371 ASP cc_start: 0.8189 (t70) cc_final: 0.7936 (t0) REVERT: B 49 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7514 (mtt90) REVERT: B 67 SER cc_start: 0.8734 (m) cc_final: 0.8331 (t) REVERT: B 103 CYS cc_start: 0.7670 (m) cc_final: 0.7266 (m) REVERT: B 169 TRP cc_start: 0.8608 (m100) cc_final: 0.8112 (m100) REVERT: B 220 GLN cc_start: 0.7939 (pt0) cc_final: 0.7585 (pt0) REVERT: B 258 ASP cc_start: 0.8124 (t70) cc_final: 0.7371 (t0) REVERT: B 304 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7953 (ttm-80) REVERT: G 28 ILE cc_start: 0.7927 (mp) cc_final: 0.7660 (mp) REVERT: R 65 TYR cc_start: 0.8007 (m-80) cc_final: 0.7484 (m-80) REVERT: R 199 PHE cc_start: 0.6850 (m-10) cc_final: 0.6458 (m-80) REVERT: R 239 THR cc_start: 0.8182 (p) cc_final: 0.7965 (p) outliers start: 19 outliers final: 13 residues processed: 213 average time/residue: 0.2811 time to fit residues: 75.8458 Evaluate side-chains 216 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 377 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129468 restraints weight = 11945.629| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.24 r_work: 0.3543 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8468 Z= 0.194 Angle : 0.563 6.667 11492 Z= 0.287 Chirality : 0.042 0.147 1295 Planarity : 0.004 0.039 1452 Dihedral : 9.328 144.002 1161 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.72 % Favored : 96.09 % Rotamer: Outliers : 3.12 % Allowed : 21.54 % Favored : 75.33 % 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: 0.10 (0.27), residues: 1022 helix: 1.36 (0.27), residues: 400 sheet: -0.06 (0.37), residues: 217 loop : -1.15 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 170 HIS 0.007 0.001 HIS A 352 PHE 0.019 0.001 PHE R 82 TYR 0.021 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7896 (ttmm) REVERT: A 289 GLU cc_start: 0.8004 (tp30) cc_final: 0.7369 (tp30) REVERT: A 309 THR cc_start: 0.8139 (t) cc_final: 0.7858 (p) REVERT: A 317 GLU cc_start: 0.6744 (mp0) cc_final: 0.6201 (mp0) REVERT: A 346 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7652 (mtt-85) REVERT: A 366 PHE cc_start: 0.7958 (t80) cc_final: 0.6933 (t80) REVERT: A 371 ASP cc_start: 0.8198 (t70) cc_final: 0.7899 (t0) REVERT: B 49 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7544 (mtt90) REVERT: B 67 SER cc_start: 0.8768 (m) cc_final: 0.8344 (t) REVERT: B 103 CYS cc_start: 0.7708 (m) cc_final: 0.7293 (m) REVERT: B 169 TRP cc_start: 0.8600 (m100) cc_final: 0.8124 (m100) REVERT: B 220 GLN cc_start: 0.7938 (pt0) cc_final: 0.7601 (pt0) REVERT: B 258 ASP cc_start: 0.8055 (t70) cc_final: 0.7390 (t0) REVERT: B 273 ILE cc_start: 0.8520 (mp) cc_final: 0.8191 (mp) REVERT: B 304 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: R 65 TYR cc_start: 0.8021 (m-80) cc_final: 0.7502 (m-80) REVERT: R 199 PHE cc_start: 0.6888 (m-10) cc_final: 0.6490 (m-80) REVERT: R 239 THR cc_start: 0.8152 (p) cc_final: 0.7943 (p) outliers start: 28 outliers final: 20 residues processed: 218 average time/residue: 0.2702 time to fit residues: 74.9319 Evaluate side-chains 222 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 377 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129238 restraints weight = 11967.133| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.24 r_work: 0.3540 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8468 Z= 0.201 Angle : 0.575 7.009 11492 Z= 0.292 Chirality : 0.043 0.145 