Starting phenix.real_space_refine on Sun Dec 29 01:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyi_26180/12_2024/7tyi_26180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyi_26180/12_2024/7tyi_26180.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/7tyi_26180/12_2024/7tyi_26180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyi_26180/12_2024/7tyi_26180.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyi_26180/12_2024/7tyi_26180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyi_26180/12_2024/7tyi_26180.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.087 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 67 5.16 5 C 6032 2.51 5 N 1603 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9413 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 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} Chain: "P" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} 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: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3039 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 208 Unusual residues: {'NAG': 2, 'PLM': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.04, per 1000 atoms: 0.64 Number of scatterers: 9413 At special positions: 0 Unit cell: (82.176, 99.296, 154.936, 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 67 16.00 O 1711 8.00 N 1603 7.00 C 6032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 39.9% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 3.517A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.576A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.870A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.688A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.707A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.642A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.851A pdb=" N LEU A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.969A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.770A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.027A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 7 No H-bonds generated for 'chain 'P' and resid 5 through 7' Processing helix chain 'P' and resid 8 through 21 Processing helix chain 'R' and resid 39 through 59 removed outlier: 3.506A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 62 No H-bonds generated for 'chain 'R' and resid 60 through 62' Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.518A pdb=" N SER R 159 " --> pdb=" O GLY R 155 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 removed outlier: 3.523A pdb=" N GLY R 177 " --> pdb=" O ARG R 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 174 through 177' Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.645A pdb=" N THR R 182 " --> pdb=" O CYS R 178 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.949A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 245 removed outlier: 3.591A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.928A 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 282 Processing helix chain 'R' and resid 287 through 291 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 329 Proline residue: R 304 - end of helix removed outlier: 3.616A pdb=" N GLU R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 347 removed outlier: 3.518A pdb=" N ILE R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 381 Processing helix chain 'R' and resid 383 through 392 Processing helix chain 'R' and resid 395 through 408 removed outlier: 3.561A pdb=" N GLN R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.775A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.775A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.855A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 4.851A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.670A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.907A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.618A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.700A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.537A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.696A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 423 hydrogen bonds defined for protein. 