Starting phenix.real_space_refine on Wed Jan 15 05:21:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yut_39582/01_2025/8yut_39582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yut_39582/01_2025/8yut_39582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yut_39582/01_2025/8yut_39582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yut_39582/01_2025/8yut_39582.map" model { file = "/net/cci-nas-00/data/ceres_data/8yut_39582/01_2025/8yut_39582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yut_39582/01_2025/8yut_39582.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 55 5.16 5 C 5212 2.51 5 N 1440 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8229 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1891 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2302 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 285} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'A1D67': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.07, per 1000 atoms: 0.62 Number of scatterers: 8229 At special positions: 0 Unit cell: (86.19, 117.624, 116.61, 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 55 16.00 O 1522 8.00 N 1440 7.00 C 5212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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=2.02 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 174 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 43.7% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 4.103A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.887A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.595A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.879A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.862A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (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 7 through 24 removed outlier: 3.513A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.879A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.705A 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 87 through 91 removed outlier: 4.102A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 46 Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 54 through 71 Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.750A pdb=" N ILE R 77 " --> pdb=" O PRO R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 122 removed outlier: 3.877A pdb=" N ILE R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP R 122 " --> pdb=" O CYS R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 130 Processing helix chain 'R' and resid 131 through 151 Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 220 removed outlier: 3.892A pdb=" N SER R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 261 removed outlier: 3.500A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE R 243 " --> pdb=" O VAL R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 262 through 265 Processing helix chain 'R' and resid 266 through 280 removed outlier: 3.703A pdb=" N ASN R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 Processing helix chain 'R' and resid 292 through 305 removed outlier: 4.439A pdb=" N PHE R 303 " --> pdb=" O TYR R 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.149A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.547A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.695A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.968A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.085A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.796A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.637A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.734A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.501A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1248 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: 2.41 Time building geometry restraints manager: 2.69 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: 1633 1.33 - 1.45: 2032 1.45 - 1.57: 4645 1.57 - 1.69: 4 1.69 - 1.81: 74 Bond restraints: 8388 Sorted by residual: bond pdb=" C06 A1D67 R 401 " pdb=" S01 A1D67 R 401 " ideal model delta sigma weight residual 1.746 1.509 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C10 A1D67 R 401 " pdb=" S01 A1D67 R 401 " ideal model delta sigma weight residual 1.740 1.536 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C08 A1D67 R 401 " pdb=" N02 A1D67 R 401 " ideal model delta sigma weight residual 1.377 1.567 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" C15 CLR R 402 " pdb=" C16 CLR R 402 " ideal model delta sigma weight residual 1.541 1.696 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C11 CLR R 402 " pdb=" C9 CLR R 402 " ideal model delta sigma weight residual 1.533 1.681 -0.148 2.00e-02 2.50e+03 5.49e+01 ... (remaining 8383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 11307 3.68 - 7.37: 60 7.37 - 11.05: 5 11.05 - 14.74: 0 14.74 - 18.42: 1 Bond angle restraints: 11373 Sorted by residual: angle pdb=" C06 A1D67 R 401 " pdb=" S01 A1D67 R 401 " pdb=" C10 A1D67 R 401 " ideal model delta sigma weight residual 89.27 107.69 -18.42 3.00e+00 1.11e-01 3.77e+01 angle pdb=" N ILE R 227 " pdb=" CA ILE R 227 " pdb=" C ILE R 