Starting phenix.real_space_refine on Fri Nov 15 01:49:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yut_39582/11_2024/8yut_39582.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yut_39582/11_2024/8yut_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yut_39582/11_2024/8yut_39582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yut_39582/11_2024/8yut_39582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yut_39582/11_2024/8yut_39582.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yut_39582/11_2024/8yut_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-5513/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: 4.95, per 1000 atoms: 0.60 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 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: 0.86 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: 2.21 Time building geometry restraints manager: 2.53 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: 0.710 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.310 ------------------------------------------------------------------------------- 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 : 0.797 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: 1.2056 time to fit residues: 207.6948 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 : 0.911 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.834 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6968 (mtmt) cc_final: 0.6704 (mmmt) REVERT: A 232 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7851 (ptp90) REVERT: B 186 ASP cc_start: 0.7710 (m-30) cc_final: 0.7335 (m-30) REVERT: B 217 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6672 (mmp) REVERT: G 21 MET cc_start: 0.6077 (ttp) cc_final: 0.5665 (tmt) REVERT: N 4 LEU cc_start: 0.8065 (mt) cc_final: 0.7727 (mt) REVERT: N 25 SER cc_start: 0.7097 (OUTLIER) cc_final: 0.6894 (p) REVERT: N 110 VAL cc_start: 0.8461 (t) cc_final: 0.8165 (m) REVERT: R 122 ASP cc_start: 0.7877 (p0) cc_final: 0.7425 (p0) outliers start: 23 outliers final: 9 residues processed: 125 average time/residue: 1.1637 time to fit residues: 155.4785 Evaluate side-chains 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8388 Z= 0.186 Angle : 0.517 8.428 11373 Z= 0.278 Chirality : 0.042 0.232 1301 Planarity : 0.003 0.044 1443 Dihedral : 4.652 45.074 1207 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.58 % Allowed : 10.44 % 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: 1.72 (0.26), residues: 1025 helix: 2.36 (0.25), residues: 414 sheet: 1.21 (0.35), residues: 194 loop : -0.13 (0.29), residues: 417 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 0.015 0.002 TYR B 105 ARG 0.004 0.000 ARG A 232 *********************** 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 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6979 (mtmt) cc_final: 0.6669 (mmmt) REVERT: A 230 GLU cc_start: 0.8078 (mt-10) cc_final: 0.6505 (tt0) REVERT: A 232 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7932 (ptp90) REVERT: B 78 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8461 (tppt) REVERT: G 21 MET cc_start: 0.6147 (ttp) cc_final: 0.5651 (tmt) REVERT: N 25 SER cc_start: 0.7570 (OUTLIER) cc_final: 0.7368 (p) REVERT: N 110 VAL cc_start: 0.8533 (t) cc_final: 0.8304 (m) REVERT: R 122 ASP cc_start: 0.7858 (p0) cc_final: 0.7413 (p0) REVERT: R 201 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7637 (m) outliers start: 23 outliers final: 10 residues processed: 124 average time/residue: 1.1497 time to fit residues: 152.7431 Evaluate side-chains 112 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 0.0170 chunk 92 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2854 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= 0.127 Angle : 0.471 11.661 11373 Z= 0.249 Chirality : 0.041 0.273 1301 Planarity : 0.003 0.042 1443 Dihedral : 4.373 47.160 1207 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.81 % Allowed : 12.01 % Favored : 85.19 % 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: 2.02 (0.26), residues: 1025 helix: 2.65 (0.25), residues: 410 sheet: 1.32 (0.35), residues: 201 loop : 0.03 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.010 0.001 TYR N 80 ARG 0.007 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 123 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8020 (mt-10) cc_final: 0.6491 (tt0) REVERT: B 59 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 78 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8323 (tppt) REVERT: G 21 MET cc_start: 0.6163 (ttp) cc_final: 0.5674 (tmt) REVERT: R 122 ASP cc_start: 0.7871 (p0) cc_final: 0.7441 (p0) REVERT: R 201 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7590 (m) outliers start: 25 outliers final: 7 residues processed: 111 average time/residue: 1.1764 time to fit residues: 139.8818 Evaluate side-chains 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 chunk 40 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8388 Z= 0.162 Angle : 0.501 13.704 11373 Z= 0.264 Chirality : 0.041 0.200 1301 