1212 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: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2487 1.33 - 1.45: 1848 1.45 - 1.58: 5184 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9615 Sorted by residual: bond pdb=" CA SER A 286 " pdb=" CB SER A 286 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.64e-02 3.72e+03 1.04e+01 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.49e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.77e+00 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.33e-02 5.65e+03 7.71e+00 bond pdb=" N VAL P 17 " pdb=" CA VAL P 17 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.67e+00 ... (remaining 9610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12585 1.50 - 2.99: 310 2.99 - 4.49: 59 4.49 - 5.99: 11 5.99 - 7.48: 2 Bond angle restraints: 12967 Sorted by residual: angle pdb=" N SER P 19 " pdb=" CA SER P 19 " pdb=" C SER P 19 " ideal model delta sigma weight residual 111.07 115.98 -4.91 1.07e+00 8.73e-01 2.11e+01 angle pdb=" CA ALA R 136 " pdb=" C ALA R 136 " pdb=" O ALA R 136 " ideal model delta sigma weight residual 121.94 117.03 4.91 1.15e+00 7.56e-01 1.82e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N PHE R 137 " pdb=" CA PHE R 137 " pdb=" C PHE R 137 " ideal model delta sigma weight residual 113.40 107.86 5.54 1.47e+00 4.63e-01 1.42e+01 angle pdb=" CA THR R 138 " pdb=" C THR R 138 " pdb=" N PRO R 139 " ideal model delta sigma weight residual 117.44 121.65 -4.21 1.13e+00 7.83e-01 1.39e+01 ... (remaining 12962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5300 17.92 - 35.85: 387 35.85 - 53.77: 69 53.77 - 71.70: 18 71.70 - 89.62: 7 Dihedral angle restraints: 5781 sinusoidal: 2415 harmonic: 3366 Sorted by residual: dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -153.21 67.21 1 1.00e+01 1.00e-02 5.88e+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 93.00 38.43 54.57 1 1.00e+01 1.00e-02 4.04e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1128 0.046 - 0.091: 210 0.091 - 0.137: 74 0.137 - 0.183: 3 0.183 - 0.229: 3 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA VAL P 32 " pdb=" N VAL P 32 " pdb=" C VAL P 32 " pdb=" CB VAL P 32 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA PHE R 102 " pdb=" N PHE R 102 " pdb=" C PHE R 102 " pdb=" CB PHE R 102 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1415 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 98 " 0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C TYR R 98 " -0.026 2.00e-02 2.50e+03 pdb=" O TYR R 98 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE R 99 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 13 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C ALA P 13 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA P 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN P 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.017 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1087 2.75 - 3.29: 9102 3.29 - 3.83: 14961 3.83 - 4.36: 18405 4.36 - 4.90: 31689 Nonbonded interactions: 75244 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.248 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.252 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.284 3.040 nonbonded pdb=" NE2 GLN A 384 " pdb=" O ILE R 248 " model vdw 2.306 3.120 ... (remaining 75239 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: 1.240 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: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.060 Find NCS groups from input model: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.004 0.053 9615 Z= 0.249 Angle : 0.568 7.483 12967 Z= 0.367 Chirality : 0.041 0.229 1418 Planarity : 0.003 0.031 1638 Dihedral : 12.810 89.619 3586 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.50 % Allowed : 4.10 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1136 helix: -2.47 (0.17), residues: 426 sheet: -0.89 (0.34), residues: 230 loop : -1.70 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 76 HIS 0.002 0.000 HIS R 121 PHE 0.010 0.001 PHE R 102 TYR 0.015 0.001 TYR R 56 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.058 Fit side-chains REVERT: P 16 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (mt) REVERT: R 113 ASP cc_start: 0.2558 (OUTLIER) cc_final: 0.2204 (p0) REVERT: R 215 ASP cc_start: 0.6546 (p0) cc_final: 0.5963 (p0) REVERT: R 229 MET cc_start: 0.8055 (tpp) cc_final: 0.7766 (mmt) REVERT: R 359 PHE cc_start: 0.7587 (m-80) cc_final: 0.7345 (m-80) REVERT: R 396 ASN cc_start: 0.7795 (t0) cc_final: 0.7582 (t0) outliers start: 15 outliers final: 6 residues processed: 158 average time/residue: 0.2722 