227 " ideal model delta sigma weight residual 108.12 115.68 -7.56 1.44e+00 4.82e-01 2.76e+01 angle pdb=" C THR R 235 " pdb=" N LEU R 236 " pdb=" CA LEU R 236 " ideal model delta sigma weight residual 120.28 114.52 5.76 1.34e+00 5.57e-01 1.85e+01 angle pdb=" N ARG R 228 " pdb=" CA ARG R 228 " pdb=" C ARG R 228 " ideal model delta sigma weight residual 108.20 115.37 -7.17 1.71e+00 3.42e-01 1.76e+01 angle pdb=" C MET R 240 " pdb=" N GLY R 241 " pdb=" CA GLY R 241 " ideal model delta sigma weight residual 119.99 124.70 -4.71 1.13e+00 7.83e-01 1.74e+01 ... (remaining 11368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4821 17.69 - 35.39: 194 35.39 - 53.08: 30 53.08 - 70.78: 7 70.78 - 88.47: 6 Dihedral angle restraints: 5058 sinusoidal: 2029 harmonic: 3029 Sorted by residual: dihedral pdb=" CA TYR R 299 " pdb=" C TYR R 299 " pdb=" N GLN R 300 " pdb=" CA GLN R 300 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 241 " pdb=" C PHE B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB CYS R 91 " pdb=" SG CYS R 91 " pdb=" SG CYS R 174 " pdb=" CB CYS R 174 " ideal model delta sinusoidal sigma weight residual 93.00 124.49 -31.49 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 5055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1056 0.063 - 0.125: 187 0.125 - 0.188: 43 0.188 - 0.251: 11 0.251 - 0.313: 4 Chirality restraints: 1301 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA LEU B 318 " pdb=" N LEU B 318 " pdb=" C LEU B 318 " pdb=" CB LEU B 318 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU R 236 " pdb=" N LEU R 236 " pdb=" C LEU R 236 " pdb=" CB LEU R 236 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1298 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 229 " 0.015 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C ASP A 229 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP A 229 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU A 230 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 165 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C SER R 165 " -0.039 2.00e-02 2.50e+03 pdb=" O SER R 165 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS R 166 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 67 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C SER B 67 " 0.034 2.00e-02 2.50e+03 pdb=" O SER B 67 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG B 68 " -0.012 2.00e-02 2.50e+03 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1299 2.76 - 3.30: 7855 3.30 - 3.83: 13572 3.83 - 4.37: 16433 4.37 - 4.90: 28411 Nonbonded interactions: 67570 Sorted by model distance: nonbonded pdb=" OD1 ASN B 340 " pdb=" ND2 ASN G 59 " model vdw 2.231 3.120 nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.258 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP A 368 " pdb=" N THR A 369 " model vdw 2.308 3.120 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.314 3.040 ... (remaining 67565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.410 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.008 0.237 8388 Z= 0.524 Angle : 0.811 18.419 11373 Z= 0.522 Chirality : 0.057 0.313 1301 Planarity : 0.004 0.047 1443 Dihedral : 10.592 88.470 3089 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 1.32 (0.26), residues: 1025 helix: 2.03 (0.26), residues: 399 sheet: 0.72 (0.33), residues: 228 loop : -0.16 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 222 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE N 68 TYR 0.026 0.002 TYR N 115 ARG 0.007 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7004 (mtmt) cc_final: 0.6763 (mmmt) REVERT: A 230 GLU cc_start: 0.6367 (mt-10) cc_final: 0.5506 (tt0) REVERT: A 344 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7523 (tp30) REVERT: A 381 ASP cc_start: 0.7554 (m-30) cc_final: 0.7338 (m-30) REVERT: B 111 TYR cc_start: 0.8402 (m-80) cc_final: 0.8196 (m-80) REVERT: B 188 MET cc_start: 0.8583 (mmm) cc_final: 0.8321 (mmm) REVERT: G 21 MET cc_start: 0.6227 (ttp) cc_final: 0.5778 (tmt) REVERT: N 21 SER cc_start: 0.8658 (t) cc_final: 0.8450 (t) REVERT: N 34 MET cc_start: 0.7460 (mmm) cc_final: 0.7247 (mmm) REVERT: R 198 MET cc_start: 0.8119 (mtp) cc_final: 0.7913 (mtp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.2459 time to fit residues: 214.9800 Evaluate side-chains 103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.191404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150662 restraints weight = 8383.085| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.95 r_work: 0.3572 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8388 Z= 0.186 Angle : 0.538 9.666 11373 Z= 0.291 Chirality : 0.042 0.145 1301 Planarity : 0.004 0.071 1443 Dihedral : 4.947 51.419 1207 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.58 % Allowed : 8.08 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1025 helix: 2.23 (0.25), residues: 410 sheet: 1.10 (0.34), residues: 209 loop : -0.20 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 222 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.002 PHE A 212 TYR 0.015 0.002 TYR B 105 ARG 0.015 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6859 (mtmt) cc_final: 