1295 Planarity : 0.003 0.038 1452 Dihedral : 9.280 143.245 1161 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.82 % Favored : 95.99 % Rotamer: Outliers : 3.35 % Allowed : 21.54 % Favored : 75.11 % 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: 0.12 (0.27), residues: 1022 helix: 1.45 (0.27), residues: 393 sheet: -0.07 (0.37), residues: 218 loop : -1.15 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 170 HIS 0.005 0.001 HIS A 352 PHE 0.015 0.001 PHE R 82 TYR 0.023 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7188 (mttm) cc_final: 0.6970 (mtmm) REVERT: A 264 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7748 (ttmm) REVERT: A 289 GLU cc_start: 0.7977 (tp30) cc_final: 0.7333 (tp30) REVERT: A 309 THR cc_start: 0.8133 (t) cc_final: 0.7846 (p) REVERT: A 317 GLU cc_start: 0.6793 (mp0) cc_final: 0.6245 (mp0) REVERT: A 346 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7633 (mtt-85) REVERT: A 366 PHE cc_start: 0.7931 (t80) cc_final: 0.6954 (t80) REVERT: A 371 ASP cc_start: 0.8202 (t70) cc_final: 0.7887 (t0) REVERT: B 49 ARG cc_start: 0.7893 (mtt90) cc_final: 0.7586 (mtt90) REVERT: B 67 SER cc_start: 0.8767 (m) cc_final: 0.8341 (t) REVERT: B 103 CYS cc_start: 0.7702 (m) cc_final: 0.7259 (m) REVERT: B 169 TRP cc_start: 0.8613 (m100) cc_final: 0.8126 (m100) REVERT: B 220 GLN cc_start: 0.7954 (pt0) cc_final: 0.7596 (pt0) REVERT: B 258 ASP cc_start: 0.8047 (t70) cc_final: 0.7360 (t0) REVERT: B 273 ILE cc_start: 0.8515 (mp) cc_final: 0.8193 (mp) REVERT: B 304 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7956 (ttm-80) REVERT: G 28 ILE cc_start: 0.7947 (mp) cc_final: 0.7675 (mp) REVERT: R 65 TYR cc_start: 0.8031 (m-80) cc_final: 0.7506 (m-80) outliers start: 30 outliers final: 24 residues processed: 223 average time/residue: 0.3655 time to fit residues: 105.7852 Evaluate side-chains 229 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 63 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.4268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 282 ASN A 377 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129556 restraints weight = 12077.735| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.25 r_work: 0.3556 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8468 Z= 0.187 Angle : 0.576 7.642 11492 Z= 0.292 Chirality : 0.042 0.149 1295 Planarity : 0.003 0.037 1452 Dihedral : 9.213 143.107 1161 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.62 % Favored : 96.18 % Rotamer: Outliers : 3.24 % Allowed : 21.99 % Favored : 74.78 % 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: 0.13 (0.27), residues: 1022 helix: 1.45 (0.27), residues: 394 sheet: -0.10 (0.37), residues: 219 loop : -1.13 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 170 HIS 0.005 0.001 HIS A 352 PHE 0.014 0.001 PHE R 82 TYR 0.024 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7117 (mttm) cc_final: 0.6864 (mttp) REVERT: A 264 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7784 (ttmm) REVERT: A 289 GLU cc_start: 0.7983 (tp30) cc_final: 0.7323 (tp30) REVERT: A 309 THR cc_start: 0.8121 (t) cc_final: 0.7829 (p) REVERT: A 317 GLU cc_start: 0.6792 (mp0) cc_final: 0.6243 (mp0) REVERT: A 346 ARG cc_start: 0.8135 (mtt-85) cc_final: 0.7664 (mtt-85) REVERT: A 366 PHE cc_start: 0.7933 (t80) cc_final: 0.6947 (t80) REVERT: A 371 ASP cc_start: 0.8204 (t70) cc_final: 0.7891 (t0) REVERT: B 49 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7578 (mtt90) REVERT: B 67 SER cc_start: 0.8776 (m) cc_final: 0.8341 (t) REVERT: B 103 CYS cc_start: 0.7740 (m) cc_final: 0.7315 (m) REVERT: B 169 TRP cc_start: 0.8620 (m100) cc_final: 0.8124 (m100) REVERT: B 220 GLN cc_start: 0.7916 (pt0) cc_final: 0.7539 (pt0) REVERT: B 234 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: B 258 ASP cc_start: 0.8036 (t70) cc_final: 0.7314 (t0) REVERT: B 259 GLN cc_start: 0.8556 (tt0) cc_final: 0.8257 (mt0) REVERT: B 273 ILE cc_start: 0.8513 (mp) cc_final: 0.8194 (mp) REVERT: B 304 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8030 (ttm-80) REVERT: G 28 ILE cc_start: 0.7948 (mp) cc_final: 0.7686 (mp) REVERT: R 65 TYR cc_start: 0.8040 (m-80) cc_final: 0.7504 (m-80) outliers start: 29 outliers final: 22 residues processed: 227 average time/residue: 0.4290 time to fit residues: 124.7500 Evaluate side-chains 231 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 377 ASN B 239 ASN N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.148165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128919 restraints weight = 12059.434| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.26 r_work: 0.3520 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8468 Z= 0.232 Angle : 0.620 13.924 11492 Z= 0.311 Chirality : 0.043 0.165 1295 Planarity : 0.004 0.038 1452 Dihedral : 9.193 142.362 1161 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 3.24 % Allowed : 22.77 % Favored : 74.00 % 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: 0.08 (0.27), residues: 1022 helix: 1.36 (0.27), residues: 394 sheet: -0.08 (0.37), residues: 217 loop : -1.13 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 170 HIS 0.006 0.001 HIS A 352 PHE 0.013 0.001 PHE B 234 TYR 0.022 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7224 (mttm) cc_final: 0.7017 (mtmm) REVERT: A 264 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7826 (ttmm) REVERT: A 289 GLU cc_start: 0.8001 (tp30) cc_final: 0.7359 (tp30) REVERT: A 309 THR cc_start: 0.8159 (t) cc_final: 0.7873 (p) REVERT: A 317 GLU cc_start: 0.6822 (mp0) cc_final: 0.6280 (mp0) REVERT: A 346 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7792 (mtt-85) REVERT: A 366 PHE cc_start: 0.7967 (t80) cc_final: 0.6993 (t80) REVERT: A 371 ASP cc_start: 0.8210 (t70) cc_final: 0.7915 (t0) REVERT: B 49 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7639 (mtt90) REVERT: B 67 SER cc_start: 0.8819 (m) cc_final: 0.8375 (t) REVERT: B 103 CYS cc_start: 0.7739 (m) cc_final: 0.7323 (m) REVERT: B 169 TRP cc_start: 0.8615 (m100) cc_final: 0.8137 (m100) REVERT: B 220 GLN cc_start: 0.7975 (pt0) cc_final: 0.7620 (pt0) REVERT: B 234 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: B 256 ARG cc_start: 0.8104 (ptp-110) cc_final: 0.7843 (ptp-110) REVERT: B 258 ASP cc_start: 0.8066 (t70) cc_final: 0.7308 (t0) REVERT: B 259 GLN cc_start: 0.8617 (tt0) cc_final: 0.8362 (mt0) REVERT: B 273 ILE cc_start: 0.8491 (mp) cc_final: 0.8169 (mp) REVERT: B 304 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: G 28 ILE cc_start: 0.8039 (mp) cc_final: 0.7779 (mp) REVERT: R 65 TYR cc_start: 0.8069 (m-80) cc_final: 0.7553 (m-80) outliers start: 29 outliers final: 23 residues processed: 227 average time/residue: 0.2705 time to fit residues: 78.7090 Evaluate side-chains 230 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.0770 chunk 78 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 282 