Planarity : 0.003 0.041 1443 Dihedral : 4.568 45.967 1207 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.69 % Allowed : 11.90 % Favored : 85.41 % 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: 2.04 (0.26), residues: 1025 helix: 2.74 (0.25), residues: 410 sheet: 1.20 (0.35), residues: 203 loop : 0.02 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 275 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR R 126 ARG 0.004 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 121 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5647 (OUTLIER) cc_final: 0.5267 (p0) REVERT: A 230 GLU cc_start: 0.8144 (mt-10) cc_final: 0.6536 (tt0) REVERT: B 45 MET cc_start: 0.8227 (mtt) cc_final: 0.7774 (mtt) REVERT: B 78 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8398 (tppt) REVERT: G 21 MET cc_start: 0.6045 (ttp) cc_final: 0.5558 (tmt) REVERT: R 122 ASP cc_start: 0.7875 (p0) cc_final: 0.7421 (p0) REVERT: R 201 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7711 (m) outliers start: 24 outliers final: 13 residues processed: 110 average time/residue: 1.0675 time to fit residues: 126.1226 Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 352 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 205 ASP 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 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 201 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 87 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8388 Z= 0.159 Angle : 0.502 13.432 11373 Z= 0.262 Chirality : 0.042 0.308 1301 Planarity : 0.003 0.042 1443 Dihedral : 4.537 45.587 1207 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 2.01 (0.26), residues: 1025 helix: 2.73 (0.25), residues: 415 sheet: 1.19 (0.34), residues: 206 loop : -0.07 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR B 105 ARG 0.004 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: 26 poor density : 95 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5586 (OUTLIER) cc_final: 0.5266 (p0) REVERT: A 230 GLU cc_start: 0.8131 (mt-10) cc_final: 0.6732 (tm-30) REVERT: A 268 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: B 45 MET cc_start: 0.8217 (mtt) cc_final: 0.7701 (mtt) REVERT: B 59 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 78 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8431 (tppt) REVERT: G 21 MET cc_start: 0.6251 (ttp) cc_final: 0.5569 (tmt) REVERT: R 122 ASP cc_start: 0.7874 (p0) cc_final: 0.7421 (p0) REVERT: R 201 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7708 (m) outliers start: 26 outliers final: 14 residues processed: 110 average time/residue: 1.0716 time to fit residues: 127.0077 Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 268 GLU Chi-restraints excluded: chain A residue 352 SER 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 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 28 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 201 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 11 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8388 Z= 0.284 Angle : 0.591 13.388 11373 Z= 0.310 Chirality : 0.044 0.280 1301 Planarity : 0.004 0.044 1443 Dihedral : 5.017 45.321 1207 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.25 % Allowed : 11.78 % Favored : 84.96 % 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: 1.85 (0.26), residues: 1025 helix: 2.62 (0.25), residues: 410 sheet: 0.98 (0.34), residues: 211 loop : -0.08 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 275 HIS 0.006 0.001 HIS B 225 PHE 0.018 0.002 PHE B 234 TYR 0.018 0.002 TYR N 117 ARG 0.003 0.000 ARG A 317 *********************** 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 131 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7008 (mtmt) cc_final: 0.6694 (mmmt) REVERT: A 229 ASP cc_start: 0.5562 (OUTLIER) cc_final: 0.5222 (p0) REVERT: A 230 GLU cc_start: 0.8225 (mt-10) cc_final: 0.6715 (tt0) REVERT: B 59 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: B 78 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8659 (tppt) REVERT: G 21 MET cc_start: 0.6082 (ttp) cc_final: 0.5645 (tmt) REVERT: N 3 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6899 (pp30) REVERT: R 122 ASP cc_start: 0.7977 (p0) cc_final: 0.7476 (p0) outliers start: 29 outliers final: 18 residues processed: 117 average time/residue: 1.0163 time to fit residues: 128.4062 Evaluate side-chains 118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 224 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 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 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 3 GLN 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 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 0.0060 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3396 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= 0.151 Angle : 0.502 14.117 11373 Z= 0.261 Chirality : 0.042 0.335 1301 Planarity : 0.003 0.043 1443 Dihedral : 4.633 47.150 1207 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.13 % Allowed : 13.47 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.10 % 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: 1.96 (0.26), residues: 1025 helix: 2.78 (0.25), residues: 405 sheet: 0.95 (0.35), residues: 216 loop : -0.02 (0.30), residues: 404 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 0.017 0.001 PHE B 234 TYR 0.011 0.001 TYR N 80 ARG 0.004 0.000 ARG A 317 *********************** 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 117 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5544 (OUTLIER) cc_final: 0.5206 (p0) REVERT: A 230 GLU cc_start: 0.8262 (mt-10) cc_final: 0.6884 (tm-30) REVERT: A 392 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 45 MET cc_start: 0.8241 (mtt) cc_final: 0.7807 (mtt) REVERT: B 59 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: B 78 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8511 (tppt) REVERT: G 21 MET cc_start: 0.6175 (ttp) cc_final: 0.5534 (tmt) REVERT: R 122 ASP cc_start: 0.7909 (p0) cc_final: 0.7438 (p0) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 1.0849 time to fit residues: 123.7722 Evaluate side-chains 111 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 28 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 121 MET 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 90 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8388 Z= 0.163 Angle : 0.509 13.885 11373 Z= 0.265 Chirality : 0.042 0.314 1301 Planarity : 0.003 0.042 1443 Dihedral : 4.608 45.302 1207 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.13 % Allowed : 13.58 % 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: 1.95 (0.26), residues: 1025 helix: 2.84 (0.25), residues: 405 sheet: 0.91 (0.35), residues: 216 loop : -0.09 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.016 0.002 PHE B 234 TYR 0.012 0.001 TYR N 80 ARG 0.003 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 115 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5545 (OUTLIER) cc_final: 0.5217 (p0) REVERT: A 230 GLU cc_start: 0.8246 (mt-10) cc_final: 0.6723 (tt0) REVERT: A 392 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 59 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: B 268 ASN cc_start: 0.8343 (p0) cc_final: 0.8073 (p0) REVERT: G 21 MET cc_start: 0.6218 (ttp) cc_final: 0.5687 (tmt) REVERT: R 122 ASP cc_start: 0.7897 (p0) cc_final: 0.7422 (p0) outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 1.0958 time to fit residues: 123.6395 Evaluate side-chains 109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 121 MET Chi-restraints excluded: chain R residue 141 LEU 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 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8388 Z= 0.152 Angle : 0.500 14.176 11373 Z= 0.260 Chirality : 0.042 0.298 1301 Planarity : 0.003 0.042 1443 Dihedral : 4.524 44.128 1207 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.13 % Allowed : 13.80 % Favored : 84.06 % 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: 1.98 (0.26), residues: 1025 helix: 2.90 (0.25), residues: 404 sheet: 0.92 (0.35), residues: 216 loop : -0.10 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE B 234 TYR 0.013 0.001 TYR N 80 ARG 0.003 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 114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5242 (p0) REVERT: A 230 GLU cc_start: 0.8243 (mt-10) cc_final: 0.6712 (tt0) REVERT: A 392 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 59 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 78 LYS cc_start: 0.8634 (tppt) cc_final: 0.8429 (tppt) REVERT: B 267 ASP cc_start: 0.7959 (m-30) cc_final: 0.7642 (m-30) REVERT: G 21 MET cc_start: 0.6189 (ttp) cc_final: 0.5634 (tmt) REVERT: R 122 ASP cc_start: 0.7883 (p0) cc_final: 0.7410 (p0) outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 1.0763 time to fit residues: 120.4723 Evaluate side-chains 110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 121 MET Chi-restraints excluded: chain R residue 141 LEU 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 73 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 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 = 0.4141 r_free = 0.4141 target = 0.189225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148273 restraints weight = 8413.250| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.97 r_work: 0.3549 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8388 Z= 0.152 Angle : 0.498 13.897 11373 Z= 0.259 Chirality : 0.042 0.291 1301 Planarity : 0.003 0.042 1443 Dihedral : 4.485 41.819 1207 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.02 % Allowed : 13.47 % Favored : 84.51 % 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: 2.01 (0.26), residues: 1025 helix: 2.93 (0.25), residues: 405 sheet: 0.93 (0.35), residues: 216 loop : -0.09 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE B 234 TYR 0.012 0.001 TYR N 80 ARG 0.003 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3055.14 seconds wall clock time: 55 minutes 3.81 seconds (3303.81 seconds total)