time to fit residues: 56.6440 Evaluate side-chains 113 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 371 ASN B 16 ASN B 62 HIS B 155 ASN B 266 HIS B 340 ASN N 35 ASN N 53 GLN N 123 GLN P 3 ASN P 14 ASN R 93 GLN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 GLN R 257 GLN R 288 ASN R 296 HIS R 377 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9615 Z= 0.366 Angle : 0.660 10.271 12967 Z= 0.348 Chirality : 0.046 0.167 1418 Planarity : 0.005 0.051 1638 Dihedral : 6.839 59.628 1453 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.60 % Allowed : 10.00 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1136 helix: -0.10 (0.23), residues: 425 sheet: -0.70 (0.34), residues: 214 loop : -1.24 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 236 HIS 0.009 0.002 HIS R 336 PHE 0.031 0.002 PHE N 108 TYR 0.031 0.002 TYR A 358 ARG 0.008 0.001 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7585 (mtm110) REVERT: B 45 MET cc_start: 0.7252 (mtm) cc_final: 0.6848 (mtp) REVERT: B 219 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: N 65 LYS cc_start: 0.8251 (tptt) cc_final: 0.7951 (tttm) REVERT: P 16 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8235 (mm) REVERT: R 113 ASP cc_start: 0.2991 (OUTLIER) cc_final: 0.2754 (m-30) REVERT: R 215 ASP cc_start: 0.6941 (p0) cc_final: 0.6732 (p0) REVERT: R 284 TYR cc_start: 0.7128 (m-10) cc_final: 0.6888 (m-10) REVERT: R 373 ASP cc_start: 0.8227 (m-30) cc_final: 0.7311 (m-30) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.2505 time to fit residues: 46.1167 Evaluate side-chains 122 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 268 ASN P 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9615 Z= 0.173 Angle : 0.508 8.516 12967 Z= 0.270 Chirality : 0.041 0.151 1418 Planarity : 0.003 0.034 1638 Dihedral : 6.223 59.235 1452 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.50 % Allowed : 12.00 % Favored : 85.50 % 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: -0.41 (0.24), residues: 1136 helix: 0.91 (0.25), residues: 424 sheet: -0.47 (0.35), residues: 205 loop : -1.17 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.005 0.001 HIS R 336 PHE 0.012 0.001 PHE N 108 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.093 Fit side-chains REVERT: A 265 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7617 (mtm110) REVERT: B 45 MET cc_start: 0.7177 (mtm) cc_final: 0.6876 (mtp) REVERT: B 70 LEU cc_start: 0.8118 (pp) cc_final: 0.7881 (pp) REVERT: B 219 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7626 (ttm-80) REVERT: P 16 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8196 (mm) REVERT: P 37 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.4165 (p90) REVERT: R 113 ASP cc_start: 0.3176 (OUTLIER) cc_final: 0.2064 (p0) REVERT: R 215 ASP cc_start: 0.6951 (p0) cc_final: 0.6385 (p0) REVERT: R 346 MET cc_start: 0.6453 (mtm) cc_final: 0.6242 (mtt) outliers start: 25 outliers final: 17 residues processed: 125 average time/residue: 0.2476 time to fit residues: 42.6094 Evaluate side-chains 118 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.1980 chunk 52 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 155 ASN P 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9615 Z= 0.151 Angle : 0.473 7.454 12967 Z= 0.252 Chirality : 0.040 0.145 1418 Planarity : 0.003 0.037 1638 Dihedral : 5.856 59.418 1452 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.80 % Allowed : 12.10 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1136 helix: 1.35 (0.26), residues: 423 sheet: -0.39 (0.35), residues: 210 loop : -0.97 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE R 137 TYR 0.013 0.001 TYR B 59 ARG 0.004 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7601 (mtm110) REVERT: B 45 MET cc_start: 0.7264 (mtm) cc_final: 0.6995 (mtp) REVERT: B 219 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7569 (ttm-80) REVERT: P 37 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.4427 (p90) REVERT: R 113 ASP cc_start: 0.3202 (OUTLIER) cc_final: 0.2134 (p0) REVERT: R 135 ASN cc_start: 0.8582 (t0) cc_final: 0.8341 (t0) REVERT: R 215 ASP cc_start: 0.7007 (p0) cc_final: 0.6413 (p0) REVERT: R 227 GLN cc_start: 0.7634 (tp40) cc_final: 0.7321 (mm-40) outliers start: 28 outliers final: 23 residues processed: 130 average time/residue: 0.2372 time to fit residues: 42.2554 Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 133 