Starting phenix.real_space_refine on Tue Apr 29 20:23:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blc_44653/04_2025/9blc_44653.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blc_44653/04_2025/9blc_44653.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/9blc_44653/04_2025/9blc_44653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blc_44653/04_2025/9blc_44653.map" model { file = "/net/cci-nas-00/data/ceres_data/9blc_44653/04_2025/9blc_44653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blc_44653/04_2025/9blc_44653.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= -0.002 sd= 0.037 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 64 5.16 5 C 5721 2.51 5 N 1582 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9015 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 234 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 16, 'TRANS': 353} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Time building chain proxies: 6.02, per 1000 atoms: 0.67 Number of scatterers: 9015 At special positions: 0 Unit cell: (81.7, 101.48, 149.64, 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 64 16.00 O 1648 8.00 N 1582 7.00 C 5721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.09 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 41.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'P' and resid 4 through 7 Processing helix chain 'P' and resid 8 through 21 removed outlier: 3.621A pdb=" N ASN P 21 " --> pdb=" O ARG P 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 62 removed outlier: 3.611A pdb=" N MET R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.640A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA R 136 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.806A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.660A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 4.089A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.700A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 221 " --> pdb=" O VAL R 217 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 285 Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.670A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.963A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 removed outlier: 4.062A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.594A pdb=" N HIS R 377 " --> pdb=" O ASP R 373 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 393 Processing helix chain 'R' and resid 395 through 413 Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.679A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.645A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.525A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.520A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.588A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.762A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 53 through 56 Processing sheet with id=AA1, first strand: chain 'R' and resid 91 through 94 removed outlier: 3.532A pdb=" N LYS R 110 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.808A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.366A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.661A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.032A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.630A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.639A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.982A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.656A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.103A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.707A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.443A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1254 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: 2.53 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2929 1.34 - 1.46: 2275 1.46 - 1.59: 3921 1.59 - 1.72: 0 1.72 - 1.85: 90 Bond restraints: 9215 Sorted by residual: bond pdb=" N PRO R 363 " pdb=" CD PRO R 363 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.481 -0.028 9.20e-03 1.18e+04 9.10e+00 bond pdb=" N TRP R 361 " pdb=" CA TRP R 361 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.55e+00 bond pdb=" N ASN R 365 " pdb=" CA ASN R 365 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.40e+00 bond pdb=" N VAL R 358 " pdb=" CA VAL R 358 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.26e+00 ... (remaining 9210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 12273 1.73 - 3.45: 188 3.45 - 5.18: 27 5.18 - 6.91: 5 6.91 - 8.63: 1 Bond angle restraints: 12494 Sorted by residual: angle pdb=" N GLY P 33 " pdb=" CA GLY P 33 " pdb=" C GLY P 33 " ideal model delta sigma weight residual 112.50 117.28 -4.78 1.16e+00 7.43e-01 1.70e+01 angle pdb=" N PRO R 360 " pdb=" CA PRO R 360 " pdb=" C PRO R 360 " ideal model delta sigma weight residual 113.40 118.51 -5.11 1.34e+00 5.57e-01 1.46e+01 angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 121.00 117.06 3.94 1.08e+00 8.57e-01 1.33e+01 angle pdb=" N LEU R 368 " pdb=" CA LEU R 368 " pdb=" C LEU R 368 " ideal model delta sigma weight residual 111.28 107.50 3.78 1.09e+00 8.42e-01 1.20e+01 angle pdb=" C ASP R 373 " pdb=" CA ASP R 373 " pdb=" CB ASP R 373 " ideal model delta sigma weight residual 110.85 116.36 -5.51 1.70e+00 3.46e-01 1.05e+01 ... (remaining 12489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4769 17.83 - 35.67: 532 35.67 - 53.50: 133 53.50 - 71.33: 22 71.33 - 89.16: 12 Dihedral angle restraints: 5468 sinusoidal: 2114 harmonic: 3354 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 93.00 178.80 -85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 154.22 -61.22 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual -86.00 -133.04 47.04 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 5465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1232 0.064 - 0.127: 147 0.127 - 0.191: 6 0.191 - 0.254: 4 0.254 - 0.318: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ASP R 373 " pdb=" N ASP R 373 " pdb=" C ASP R 373 " pdb=" CB ASP R 373 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA PHE R 359 " pdb=" N PHE R 359 " pdb=" C PHE R 359 " pdb=" CB PHE R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PRO R 360 " pdb=" N PRO R 360 " pdb=" C PRO R 360 " pdb=" CB PRO R 360 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1388 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 362 " -0.069 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO R 363 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO R 363 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO R 363 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO G 60 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 194 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.025 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 227 2.70 - 3.25: 8695 3.25 - 3.80: 14049 3.80 - 4.35: 18129 4.35 - 4.90: 31075 Nonbonded interactions: 72175 Sorted by model distance: nonbonded pdb=" OE1 GLN R 408 " pdb=" O ALA B 309 " model vdw 2.146 3.040 nonbonded pdb=" O ASP A 215 " pdb=" OD1 ASP A 215 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP R 103 " pdb=" N SER R 105 " model vdw 2.238 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.258 3.040 ... (remaining 72170 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=0.00 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: 1.890 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 0.093 9223 Z= 0.200 Angle : 0.531 8.634 12508 Z= 0.314 Chirality : 0.043 0.318 1391 Planarity : 0.004 0.107 1599 Dihedral : 16.165 89.163 3275 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 0.84 % Allowed : 22.44 % Favored : 76.71 % Cbeta Deviations : 0.09 % 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: 0.21 (0.25), residues: 1132 helix: 1.51 (0.25), residues: 436 sheet: -0.52 (0.34), residues: 233 loop : -0.76 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.006 0.001 HIS R 184 PHE 0.018 0.001 PHE R 285 TYR 0.010 0.001 TYR N 95 ARG 0.004 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.22604 ( 437) hydrogen bonds : angle 7.22377 ( 1254) SS BOND : bond 0.02062 ( 7) SS BOND : angle 2.53049 ( 14) covalent geometry : bond 0.00291 ( 9215) covalent geometry : angle 0.52468 (12494) Misc. bond : bond 0.09346 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 9 ILE cc_start: 0.6924 (tt) cc_final: 0.5778 (tp) REVERT: G 14 LYS cc_start: 0.7563 (ptmt) cc_final: 0.7203 (ptmt) REVERT: G 16 VAL cc_start: 0.8076 (t) cc_final: 0.7840 (p) REVERT: G 20 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7812 (mtmm) outliers start: 8 outliers final: 3 residues processed: 230 average time/residue: 0.2656 time to fit residues: 79.5724 Evaluate side-chains 173 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS R 194 ASN R 257 GLN A 19 GLN A 220 HIS A 278 ASN B 44 GLN B 75 GLN B 88 ASN N 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.121663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.090463 restraints weight = 16119.068| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.68 r_work: 0.3063 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9223 Z= 0.191 Angle : 0.591 7.337 12508 Z= 0.318 Chirality : 0.043 0.176 1391 Planarity : 0.005 0.078 1599 Dihedral : 3.946 19.380 1250 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.95 % Allowed : 21.07 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1132 helix: 1.93 (0.25), residues: 449 sheet: -0.60 (0.33), residues: 238 loop : -0.83 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 82 HIS 0.004 