0.6306 (mmmt) REVERT: A 232 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8131 (ptp90) REVERT: B 186 ASP cc_start: 0.8150 (m-30) cc_final: 0.7850 (m-30) REVERT: B 195 ASP cc_start: 0.6982 (p0) cc_final: 0.6730 (p0) REVERT: B 197 ARG cc_start: 0.7332 (mmm160) cc_final: 0.7042 (mmp80) REVERT: B 217 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6163 (mmp) REVERT: B 259 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: B 291 ASP cc_start: 0.6874 (m-30) cc_final: 0.6663 (p0) REVERT: G 21 MET cc_start: 0.6373 (ttp) cc_final: 0.5473 (tmt) REVERT: N 4 LEU cc_start: 0.7884 (mt) cc_final: 0.7577 (mt) REVERT: N 21 SER cc_start: 0.8654 (t) cc_final: 0.8411 (t) REVERT: N 25 SER cc_start: 0.7046 (OUTLIER) cc_final: 0.6757 (p) REVERT: N 110 VAL cc_start: 0.8525 (t) cc_final: 0.8116 (m) REVERT: R 122 ASP cc_start: 0.8275 (p0) cc_final: 0.7800 (p0) outliers start: 23 outliers final: 9 residues processed: 125 average time/residue: 1.1673 time to fit residues: 156.0130 Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 272 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.190628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149661 restraints weight = 8522.461| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.90 r_work: 0.3558 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8388 Z= 0.167 Angle : 0.502 8.308 11373 Z= 0.270 Chirality : 0.042 0.195 1301 Planarity : 0.003 0.044 1443 Dihedral : 4.562 45.033 1207 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.47 % Allowed : 10.55 % Favored : 86.98 % 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: 1.76 (0.26), residues: 1025 helix: 2.41 (0.25), residues: 414 sheet: 1.18 (0.35), residues: 196 loop : -0.10 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 275 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.014 0.001 TYR B 105 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8273 (mt-10) cc_final: 0.6335 (tt0) REVERT: A 232 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8192 (ptp90) REVERT: B 45 MET cc_start: 0.8454 (mtt) cc_final: 0.8073 (mtt) REVERT: B 78 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8512 (tppt) REVERT: B 97 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7924 (t) REVERT: B 259 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: G 21 MET cc_start: 0.6450 (ttp) cc_final: 0.5482 (tmt) REVERT: N 21 SER cc_start: 0.8668 (t) cc_final: 0.8443 (t) REVERT: N 25 SER cc_start: 0.7444 (OUTLIER) cc_final: 0.7162 (p) REVERT: N 110 VAL cc_start: 0.8536 (t) cc_final: 0.8231 (m) REVERT: R 122 ASP cc_start: 0.8327 (p0) cc_final: 0.7850 (p0) REVERT: R 201 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7838 (m) outliers start: 22 outliers final: 9 residues processed: 123 average time/residue: 1.1441 time to fit residues: 150.7973 Evaluate side-chains 110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.185378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145077 restraints weight = 8463.080| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.03 r_work: 0.3506 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.004 0.045 8388 Z= 0.264 Angle : 0.576 9.799 11373 Z= 0.305 Chirality : 0.044 0.280 1301 Planarity : 0.004 0.044 1443 Dihedral : 4.875 46.551 1207 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.15 % Allowed : 11.22 % Favored : 84.62 % 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: 1.76 (0.26), residues: 1025 helix: 2.49 (0.25), residues: 408 sheet: 1.07 (0.34), residues: 199 loop : -0.09 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 275 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.002 PHE N 68 TYR 0.019 0.002 TYR B 105 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6932 (mtmt) cc_final: 0.6342 (mmmt) REVERT: A 229 ASP cc_start: 0.5535 (OUTLIER) cc_final: 0.5186 (p0) REVERT: A 230 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 268 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: B 59 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: B 78 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8654 (tppt) REVERT: B 268 ASN cc_start: 0.7474 (m-40) cc_final: 0.7191 (p0) REVERT: G 21 MET cc_start: 0.6380 (ttp) cc_final: 0.5395 (tmt) REVERT: N 25 SER cc_start: 0.7688 (OUTLIER) cc_final: 0.7467 (p) REVERT: R 122 ASP cc_start: 0.8389 (p0) cc_final: 0.7861 (p0) REVERT: R 171 THR cc_start: 0.6407 (OUTLIER) cc_final: 0.6022 (t) outliers start: 37 outliers final: 16 residues processed: 122 average time/residue: 1.0320 time to fit residues: 135.6498 Evaluate side-chains 116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.188826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147685 restraints weight = 8486.573| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.90 r_work: 0.3540 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 8388 Z= 0.157 Angle : 0.509 14.328 11373 Z= 0.267 Chirality : 0.042 0.291 1301 Planarity : 0.003 0.044 1443 Dihedral : 4.697 47.978 1207 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.92 % Allowed : 12.01 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.87 (0.26), residues: 1025 helix: 2.62 (0.25), residues: 414 sheet: 1.04 (0.34), residues: 209 loop : -0.10 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR N 80 ARG 0.005 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5540 (OUTLIER) cc_final: 0.5239 (p0) REVERT: A 230 GLU cc_start: 0.8385 (mt-10) cc_final: 0.6540 (tm-30) REVERT: B 45 MET cc_start: 0.8527 (mtt) cc_final: 0.8113 (mtt) REVERT: B 59 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: B 78 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8532 (tppt) REVERT: B 217 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7363 (ppp) REVERT: B 259 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: B 268 ASN cc_start: 0.7474 (m-40) cc_final: 0.7177 (p0) REVERT: G 21 MET cc_start: 0.6371 (ttp) cc_final: 0.5382 (tmt) REVERT: R 122 ASP cc_start: 0.8319 (p0) cc_final: 0.7807 (p0) REVERT: R 171 THR cc_start: 0.6365 (OUTLIER) cc_final: 0.5992 (t) outliers start: 26 outliers final: 13 residues processed: 111 average time/residue: 1.1228 time to fit residues: 133.5030 Evaluate side-chains 109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.187921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146413 restraints weight = 8474.904| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.91 r_work: 0.3524 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8388 Z= 0.176 Angle : 0.515 13.632 11373 Z= 0.272 Chirality : 0.042 0.246 1301 Planarity : 0.003 0.043 1443 Dihedral : 4.695 47.255 1207 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.25 % Allowed : 12.01 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.87 (0.26), residues: 1025 helix: 2.63 (0.25), residues: 415 sheet: 1.09 (0.34), residues: 207 loop : -0.15 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.002 PHE A 212 TYR 0.010 0.001 TYR B 105 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5503 (OUTLIER) cc_final: 0.5198 (p0) REVERT: A 230 GLU cc_start: 0.8380 (mt-10) cc_final: 0.6519 (tm-30) REVERT: B 45 MET cc_start: 0.8534 (mtt) cc_final: 0.8116 (mtt) REVERT: B 59 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: B 78 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8584 (tppt) REVERT: B 153 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7519 (p0) REVERT: B 217 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7491 (ppp) REVERT: B 259 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: B 268 ASN cc_start: 0.7474 (m-40) cc_final: 0.7173 (p0) REVERT: G 21 MET cc_start: 0.6431 (ttp) cc_final: 0.5393 (tmt) REVERT: R 122 ASP cc_start: 0.8338 (p0) cc_final: 0.7829 (p0) REVERT: R 171 THR cc_start: 0.6359 (OUTLIER) cc_final: 0.5978 (t) outliers start: 29 outliers final: 16 residues processed: 109 average time/residue: 1.1090 time to fit residues: 129.9369 Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 15 optimal weight: 0.0970 chunk 99 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.181756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142511 restraints weight = 8476.656| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.00 r_work: 0.3469 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8388 Z= 0.408 Angle : 0.676 14.328 11373 Z= 0.353 Chirality : 0.048 0.351 1301 Planarity : 0.005 0.046 1443 Dihedral : 5.378 47.360 1207 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.93 % Allowed : 11.67 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.50 (0.25), residues: 1025 helix: 2.34 (0.25), residues: 409 sheet: 0.87 (0.34), residues: 211 loop : -0.32 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.008 0.002 HIS B 225 PHE 0.022 0.002 PHE N 68 TYR 0.021 0.003 TYR N 117 ARG 0.003 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6939 (mtmt) cc_final: 0.6329 (mmmt) REVERT: A 229 ASP cc_start: 0.5628 (OUTLIER) cc_final: 0.5330 (p0) REVERT: A 230 GLU cc_start: 0.8327 (mt-10) cc_final: 0.6406 (tm-30) REVERT: B 59 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: B 78 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8792 (tppt) REVERT: B 96 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7632 (mtm-85) REVERT: B 219 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6870 (mtm-85) REVERT: B 259 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: B 318 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8295 (mt) REVERT: G 21 MET cc_start: 0.6510 (ttp) cc_final: 0.5569 (tmt) REVERT: R 122 ASP cc_start: 0.8440 (p0) cc_final: 0.7912 (p0) REVERT: R 160 SER cc_start: 0.8110 (m) cc_final: 0.7616 (p) REVERT: R 171 THR cc_start: 0.6357 (OUTLIER) cc_final: 0.5976 (t) outliers start: 35 outliers final: 19 residues processed: 120 average time/residue: 1.0937 time to fit residues: 140.8368 Evaluate side-chains 124 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.187501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146380 restraints weight = 8527.667| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.99 r_work: 0.3525 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8388 Z= 0.161 Angle : 0.520 15.047 11373 Z= 0.272 Chirality : 0.042 0.297 1301 Planarity : 0.003 0.044 1443 Dihedral : 4.831 50.022 1207 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.47 % Allowed : 13.58 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.75 (0.26), residues: 1025 helix: 2.61 (0.25), residues: 411 sheet: 0.93 (0.35), residues: 211 loop : -0.23 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE A 212 TYR 0.013 0.001 TYR N 80 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6894 (mtmt) cc_final: 0.6252 (mmmt) REVERT: A 230 GLU cc_start: 0.8413 (mt-10) cc_final: 0.6518 (tm-30) REVERT: A 342 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7671 (ttp-170) REVERT: B 59 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: B 153 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7542 (p0) REVERT: B 259 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: G 21 MET cc_start: 0.6461 (ttp) cc_final: 0.5542 (tmt) REVERT: R 122 ASP cc_start: 0.8383 (p0) cc_final: 0.7869 (p0) REVERT: R 171 THR cc_start: 0.6252 (OUTLIER) cc_final: 0.5896 (t) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 1.1926 time to fit residues: 145.7423 Evaluate side-chains 115 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.187504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146178 restraints weight = 8543.305| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.94 r_work: 0.3515 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8388 Z= 0.168 Angle : 0.518 14.847 11373 Z= 0.271 Chirality : 0.042 0.276 1301 Planarity : 0.003 0.043 1443 Dihedral : 4.719 47.737 1207 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.47 % Allowed : 13.24 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.78 (0.26), residues: 1025 helix: 2.65 (0.25), residues: 415 sheet: 0.91 (0.35), residues: 211 loop : -0.26 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR N 80 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6869 (mtmt) cc_final: 0.6217 (mmmt) REVERT: A 229 ASP cc_start: 0.5640 (OUTLIER) cc_final: 0.5331 (p0) REVERT: A 230 GLU cc_start: 0.8340 (mt-10) cc_final: 0.6401 (tm-30) REVERT: A 342 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7661 (ttp-170) REVERT: B 59 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: B 96 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7797 (mtm-85) REVERT: B 259 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: G 21 MET cc_start: 0.6359 (ttp) cc_final: 0.5402 (tmt) REVERT: R 122 ASP cc_start: 0.8329 (p0) cc_final: 0.7818 (p0) REVERT: R 171 THR cc_start: 0.6283 (OUTLIER) cc_final: 0.5863 (t) outliers start: 22 outliers final: 15 residues processed: 109 average time/residue: 1.1825 time to fit residues: 137.7846 Evaluate side-chains 116 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 7.9990 chunk 9 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.189711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148552 restraints weight = 8440.334| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.90 r_work: 0.3554 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8388 Z= 0.136 Angle : 0.493 15.173 11373 Z= 0.255 Chirality : 0.042 0.345 1301 Planarity : 0.003 0.043 1443 Dihedral : 4.517 46.937 1207 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.02 % Allowed : 13.69 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 1.93 (0.26), residues: 1025 helix: 2.84 (0.25), residues: 410 sheet: 0.89 (0.35), residues: 216 loop : -0.16 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR N 80 ARG 0.002 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8408 (mt-10) cc_final: 0.6492 (tm-30) REVERT: A 342 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7607 (ttp-170) REVERT: B 45 MET cc_start: 0.8473 (mtt) cc_final: 0.8032 (mtt) REVERT: B 59 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: B 259 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: B 267 ASP cc_start: 0.8205 (m-30) cc_final: 0.7902 (m-30) REVERT: G 21 MET cc_start: 0.6328 (ttp) cc_final: 0.5366 (tmt) REVERT: R 122 ASP cc_start: 0.8279 (p0) cc_final: 0.7790 (p0) REVERT: R 171 THR cc_start: 0.6270 (OUTLIER) cc_final: 0.5910 (t) outliers start: 18 outliers final: 11 residues processed: 107 average time/residue: 1.1973 time to fit residues: 137.0123 Evaluate side-chains 112 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 chunk 41 optimal weight: 0.0070 chunk 32 optimal weight: 0.0670 chunk 85 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.193076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152498 restraints weight = 8614.427| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.85 r_work: 0.3596 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8388 Z= 0.113 Angle : 0.468 15.314 11373 Z= 0.241 Chirality : 0.041 0.326 1301 Planarity : 0.003 0.042 1443 Dihedral : 4.280 43.973 1207 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.57 % Allowed : 14.37 % Favored : 84.06 % 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: 2.17 (0.27), residues: 1025 helix: 3.17 (0.25), residues: 399 sheet: 0.89 (0.36), residues: 215 loop : 0.00 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.002 0.000 HIS B 183 PHE 0.013 0.001 PHE A 212 TYR 0.012 0.001 TYR N 80 ARG 0.002 0.000 ARG R 293 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 6583.56 seconds wall clock time: 116 minutes 10.26 seconds (6970.26 seconds total)