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN P 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9615 Z= 0.167 Angle : 0.472 5.866 12967 Z= 0.251 Chirality : 0.040 0.145 1418 Planarity : 0.003 0.044 1638 Dihedral : 5.729 59.671 1450 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.50 % Allowed : 12.20 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1136 helix: 1.47 (0.26), residues: 424 sheet: -0.37 (0.35), residues: 210 loop : -0.90 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.008 0.001 HIS A 220 PHE 0.013 0.001 PHE A 222 TYR 0.010 0.001 TYR N 94 ARG 0.009 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7597 (mtm110) REVERT: B 45 MET cc_start: 0.7330 (mtm) cc_final: 0.7065 (mtp) REVERT: B 59 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7731 (t80) REVERT: B 219 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7674 (ttm-80) REVERT: P 16 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8177 (mm) REVERT: P 37 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.4404 (p90) REVERT: R 113 ASP cc_start: 0.3429 (OUTLIER) cc_final: 0.2338 (p0) REVERT: R 135 ASN cc_start: 0.8602 (t0) cc_final: 0.8394 (t0) REVERT: R 215 ASP cc_start: 0.7040 (p0) cc_final: 0.6425 (p0) REVERT: R 227 GLN cc_start: 0.7620 (tp40) cc_final: 0.7290 (mm-40) outliers start: 35 outliers final: 25 residues processed: 131 average time/residue: 0.2433 time to fit residues: 43.7859 Evaluate side-chains 131 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN P 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9615 Z= 0.153 Angle : 0.478 9.908 12967 Z= 0.250 Chirality : 0.039 0.174 1418 Planarity : 0.003 0.040 1638 Dihedral : 5.596 59.513 1450 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.20 % Allowed : 13.10 % Favored : 83.70 % 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: 0.25 (0.25), residues: 1136 helix: 1.61 (0.26), residues: 424 sheet: -0.32 (0.35), residues: 203 loop : -0.85 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE N 108 TYR 0.009 0.001 TYR B 59 ARG 0.007 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7318 (mtm) cc_final: 0.7057 (mtp) REVERT: B 59 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 70 LEU cc_start: 0.8150 (pp) cc_final: 0.7929 (pp) REVERT: B 219 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7669 (ttm-80) REVERT: P 16 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8255 (mm) REVERT: P 37 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.4387 (p90) REVERT: R 48 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7567 (mtm) REVERT: R 113 ASP cc_start: 0.3455 (OUTLIER) cc_final: 0.2331 (p0) REVERT: R 215 ASP cc_start: 0.6993 (p0) cc_final: 0.6402 (p0) REVERT: R 227 GLN cc_start: 0.7708 (tp40) cc_final: 0.7358 (mm-40) outliers start: 32 outliers final: 22 residues processed: 129 average time/residue: 0.2504 time to fit residues: 43.8976 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9615 Z= 0.145 Angle : 0.470 8.689 12967 Z= 0.247 Chirality : 0.039 0.148 1418 Planarity : 0.003 0.040 1638 Dihedral : 5.454 59.263 1450 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.20 % Allowed : 13.50 % Favored : 83.30 % 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: 0.35 (0.25), residues: 1136 helix: 1.72 (0.26), residues: 424 sheet: -0.29 (0.35), residues: 203 loop : -0.80 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE N 108 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.7333 (mtm) cc_final: 0.7091 (mtp) REVERT: B 59 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7687 (t80) REVERT: B 70 LEU cc_start: 0.8193 (pp) cc_final: 0.7989 (pp) REVERT: B 118 ASP cc_start: 0.6737 (p0) cc_final: 0.6478 (p0) REVERT: B 219 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7609 (ttm-80) REVERT: P 37 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.4401 (p90) REVERT: R 48 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7638 (mtm) REVERT: R 113 ASP cc_start: 0.3559 (OUTLIER) cc_final: 0.2237 (p0) REVERT: R 215 ASP cc_start: 0.7011 (p0) cc_final: 0.6410 (p0) REVERT: R 227 GLN cc_start: 0.7638 (tp40) cc_final: 0.7340 (mm-40) outliers start: 32 outliers final: 24 residues processed: 125 average time/residue: 0.2491 time to fit residues: 42.4153 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.0010 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9615 Z= 0.142 Angle : 0.471 8.522 12967 Z= 0.247 Chirality : 0.039 