Starting phenix.real_space_refine on Fri Feb 14 01:02:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ha0_34585/02_2025/8ha0_34585_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ha0_34585/02_2025/8ha0_34585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ha0_34585/02_2025/8ha0_34585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ha0_34585/02_2025/8ha0_34585.map" model { file = "/net/cci-nas-00/data/ceres_data/8ha0_34585/02_2025/8ha0_34585_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ha0_34585/02_2025/8ha0_34585_neut.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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 60 5.16 5 C 6013 2.51 5 N 1616 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9385 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 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: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 289 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 2947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2947 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 11, 'TRANS': 347} Chain breaks: 4 Chain: "R" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 166 Unusual residues: {'CLR': 4, 'PLM': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 6.13, per 1000 atoms: 0.65 Number of scatterers: 9385 At special positions: 0 Unit cell: (159.856, 114.536, 102.176, 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 60 16.00 O 1696 8.00 N 1616 7.00 C 6013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.08 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.06 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 992.8 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 42.3% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 252 through 278 removed outlier: 4.229A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.560A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.380A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.617A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.775A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.546A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.550A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.652A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 34 removed outlier: 4.128A pdb=" N ASN P 33 " --> pdb=" O GLN P 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 48 removed outlier: 3.778A pdb=" N CYS R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 212 Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.590A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 347 removed outlier: 4.142A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 4.397A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 393 removed outlier: 3.658A pdb=" N GLN R 364 " --> pdb=" O LYS R 360 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 434 through 461 removed outlier: 4.109A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.589A pdb=" N VAL A 224 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG A 35 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 245 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 37 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL A 247 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 39 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASP A 249 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.450A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.507A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.806A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.821A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.989A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.703A 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: 6.400A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.821A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.854A 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 removed outlier: 3.536A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.731A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.555A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 128 through 130 468 hydrogen bonds defined for protein. 