0.001 HIS R 201 PHE 0.015 0.002 PHE R 119 TYR 0.011 0.001 TYR A 339 ARG 0.005 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 437) hydrogen bonds : angle 4.82799 ( 1254) SS BOND : bond 0.00437 ( 7) SS BOND : angle 1.14354 ( 14) covalent geometry : bond 0.00438 ( 9215) covalent geometry : angle 0.59059 (12494) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 82 TRP cc_start: 0.5929 (m100) cc_final: 0.5328 (m-10) REVERT: B 13 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8302 (mm-40) REVERT: B 59 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: B 258 ASP cc_start: 0.7936 (t0) cc_final: 0.7551 (t0) REVERT: G 16 VAL cc_start: 0.9112 (t) cc_final: 0.8875 (p) REVERT: G 20 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8304 (mtmm) REVERT: N 70 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7364 (mp) outliers start: 47 outliers final: 23 residues processed: 202 average time/residue: 0.2206 time to fit residues: 60.9749 Evaluate side-chains 184 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 392 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.126207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094705 restraints weight = 17148.497| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.88 r_work: 0.3203 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9223 Z= 0.184 Angle : 0.559 7.818 12508 Z= 0.300 Chirality : 0.043 0.145 1391 Planarity : 0.004 0.058 1599 Dihedral : 4.005 20.205 1247 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.11 % Allowed : 21.29 % Favored : 74.60 % 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: 0.49 (0.26), residues: 1132 helix: 2.01 (0.25), residues: 449 sheet: -0.56 (0.32), residues: 248 loop : -0.89 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 121 PHE 0.012 0.001 PHE N 108 TYR 0.012 0.001 TYR N 80 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 437) hydrogen bonds : angle 4.59774 ( 1254) SS BOND : bond 0.00363 ( 7) SS BOND : angle 1.61681 ( 14) covalent geometry : bond 0.00427 ( 9215) covalent geometry : angle 0.55626 (12494) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 373 ASP cc_start: 0.8691 (p0) cc_final: 0.8364 (p0) REVERT: A 317 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8028 (tmm160) REVERT: B 13 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8318 (mm-40) REVERT: B 59 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: B 173 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8844 (m) REVERT: B 175 GLN cc_start: 0.8401 (pm20) cc_final: 0.7991 (pm20) REVERT: B 217 MET cc_start: 0.8664 (ppp) cc_final: 0.8311 (ppp) REVERT: B 258 ASP cc_start: 0.8113 (t0) cc_final: 0.7677 (t0) REVERT: G 16 VAL cc_start: 0.9177 (t) cc_final: 0.8786 (p) REVERT: G 17 GLU cc_start: 0.8527 (pp20) cc_final: 0.8188 (pp20) REVERT: G 20 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8300 (mtmm) REVERT: N 46 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7286 (mm-30) outliers start: 39 outliers final: 23 residues processed: 197 average time/residue: 0.2192 time to fit residues: 58.6830 Evaluate side-chains 185 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 288 ASN Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.125660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094771 restraints weight = 16891.703| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.89 r_work: 0.3215 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9223 Z= 0.113 Angle : 0.515 7.436 12508 Z= 0.277 Chirality : 0.041 0.135 1391 Planarity : 0.004 0.048 1599 Dihedral : 3.873 19.606 1247 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.79 % Allowed : 22.13 % Favored : 74.08 % 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: 0.64 (0.26), residues: 1132 helix: 2.16 (0.25), residues: 447 sheet: -0.45 (0.32), residues: 243 loop : -0.85 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.011 0.001 PHE R 224 TYR 0.015 0.001 TYR R 98 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 437) hydrogen bonds : angle 4.35892 ( 1254) SS BOND : bond 0.00367 ( 7) SS BOND : angle 2.62520 ( 14) covalent geometry : bond 0.00246 ( 9215) covalent geometry : angle 0.50794 (12494) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 373 ASP cc_start: 0.8687 (p0) cc_final: 0.8322 (p0) REVERT: A 317 ARG cc_start: 0.8629 (tpp80) cc_final: 0.8107 (tmm160) REVERT: B 13 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8339 (mm-40) REVERT: B 59 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: B 173 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8907 (m) REVERT: B 175 GLN cc_start: 0.8434 (pm20) cc_final: 0.8017 (pm20) REVERT: B 258 ASP cc_start: 0.8075 (t0) cc_final: 0.7578 (t0) REVERT: G 16 VAL cc_start: 0.9175 (t) cc_final: 0.8860 (p) REVERT: G 17 GLU cc_start: 0.8591 (pp20) cc_final: 