ASN A 377 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129147 restraints weight = 11996.062| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.24 r_work: 0.3527 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8468 Z= 0.202 Angle : 0.609 13.522 11492 Z= 0.307 Chirality : 0.043 0.155 1295 Planarity : 0.004 0.038 1452 Dihedral : 9.127 142.414 1161 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 3.24 % Allowed : 22.10 % 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: 0.09 (0.27), residues: 1022 helix: 1.37 (0.27), residues: 394 sheet: -0.11 (0.37), residues: 217 loop : -1.12 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 170 HIS 0.007 0.001 HIS A 352 PHE 0.014 0.001 PHE N 108 TYR 0.029 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.7185 (mttm) cc_final: 0.6971 (mtmm) REVERT: A 264 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7805 (ttmm) REVERT: A 289 GLU cc_start: 0.7999 (tp30) cc_final: 0.7352 (tp30) REVERT: A 317 GLU cc_start: 0.6821 (mp0) cc_final: 0.6276 (mp0) REVERT: A 346 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7731 (mtt-85) REVERT: A 366 PHE cc_start: 0.7942 (t80) cc_final: 0.6957 (t80) REVERT: A 371 ASP cc_start: 0.8214 (t70) cc_final: 0.7931 (t0) REVERT: B 49 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7640 (mtt90) REVERT: B 61 MET cc_start: 0.7841 (ppp) cc_final: 0.7298 (ppp) REVERT: B 67 SER cc_start: 0.8823 (m) cc_final: 0.8376 (t) REVERT: B 103 CYS cc_start: 0.7744 (m) cc_final: 0.7337 (m) REVERT: B 169 TRP cc_start: 0.8596 (m100) cc_final: 0.8149 (m100) REVERT: B 220 GLN cc_start: 0.7957 (pt0) cc_final: 0.7597 (pt0) REVERT: B 234 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 256 ARG cc_start: 0.8117 (ptp-110) cc_final: 0.7877 (ptp-110) REVERT: B 258 ASP cc_start: 0.8071 (t70) cc_final: 0.7301 (t0) REVERT: B 259 GLN cc_start: 0.8617 (tt0) cc_final: 0.8374 (mt0) REVERT: B 273 ILE cc_start: 0.8457 (mp) cc_final: 0.8130 (mp) REVERT: B 304 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: G 28 ILE cc_start: 0.8010 (mp) cc_final: 0.7748 (mp) REVERT: R 65 TYR cc_start: 0.8057 (m-80) cc_final: 0.7541 (m-80) REVERT: R 272 MET cc_start: 0.7769 (mtt) cc_final: 0.7301 (mmm) outliers start: 29 outliers final: 26 residues processed: 233 average time/residue: 0.2658 time to fit residues: 79.4366 Evaluate side-chains 240 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ARG Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 0.0670 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 282 ASN A 377 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129549 restraints weight = 12146.216| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.25 r_work: 0.3529 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8468 Z= 0.190 Angle : 0.612 13.097 11492 Z= 0.309 Chirality : 0.043 0.147 1295 Planarity : 0.004 0.037 1452 Dihedral : 9.057 142.538 1161 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.52 % Favored : 96.28 % Rotamer: Outliers : 2.79 % Allowed : 22.99 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 1022 helix: 1.41 (0.27), residues: 394 sheet: -0.09 (0.37), residues: 217 loop : -1.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 170 HIS 0.007 0.001 HIS A 352 PHE 0.029 0.001 PHE R 199 TYR 0.027 0.001 TYR R 32 ARG 0.003 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4879.24 seconds wall clock time: 86 minutes 46.46 seconds (5206.46 seconds total)