0.142 1418 Planarity : 0.003 0.052 1638 Dihedral : 5.410 58.909 1450 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.30 % Allowed : 13.70 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1136 helix: 1.82 (0.26), residues: 423 sheet: -0.29 (0.34), residues: 203 loop : -0.78 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE B 199 TYR 0.008 0.001 TYR R 149 ARG 0.011 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.7345 (mtm) cc_final: 0.7105 (mtp) REVERT: B 59 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 118 ASP cc_start: 0.6715 (p0) cc_final: 0.6467 (p0) REVERT: B 219 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7595 (ttm-80) REVERT: R 48 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7679 (mtm) REVERT: R 113 ASP cc_start: 0.3608 (OUTLIER) cc_final: 0.2249 (p0) REVERT: R 215 ASP cc_start: 0.7010 (p0) cc_final: 0.6411 (p0) REVERT: R 227 GLN cc_start: 0.7637 (tp40) cc_final: 0.7336 (mm-40) outliers start: 33 outliers final: 25 residues processed: 128 average time/residue: 0.2460 time to fit residues: 43.2108 Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9615 Z= 0.196 Angle : 0.500 6.998 12967 Z= 0.263 Chirality : 0.040 0.144 1418 Planarity : 0.003 0.050 1638 Dihedral : 5.523 59.834 1448 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.10 % Allowed : 13.60 % Favored : 83.30 % 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: 0.33 (0.25), residues: 1136 helix: 1.73 (0.26), residues: 424 sheet: -0.37 (0.34), residues: 204 loop : -0.81 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 236 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE N 108 TYR 0.011 0.001 TYR R 338 ARG 0.010 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7769 (t80) REVERT: B 219 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7616 (ttm-80) REVERT: R 48 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7700 (mtm) REVERT: R 113 ASP cc_start: 0.3655 (OUTLIER) cc_final: 0.2101 (p0) REVERT: R 215 ASP cc_start: 0.7027 (p0) cc_final: 0.6444 (p0) REVERT: R 227 GLN cc_start: 0.7666 (tp40) cc_final: 0.7390 (mm-40) outliers start: 31 outliers final: 25 residues processed: 126 average time/residue: 0.2502 time to fit residues: 43.2335 Evaluate side-chains 127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9615 Z= 0.163 Angle : 0.490 10.510 12967 Z= 0.255 Chirality : 0.040 0.141 1418 Planarity : 0.003 0.044 1638 Dihedral : 5.449 59.880 1448 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.70 % Allowed : 14.10 % Favored : 83.20 % 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: 0.41 (0.25), residues: 1136 helix: 1.84 (0.26), residues: 423 sheet: -0.37 (0.34), residues: 202 loop : -0.78 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 222 TYR 0.009 0.001 TYR R 191 ARG 0.010 0.000 ARG R 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7731 (t80) REVERT: B 70 LEU cc_start: 0.8221 (pp) cc_final: 0.8017 (pp) REVERT: B 118 ASP cc_start: 0.6768 (p0) cc_final: 0.6511 (p0) REVERT: B 219 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7591 (ttm-80) REVERT: R 48 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7724 (mtm) REVERT: R 113 ASP cc_start: 0.3661 (OUTLIER) cc_final: 0.2054 (p0) REVERT: R 213 ARG cc_start: 0.6910 (ttp80) cc_final: 0.6451 (ttp80) REVERT: R 215 ASP cc_start: 0.7056 (p0) cc_final: 0.6483 (p0) REVERT: R 227 GLN cc_start: 0.7694 (tp40) cc_final: 0.7404 (mm-40) outliers start: 27 outliers final: 23 residues processed: 120 average time/residue: 0.2524 time to fit residues: 41.2201 Evaluate side-chains 126 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.193073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142731 restraints weight = 10363.111| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.11 r_work: 0.3420 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9615 Z= 0.169 Angle : 0.495 9.873 12967 Z= 0.258 Chirality : 0.040 0.142 1418 Planarity : 0.003 0.045 1638 Dihedral : 5.469 59.690 1447 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.90 % Allowed : 14.00 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1136 helix: 1.84 (0.26), residues: 423 sheet: -0.39 (0.34), residues: 202 loop : -0.78 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE A 222 TYR 0.010 0.001 TYR R 262 ARG 0.010 0.000 ARG R 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.47 seconds wall clock time: 41 minutes 40.96 seconds (2500.96 seconds total)