0.8210 (pp20) REVERT: G 20 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8338 (mtmm) REVERT: N 46 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7244 (mm-30) REVERT: N 88 PRO cc_start: 0.8564 (Cg_exo) cc_final: 0.8351 (Cg_endo) outliers start: 36 outliers final: 24 residues processed: 205 average time/residue: 0.2191 time to fit residues: 61.7200 Evaluate side-chains 183 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN R 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.122697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091535 restraints weight = 16748.908| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.87 r_work: 0.3179 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9223 Z= 0.160 Angle : 0.547 7.339 12508 Z= 0.292 Chirality : 0.042 0.149 1391 Planarity : 0.004 0.049 1599 Dihedral : 3.972 21.470 1247 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.32 % Allowed : 21.39 % Favored : 74.29 % 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 (0.26), residues: 1132 helix: 2.05 (0.24), residues: 451 sheet: -0.66 (0.32), residues: 253 loop : -0.81 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 201 PHE 0.014 0.001 PHE N 108 TYR 0.013 0.001 TYR N 60 ARG 0.004 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 437) hydrogen bonds : angle 4.34795 ( 1254) SS BOND : bond 0.00433 ( 7) SS BOND : angle 1.64700 ( 14) covalent geometry : bond 0.00372 ( 9215) covalent geometry : angle 0.54489 (12494) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 LEU cc_start: 0.7628 (mt) cc_final: 0.7405 (mt) REVERT: R 373 ASP cc_start: 0.8583 (p0) cc_final: 0.8335 (p0) REVERT: R 408 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7235 (mp10) REVERT: B 13 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8466 (mm-40) REVERT: B 59 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8661 (m-80) REVERT: B 173 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8858 (m) REVERT: B 175 GLN cc_start: 0.8429 (pm20) cc_final: 0.8129 (pm20) REVERT: B 217 MET cc_start: 0.8573 (ppp) cc_final: 0.8264 (ppp) REVERT: B 258 ASP cc_start: 0.8186 (t0) cc_final: 0.7745 (t0) REVERT: G 17 GLU cc_start: 0.8659 (pp20) cc_final: 0.8355 (pp20) REVERT: G 20 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8323 (mtmm) REVERT: N 46 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7259 (mm-30) outliers start: 41 outliers final: 31 residues processed: 203 average time/residue: 0.2584 time to fit residues: 72.0967 Evaluate side-chains 192 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.125983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094710 restraints weight = 16823.470| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.86 r_work: 0.3201 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9223 Z= 0.122 Angle : 0.536 8.106 12508 Z= 0.286 Chirality : 0.041 0.153 1391 Planarity : 0.003 0.043 1599 Dihedral : 3.882 19.965 1247 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.43 % Allowed : 21.92 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1132 helix: 2.19 (0.25), residues: 447 sheet: -0.72 (0.32), residues: 251 loop : -0.75 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.011 0.001 PHE R 224 TYR 0.013 0.001 TYR N 80 ARG 0.004 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 437) hydrogen bonds : angle 4.24508 ( 1254) SS BOND : bond 0.00317 ( 7) SS BOND : angle 2.54075 ( 14) covalent geometry : bond 0.00279 ( 9215) covalent geometry : angle 0.52934 (12494) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 101 ASP cc_start: 0.7817 (t0) cc_final: 0.7507 (t0) REVERT: R 211 LEU cc_start: 0.7644 (mt) cc_final: 0.7424 (mt) REVERT: R 373 ASP cc_start: 0.8584 (p0) cc_final: 0.8320 (p0) REVERT: B 13 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8438 (mm-40) REVERT: B 59 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: B 173 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8794 (m) REVERT: B 175 GLN cc_start: 0.8413 (pm20) cc_final: 0.8096 (pm20) REVERT: B 258 ASP cc_start: 0.8139 (t0) cc_final: 0.7722 (t0) REVERT: G 17 GLU cc_start: 0.8631 (pp20) cc_final: 0.8335 (pp20) REVERT: G 20 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8405 (mtmm) REVERT: N 46 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7232 (mm-30) REVERT: N 127 SER cc_start: 0.6906 (OUTLIER) cc_final: 0.6618 (p) outliers start: 42 outliers final: 33 residues processed: 198 average time/residue: 0.1974 time to fit residues: 54.3902 Evaluate side-chains 195 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 85 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 383 GLN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095320 restraints weight = 17088.303| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.90 r_work: 0.3210 