1344 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: 2.60 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3009 1.34 - 1.49: 2470 1.49 - 1.63: 4035 1.63 - 1.77: 0 1.77 - 1.92: 86 Bond restraints: 9600 Sorted by residual: bond pdb=" N ASP R 149 " pdb=" CA ASP R 149 " ideal model delta sigma weight residual 1.457 1.559 -0.102 1.29e-02 6.01e+03 6.21e+01 bond pdb=" CA MET R 312 " pdb=" C MET R 312 " ideal model delta sigma weight residual 1.522 1.414 0.108 1.43e-02 4.89e+03 5.69e+01 bond pdb=" CA CYS R 148 " pdb=" CB CYS R 148 " ideal model delta sigma weight residual 1.524 1.620 -0.095 1.30e-02 5.92e+03 5.38e+01 bond pdb=" CA CYS R 148 " pdb=" C CYS R 148 " ideal model delta sigma weight residual 1.530 1.607 -0.076 1.14e-02 7.69e+03 4.50e+01 bond pdb=" N ALA R 313 " pdb=" CA ALA R 313 " ideal model delta sigma weight residual 1.457 1.374 0.084 1.29e-02 6.01e+03 4.19e+01 ... (remaining 9595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 12944 4.80 - 9.61: 48 9.61 - 14.41: 8 14.41 - 19.21: 1 19.21 - 24.01: 1 Bond angle restraints: 13002 Sorted by residual: angle pdb=" N TYR R 320 " pdb=" CA TYR R 320 " pdb=" C TYR R 320 " ideal model delta sigma weight residual 112.30 88.29 24.01 1.36e+00 5.41e-01 3.12e+02 angle pdb=" N LYS R 318 " pdb=" CA LYS R 318 " pdb=" C LYS R 318 " ideal model delta sigma weight residual 113.02 100.05 12.97 1.49e+00 4.50e-01 7.58e+01 angle pdb=" N CYS R 148 " pdb=" CA CYS R 148 " pdb=" C CYS R 148 " ideal model delta sigma weight residual 110.68 99.56 11.12 1.39e+00 5.18e-01 6.40e+01 angle pdb=" C TYR R 320 " pdb=" N LEU R 321 " pdb=" CA LEU R 321 " ideal model delta sigma weight residual 120.54 130.92 -10.38 1.35e+00 5.49e-01 5.91e+01 angle pdb=" N ALA R 313 " pdb=" CA ALA R 313 " pdb=" C ALA R 313 " ideal model delta sigma weight residual 110.80 94.83 15.97 2.13e+00 2.20e-01 5.62e+01 ... (remaining 12997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5385 17.52 - 35.03: 341 35.03 - 52.55: 108 52.55 - 70.06: 40 70.06 - 87.58: 6 Dihedral angle restraints: 5880 sinusoidal: 2519 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS R 108 " pdb=" SG CYS R 108 " pdb=" SG CYS R 148 " pdb=" CB CYS R 148 " ideal model delta sinusoidal sigma weight residual 93.00 142.85 -49.85 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 117 " pdb=" CB CYS R 117 " ideal model delta sinusoidal sigma weight residual 93.00 134.90 -41.90 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" N TYR R 320 " pdb=" C TYR R 320 " pdb=" CA TYR R 320 " pdb=" CB TYR R 320 " ideal model delta harmonic sigma weight residual 122.80 111.03 11.77 0 2.50e+00 1.60e-01 2.21e+01 ... (remaining 5877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1348 0.097 - 0.195: 71 0.195 - 0.292: 10 0.292 - 0.389: 6 0.389 - 0.487: 3 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA LEU R 116 " pdb=" N LEU R 116 " pdb=" C LEU R 116 " pdb=" CB LEU R 116 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA CYS R 460 " pdb=" N CYS R 460 " pdb=" C CYS R 460 " pdb=" CB CYS R 460 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 1435 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 311 " -0.054 2.00e-02 2.50e+03 1.07e-01 1.14e+02 pdb=" C PHE R 311 " 0.184 2.00e-02 2.50e+03 pdb=" O PHE R 311 " -0.072 2.00e-02 2.50e+03 pdb=" N MET R 312 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 114 " -0.029 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C HIS R 114 " 0.100 2.00e-02 2.50e+03 pdb=" O HIS R 114 " -0.038 2.00e-02 2.50e+03 pdb=" N ILE R 115 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 109 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO R 110 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO R 110 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO R 110 " 0.060 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 19 2.33 - 2.97: 4675 2.97 - 3.62: 13823 3.62 - 4.26: 21858 4.26 - 4.90: 36817 Nonbonded interactions: 77192 Sorted by model distance: nonbonded pdb=" O PRO R 110 " pdb=" CZ3 TRP R 154 " model vdw 1.689 3.340 nonbonded pdb=" O PRO R 110 " pdb=" CH2 TRP R 154 " model vdw 1.747 3.340 nonbonded pdb=" SD MET R 189 " pdb=" C2 CLR R1504 " model vdw 1.936 3.040 nonbonded pdb=" N TYR R 320 " pdb=" N LEU R 321 " model vdw 2.091 2.560 nonbonded pdb=" C LYS R 50 " pdb=" CD LYS R 50 " model vdw 2.097 3.670 ... (remaining 77187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.230 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.005 0.109 9600 Z= 0.329 Angle : 0.783 24.015 13002 Z= 0.488 Chirality : 0.053 0.487 1438 Planarity : 0.005 0.117 1626 Dihedral : 13.582 87.580 3696 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.62 % Allowed : 2.21 % Favored : 97.18 % Rotamer: Outliers : 4.53 % Allowed : 5.14 % Favored : 90.33 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1133 helix: 0.83 (0.24), residues: 455 sheet: -0.57 (0.31), residues: 216 loop : -1.69 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 118 HIS 0.008 0.001 HIS P 14 PHE 0.017 0.001 PHE R 335 TYR 0.018 0.001 TYR R 191 ARG 0.010 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7478 (tp40) cc_final: 0.7131 (tp40) REVERT: A 344 GLU cc_start: 0.7261 (tp30) cc_final: 0.6822 (tp30) REVERT: A 381 ASP cc_start: 0.8332 (t0) cc_final: 0.8124 (t70) REVERT: B 16 ASN cc_start: 0.7864 (m-40) cc_final: 0.7541 (m110) REVERT: B 137 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7357 (tpp-160) REVERT: B 156 GLN cc_start: 0.8213 (mt0) cc_final: 0.7981 (mt0) REVERT: B 334 SER cc_start: 0.8030 (m) cc_final: 0.7711 (p) REVERT: B 340 ASN cc_start: 0.7953 (t0) cc_final: 0.7744 (t0) REVERT: R 40 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7053 (tt) REVERT: R 112 TRP cc_start: -0.0842 (OUTLIER) cc_final: -0.3361 (m100) outliers start: 45 outliers final: 22 residues processed: 280 average time/residue: 1.3717 time to fit residues: 408.5801 Evaluate side-chains 221 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 108 CYS Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 146 ARG Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 154 TRP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 13 GLN B 36 ASN B 268 ASN B 311 HIS P 6 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.142039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117824 restraints weight = 12988.228| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.70 r_work: 0.3451 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 9600 Z= 0.258 Angle : 0.593 7.194 13002 Z= 0.312 Chirality : 0.043 0.174 1438 Planarity : 0.005 0.097 1626 Dihedral : 9.692 59.649 1636 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 4.43 % Allowed : 13.39 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1133 helix: 2.27 (0.24), residues: 449 sheet: 0.10 (0.33), residues: 224 loop : -1.18 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.002 HIS B 91 PHE 0.032 0.002 PHE R 311 TYR 0.021 0.002 TYR R 191 ARG 0.007 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7786 (ttt-90) REVERT: A 39 LEU cc_start: 0.8337 (mt) cc_final: 0.8067 (mp) REVERT: A 210 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 230 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: A 274 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8336 (ttpp) REVERT: A 344 GLU cc_start: 0.8164 (tp30) cc_final: 0.7803 (tp30) REVERT: B 74 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8277 (p) REVERT: B 76 ASP cc_start: 0.8309 (p0) cc_final: 0.7967 (p0) REVERT: B 137 ARG cc_start: 0.7988 (tpp-160) cc_final: 0.7629 (tpp-160) REVERT: B 333 ASP cc_start: 0.8084 (p0) cc_final: 0.7876 (p0) REVERT: N 52 SER cc_start: 0.8383 (t) cc_final: 0.8136 (m) REVERT: R 112 TRP cc_start: -0.0627 (OUTLIER) cc_final: -0.4054 (m100) REVERT: R 154 TRP cc_start: 0.5702 (OUTLIER) cc_final: 0.5188 (m100) REVERT: R 450 PHE cc_start: 0.8080 (m-80) cc_final: 0.7871 (m-80) REVERT: R 469 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7614 (mm-30) outliers start: 44 outliers final: 27 residues processed: 221 average time/residue: 1.3024 time to fit residues: 307.5768 Evaluate side-chains 209 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 154 TRP Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 460 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 16 ASN B 220 GLN B 340 ASN R 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115513 restraints weight = 13014.944| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.68 r_work: 0.3420 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9600 Z= 0.255 Angle : 0.556 6.682 13002 Z= 0.294 Chirality : 0.042 0.198 1438 Planarity : 0.005 0.096 1626 Dihedral : 8.617 59.067 1618 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.82 % Rotamer: Outliers : 4.63 % Allowed : 15.11 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1133 helix: 2.71 (0.24), residues: 448 sheet: 0.30 (0.33), residues: 224 loop : -1.07 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.022 0.002 PHE R 311 TYR 0.022 0.002 TYR R 191 ARG 0.008 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7908 (mtpm) REVERT: A 26 ASP cc_start: 0.7872 (m-30) cc_final: 0.7623 (m-30) REVERT: A 39 LEU cc_start: 0.8307 (mt) cc_final: 0.8049 (mp) REVERT: A 230 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: A 275 SER cc_start: 0.8675 (t) cc_final: 0.8462 (m) REVERT: A 276 ILE cc_start: 0.8603 (mt) cc_final: 0.8400 (mp) REVERT: A 344 GLU cc_start: 0.8135 (tp30) cc_final: 0.7783 (tp30) REVERT: A 370 GLU cc_start: 0.6790 (tt0) cc_final: 0.6472 (tm-30) REVERT: B 22 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8191 (mtt180) REVERT: B 74 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8267 (p) REVERT: B 76 ASP cc_start: 0.8356 (p0) cc_final: 0.7902 (p0) REVERT: B 137 ARG cc_start: 0.7914 (tpp-160) cc_final: 0.7664 (tpp-160) REVERT: N 31 ASN cc_start: 0.8385 (m-40) cc_final: 0.8133 (m110) REVERT: R 36 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.4989 (mt-10) REVERT: R 112 TRP cc_start: -0.0588 (OUTLIER) cc_final: -0.4314 (m100) outliers start: 46 outliers final: 26 residues processed: 198 average time/residue: 