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9223 Z= 0.116 Angle : 0.529 8.126 12508 Z= 0.281 Chirality : 0.041 0.157 1391 Planarity : 0.003 0.042 1599 Dihedral : 3.834 20.359 1247 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.11 % Allowed : 22.76 % Favored : 73.13 % 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: 0.70 (0.26), residues: 1132 helix: 2.29 (0.25), residues: 442 sheet: -0.71 (0.32), residues: 250 loop : -0.67 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.011 0.001 PHE R 224 TYR 0.014 0.001 TYR N 80 ARG 0.006 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 437) hydrogen bonds : angle 4.17220 ( 1254) SS BOND : bond 0.00278 ( 7) SS BOND : angle 1.14947 ( 14) covalent geometry : bond 0.00263 ( 9215) covalent geometry : angle 0.52744 (12494) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 LEU cc_start: 0.7637 (mt) cc_final: 0.7368 (mt) REVERT: R 373 ASP cc_start: 0.8570 (p0) cc_final: 0.8305 (p0) REVERT: R 408 GLN cc_start: 0.7513 (mp10) cc_final: 0.7061 (mp10) REVERT: B 13 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8429 (mm-40) REVERT: B 59 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8661 (m-80) REVERT: B 173 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8734 (m) REVERT: B 175 GLN cc_start: 0.8381 (pm20) cc_final: 0.8068 (pm20) REVERT: B 258 ASP cc_start: 0.8115 (t0) cc_final: 0.7717 (t0) REVERT: G 17 GLU cc_start: 0.8660 (pp20) cc_final: 0.8393 (pp20) REVERT: G 20 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8419 (mtmm) REVERT: N 46 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7232 (mm-30) outliers start: 39 outliers final: 37 residues processed: 200 average time/residue: 0.2080 time to fit residues: 57.9246 Evaluate side-chains 199 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 383 GLN B 32 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094696 restraints weight = 16909.765| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.89 r_work: 0.3220 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9223 Z= 0.123 Angle : 0.545 11.858 12508 Z= 0.286 Chirality : 0.041 0.163 1391 Planarity : 0.003 0.042 1599 Dihedral : 3.804 19.586 1247 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.21 % Allowed : 22.66 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1132 helix: 2.34 (0.25), residues: 442 sheet: -0.69 (0.32), residues: 249 loop : -0.64 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 184 PHE 0.011 0.001 PHE R 224 TYR 0.013 0.001 TYR N 80 ARG 0.006 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 437) hydrogen bonds : angle 4.12359 ( 1254) SS BOND : bond 0.00292 ( 7) SS BOND : angle 1.58141 ( 14) covalent geometry : bond 0.00283 ( 9215) covalent geometry : angle 0.54298 (12494) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 LEU cc_start: 0.7656 (mt) cc_final: 0.7420 (mt) REVERT: R 373 ASP cc_start: 0.8554 (p0) cc_final: 0.8265 (p0) REVERT: A 13 ARG cc_start: 0.7759 (mpp-170) cc_final: 0.7546 (mpp-170) REVERT: B 13 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8432 (mm-40) REVERT: B 59 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.8639 (m-80) REVERT: B 173 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8739 (m) REVERT: B 175 GLN cc_start: 0.8388 (pm20) cc_final: 0.8059 (pm20) REVERT: B 258 ASP cc_start: 0.8114 (t0) cc_final: 0.7716 (t0) REVERT: G 17 GLU cc_start: 0.8653 (pp20) cc_final: 0.8417 (pp20) REVERT: G 20 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8409 (mtmm) REVERT: G 22 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8085 (mp0) REVERT: N 46 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7247 (mm-30) REVERT: N 99 CYS cc_start: 0.6568 (t) cc_final: 0.6312 (t) outliers start: 40 outliers final: 37 residues processed: 201 average time/residue: 0.2128 time to fit residues: 59.1711 Evaluate side-chains 202 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 87 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094340 restraints weight = 16682.624| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.87 r_work: 0.3224 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9223 Z= 0.108 Angle : 0.539 11.613 12508 Z= 0.282 Chirality : 0.041 0.167 1391 Planarity : 0.003 0.042 1599 Dihedral : 3.723 18.307 1247 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.64 % Allowed : 22.44 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1132 helix: 2.36 (0.25), residues: 444 sheet: -0.59 (0.32), residues: 246 loop : -0.70 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.000 HIS R 377 PHE 0.011 0.001 PHE R 224 TYR 0.013 0.001 TYR N 80 ARG 0.006 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 437) hydrogen bonds : angle 4.05049 ( 1254) SS BOND : bond 0.00217 ( 7) SS BOND : angle 1.32289 ( 14) covalent geometry : bond 0.00244 ( 9215) covalent geometry : angle 0.53734 (12494) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 79 TRP cc_start: 0.7926 (m100) cc_final: 0.7722 (m100) REVERT: R 211 LEU cc_start: 0.7657 (mt) cc_final: 0.7430 (mt) REVERT: R 373 ASP cc_start: 0.8549 (p0) cc_final: 0.8266 (p0) REVERT: R 408 GLN cc_start: 0.7455 (mp10) cc_final: 0.6935 (pp30) REVERT: B 13 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8389 (mm-40) REVERT: B 59 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: B 173 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (m) REVERT: B 175 GLN cc_start: 0.8334 (pm20) cc_final: 0.7989 (pm20) REVERT: B 258 ASP cc_start: 0.8101 (t0) cc_final: 0.7728 (t0) REVERT: G 17 GLU cc_start: 0.8606 (pp20) cc_final: 0.8393 (pp20) REVERT: G 20 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8457 (mtmm) REVERT: G 22 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8105 (mp0) REVERT: N 19 ARG cc_start: 0.7828 (tpp-160) cc_final: 0.7431 (tpp-160) REVERT: N 34 MET cc_start: 0.8211 (mmm) cc_final: 0.8010 (mmp) REVERT: N 46 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7218 (mm-30) REVERT: N 127 SER cc_start: 0.6807 (OUTLIER) cc_final: 0.6508 (p) outliers start: 44 outliers final: 37 residues processed: 211 average time/residue: 0.2059 time to fit residues: 59.9946 Evaluate side-chains 211 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.125177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094203 restraints weight = 16727.971| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.89 r_work: 0.3222 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9223 Z= 0.129 Angle : 0.558 10.346 12508 Z= 0.294 Chirality : 0.041 0.170 1391 Planarity : 0.004 0.042 1599 Dihedral : 3.725 20.049 1247 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.43 % Allowed : 23.18 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1132 helix: 2.38 (0.25), residues: 444 sheet: -0.70 (0.32), residues: 249 loop : -0.64 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 377 PHE 0.020 0.001 PHE R 161 TYR 0.014 0.001 TYR N 80 ARG 0.006 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 437) hydrogen bonds : angle 4.07511 ( 1254) SS BOND : bond 0.00242 ( 7) SS BOND : angle 1.35195 ( 14) covalent geometry : bond 0.00301 ( 9215) covalent geometry : angle 0.55649 (12494) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 LEU cc_start: 0.7681 (mt) cc_final: 0.7444 (mt) REVERT: R 373 ASP cc_start: 0.8555 (p0) cc_final: 0.8300 (p0) REVERT: R 408 GLN cc_start: 0.7448 (mp10) cc_final: 0.7050 (mp10) REVERT: B 13 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8428 (mm-40) REVERT: B 59 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: B 173 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8704 (m) REVERT: B 175 GLN cc_start: 0.8352 (pm20) cc_final: 0.8012 (pm20) REVERT: B 217 MET cc_start: 0.8605 (ppp) cc_final: 0.8299 (ppp) REVERT: B 258 ASP cc_start: 0.8120 (t0) cc_final: 0.7755 (t0) REVERT: G 17 GLU cc_start: 0.8622 (pp20) cc_final: 0.8421 (pp20) REVERT: G 20 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8459 (mtmm) REVERT: G 22 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8113 (mp0) REVERT: N 34 MET cc_start: 0.8241 (mmm) cc_final: 0.8039 (mmp) REVERT: N 46 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7215 (mm-30) REVERT: N 127 SER cc_start: 0.6857 (OUTLIER) cc_final: 0.6537 (p) outliers start: 42 outliers final: 37 residues processed: 207 average time/residue: 0.2075 time to fit residues: 59.1200 Evaluate side-chains 209 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 30.0000 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 381 HIS B 32 GLN N 1 GLN N 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095962 restraints weight = 16880.297| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.88 r_work: 0.3239 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9223 Z= 0.112 Angle : 0.545 10.307 12508 Z= 0.289 Chirality : 0.041 0.169 1391 Planarity : 0.004 0.042 1599 Dihedral : 3.663 17.568 1247 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.00 % Allowed : 23.50 % Favored : 72.50 % 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: 0.82 (0.26), residues: 1132 helix: 2.40 (0.25), residues: 444 sheet: -0.61 (0.32), residues: 246 loop : -0.67 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS R 377 PHE 0.020 0.001 PHE R 161 TYR 0.013 0.001 TYR N 80 ARG 0.008 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 437) hydrogen bonds : angle 4.02810 ( 1254) SS BOND : bond 0.00241 ( 7) SS BOND : angle 1.59342 ( 14) covalent geometry : bond 0.00254 ( 9215) covalent geometry : angle 0.54234 (12494) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.01 seconds wall clock time: 77 minutes 44.23 seconds (4664.23 seconds total)