1.4725 time to fit residues: 308.2481 Evaluate side-chains 188 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 36 GLU Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 77 ASN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113736 restraints weight = 12855.353| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.68 r_work: 0.3387 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9600 Z= 0.342 Angle : 0.590 6.297 13002 Z= 0.312 Chirality : 0.044 0.181 1438 Planarity : 0.005 0.097 1626 Dihedral : 8.212 59.568 1609 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.35 % Favored : 96.29 % Rotamer: Outliers : 4.63 % Allowed : 15.31 % Favored : 80.06 % 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: 1.15 (0.25), residues: 1133 helix: 2.69 (0.24), residues: 448 sheet: 0.36 (0.33), residues: 221 loop : -1.02 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.025 0.002 PHE R 311 TYR 0.023 0.002 TYR R 191 ARG 0.007 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7851 (m-30) cc_final: 0.7629 (m-30) REVERT: A 39 LEU cc_start: 0.8479 (mt) cc_final: 0.8236 (mp) REVERT: A 230 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: A 275 SER cc_start: 0.8686 (t) cc_final: 0.8479 (m) REVERT: A 293 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8452 (mtpt) REVERT: A 344 GLU cc_start: 0.8158 (tp30) cc_final: 0.7876 (tp30) REVERT: A 370 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: B 22 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8150 (mtt180) REVERT: B 137 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.7624 (tpp-160) REVERT: B 325 MET cc_start: 0.8384 (mmm) cc_final: 0.8114 (mmt) REVERT: R 36 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5118 (mt-10) REVERT: R 112 TRP cc_start: -0.0076 (OUTLIER) cc_final: -0.4466 (m100) outliers start: 46 outliers final: 30 residues processed: 200 average time/residue: 1.5964 time to fit residues: 336.3687 Evaluate side-chains 200 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 36 GLU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115249 restraints weight = 12736.497| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.70 r_work: 0.3407 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9600 Z= 0.244 Angle : 0.538 6.000 13002 Z= 0.285 Chirality : 0.042 0.173 1438 Planarity : 0.005 0.094 1626 Dihedral : 7.920 58.689 1609 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.00 % Favored : 96.65 % Rotamer: Outliers : 4.63 % Allowed : 16.92 % Favored : 78.45 % 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 (0.25), residues: 1133 helix: 2.83 (0.24), residues: 450 sheet: 0.50 (0.34), residues: 220 loop : -0.96 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8053 (ttt-90) cc_final: 0.7810 (ttt-90) REVERT: A 39 LEU cc_start: 0.8439 (mt) cc_final: 0.8198 (mp) REVERT: A 230 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: A 275 SER cc_start: 0.8687 (t) cc_final: 0.8457 (m) REVERT: A 344 GLU cc_start: 0.8093 (tp30) cc_final: 0.7787 (tp30) REVERT: A 370 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: B 22 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8135 (mtt-85) REVERT: B 137 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.7631 (tpp-160) REVERT: B 325 MET cc_start: 0.8358 (mmm) cc_final: 0.7980 (mmt) REVERT: R 40 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7284 (tt) REVERT: R 112 TRP cc_start: -0.0232 (OUTLIER) cc_final: -0.4515 (m100) REVERT: R 214 ARG cc_start: 0.7718 (ttt180) cc_final: 0.7469 (ttt180) outliers start: 46 outliers final: 29 residues processed: 195 average time/residue: 1.6386 time to fit residues: 336.7690 Evaluate side-chains 192 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 ASN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114616 restraints weight = 12767.052| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.69 r_work: 0.3403 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9600 Z= 0.276 Angle : 0.550 6.046 13002 Z= 0.291 Chirality : 0.042 0.177 1438 Planarity : 0.005 0.093 1626 Dihedral : 7.816 59.493 1609 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 4.43 % Allowed : 17.02 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1133 helix: 2.85 (0.24), residues: 450 sheet: 0.45 (0.34), residues: 220 loop : -0.91 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8067 (ttt-90) cc_final: 0.7815 (ttt-90) REVERT: A 39 LEU cc_start: 0.8452 (mt) cc_final: 0.8224 (mp) REVERT: A 227 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8086 (tp40) REVERT: A 230 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: A 275 SER cc_start: 0.8697 (t) cc_final: 0.8481 (m) REVERT: A 344 GLU cc_start: 0.8109 (tp30) cc_final: 0.7811 (tp30) REVERT: A 370 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: B 22 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8156 (mtt180) REVERT: B 137 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7713 (tpp-160) REVERT: B 325 MET cc_start: 0.8419 (mmm) cc_final: 0.8142 (mmt) REVERT: R 40 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7257 (tt) REVERT: R 112 TRP cc_start: -0.0228 (OUTLIER) cc_final: -0.4435 (m100) REVERT: R 214 ARG cc_start: 0.7767 (ttt180) cc_final: 0.7550 (ttt180) outliers start: 44 outliers final: 32 residues processed: 198 average time/residue: 1.6670 time to fit residues: 346.9914 Evaluate side-chains 199 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114665 restraints weight = 12822.609| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.68 r_work: 0.3406 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9600 Z= 0.257 Angle : 0.541 6.197 13002 Z= 0.287 Chirality : 0.042 0.177 1438 Planarity : 0.005 0.093 1626 Dihedral : 7.361 56.305 1603 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.82 % Rotamer: Outliers : 4.03 % Allowed : 17.82 % Favored : 78.15 % 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: 1.40 (0.26), residues: 1133 helix: 2.90 (0.24), residues: 450 sheet: 0.46 (0.34), residues: 220 loop : -0.88 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 47 HIS 0.005 0.001 HIS P 14 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8051 (ttt-90) cc_final: 0.7794 (ttt-90) REVERT: A 39 LEU cc_start: 0.8439 (mt) cc_final: 0.8213 (mp) REVERT: A 227 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8020 (tp40) REVERT: A 230 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: A 231 ARG cc_start: 0.8546 (ptp-170) cc_final: 0.8199 (ptt180) REVERT: A 275 SER cc_start: 0.8698 (t) cc_final: 0.8475 (m) REVERT: A 344 GLU cc_start: 0.8067 (tp30) cc_final: 0.7776 (tp30) REVERT: A 370 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6448 (tm-30) REVERT: B 137 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.7634 (tpp-160) REVERT: B 325 MET cc_start: 0.8380 (mmm) cc_final: 0.8041 (mmt) REVERT: R 40 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7308 (tt) REVERT: R 112 TRP cc_start: -0.0245 (OUTLIER) cc_final: -0.4364 (m100) REVERT: R 214 ARG cc_start: 0.7772 (ttt180) cc_final: 0.7557 (ttt180) outliers start: 40 outliers final: 31 residues processed: 192 average time/residue: 1.6542 time to fit residues: 334.3355 Evaluate side-chains 203 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 0.0000 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 ASN R 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.140802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115986 restraints weight = 12923.737| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.71 r_work: 0.3423 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9600 Z= 0.192 Angle : 0.514 5.965 13002 Z= 0.272 Chirality : 0.040 0.180 1438 Planarity : 0.005 0.093 1626 Dihedral : 7.100 56.345 1602 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.00 % Favored : 96.65 % Rotamer: Outliers : 3.73 % Allowed : 18.13 % Favored : 78.15 % 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: 1.55 (0.26), residues: 1133 helix: 3.02 (0.24), residues: 453 sheet: 0.52 (0.34), residues: 220 loop : -0.81 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS P 14 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8000 (ttt-90) cc_final: 0.7747 (ttt-90) REVERT: A 39 LEU cc_start: 0.8350 (mt) cc_final: 0.8102 (mp) REVERT: A 227 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7973 (tp40) REVERT: A 230 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: A 231 ARG cc_start: 0.8516 (ptp-170) cc_final: 0.8117 (ptt90) REVERT: A 275 SER cc_start: 0.8696 (t) cc_final: 0.8467 (m) REVERT: A 344 GLU cc_start: 0.8058 (tp30) cc_final: 0.7749 (tp30) REVERT: A 370 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: B 137 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7660 (tpp-160) REVERT: B 325 MET cc_start: 0.8346 (mmm) cc_final: 0.8077 (mmt) REVERT: P 19 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: R 40 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7327 (tt) REVERT: R 112 TRP cc_start: -0.0380 (OUTLIER) cc_final: -0.4408 (m100) REVERT: R 214 ARG cc_start: 0.7816 (ttt180) cc_final: 0.7615 (ttt180) outliers start: 37 outliers final: 28 residues processed: 188 average time/residue: 1.7105 time to fit residues: 337.8561 Evaluate side-chains 193 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 GLU Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 39 PHE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 96 optimal weight: 0.0060 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115909 restraints weight = 12750.930| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.69 r_work: 0.3417 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9600 Z= 0.224 Angle : 0.527 6.324 13002 Z= 0.279 Chirality : 0.041 0.183 1438 Planarity : 0.005 0.094 1626 Dihedral : 7.054 56.623 1602 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.27 % Favored : 96.38 % Rotamer: Outliers : 3.63 % Allowed : 18.63 % Favored : 77.74 % 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: 1.55 (0.26), residues: 1133 helix: 3.06 (0.24), residues: 450 sheet: 0.52 (0.34), residues: 220 loop : -0.83 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7749 (ttt-90) REVERT: A 39 LEU cc_start: 0.8338 (mt) cc_final: 0.8095 (mp) REVERT: A 227 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7916 (tp40) REVERT: A 230 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 232 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8141 (ptt180) REVERT: A 275 SER cc_start: 0.8679 (t) cc_final: 0.8467 (m) REVERT: A 344 GLU cc_start: 0.8076 (tp30) cc_final: 0.7768 (tp30) REVERT: A 370 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: B 137 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7664 (tpp-160) REVERT: B 325 MET cc_start: 0.8335 (mmm) cc_final: 0.8017 (mmt) REVERT: R 40 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7321 (tt) REVERT: R 112 TRP cc_start: -0.0420 (OUTLIER) cc_final: -0.4391 (m100) outliers start: 36 outliers final: 27 residues processed: 201 average time/residue: 1.7292 time to fit residues: 365.5747 Evaluate side-chains 209 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 218 ASN A 220 HIS A 236 GLN A 294 GLN A 390 GLN B 340 ASN R 143 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.140348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115436 restraints weight = 12973.573| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.72 r_work: 0.3410 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9600 Z= 0.230 Angle : 0.537 6.526 13002 Z= 0.283 Chirality : 0.041 0.186 1438 Planarity : 0.005 0.094 1626 Dihedral : 6.911 57.220 1598 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.09 % Favored : 96.56 % Rotamer: Outliers : 3.42 % Allowed : 18.93 % Favored : 77.64 % 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: 1.55 (0.26), residues: 1133 helix: 3.06 (0.24), residues: 450 sheet: 0.50 (0.35), residues: 220 loop : -0.82 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS P 14 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.010 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8003 (ttt-90) cc_final: 0.7752 (ttt-90) REVERT: A 21 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7910 (mtpm) REVERT: A 39 LEU cc_start: 0.8377 (mt) cc_final: 0.8147 (mp) REVERT: A 227 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6575 (mp10) REVERT: A 230 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: A 231 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8243 (ptt180) REVERT: A 232 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8152 (ptt90) REVERT: A 275 SER cc_start: 0.8678 (t) cc_final: 0.8471 (m) REVERT: A 344 GLU cc_start: 0.8085 (tp30) cc_final: 0.7797 (tp30) REVERT: A 370 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: B 137 ARG cc_start: 0.7936 (tpp-160) cc_final: 0.7668 (tpp-160) REVERT: B 325 MET cc_start: 0.8370 (mmm) cc_final: 0.8103 (mmt) REVERT: P 19 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: R 112 TRP cc_start: -0.0489 (OUTLIER) cc_final: -0.4322 (m100) outliers start: 34 outliers final: 27 residues processed: 198 average time/residue: 1.6917 time to fit residues: 352.1669 Evaluate side-chains 208 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 GLU Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 218 ASN A 220 HIS A 236 GLN A 294 GLN A 390 GLN B 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.140505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115695 restraints weight = 12789.061| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.70 r_work: 0.3414 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9600 Z= 0.223 Angle : 0.536 6.944 13002 Z= 0.284 Chirality : 0.041 0.185 1438 Planarity : 0.005 0.095 1626 Dihedral : 6.860 59.961 1598 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.27 % Favored : 96.47 % Rotamer: Outliers : 3.73 % Allowed : 18.53 % Favored : 77.74 % 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: 1.60 (0.26), residues: 1133 helix: 3.07 (0.24), residues: 450 sheet: 0.54 (0.36), residues: 217 loop : -0.75 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 118 HIS 0.004 0.001 HIS A 357 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.010 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9621.15 seconds wall clock time: 169 minutes 51.67 seconds (10191.67 seconds total)