Starting phenix.real_space_refine on Fri Mar 14 04:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ha0_34585/03_2025/8ha0_34585_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ha0_34585/03_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_34585/03_2025/8ha0_34585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ha0_34585/03_2025/8ha0_34585.map" model { file = "/net/cci-nas-00/data/ceres_data/8ha0_34585/03_2025/8ha0_34585_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ha0_34585/03_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-5624/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: 5.97, per 1000 atoms: 0.64 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.38 Time building geometry restraints manager: 3.12 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: 1.690 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- 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 : 0.920 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: 1.2849 time to fit residues: 383.1294 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 : 1.069 ------------------------------------------------------------------------------- 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 = 0.142041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117795 restraints weight = 12988.304| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.71 r_work: 0.3451 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- 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 59.650 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 : 1.037 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: 0.8337 (ttpp) REVERT: A 344 GLU cc_start: 0.8164 (tp30) cc_final: 0.7804 (tp30) REVERT: B 74 SER cc_start: 0.8477 (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: 0.7628 (tpp-160) REVERT: B 333 ASP cc_start: 0.8084 (p0) cc_final: 0.7875 (p0) REVERT: N 52 SER cc_start: 0.8382 (t) cc_final: 0.8135 (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: 0.5189 (m100) REVERT: R 450 PHE cc_start: 0.8080 (m-80) cc_final: 0.7872 (m-80) REVERT: R 469 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7614 (mm-30) outliers start: 44 outliers final: 27 residues processed: 221 average time/residue: 1.2300 time to fit residues: 290.2061 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 : 0.964 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 340 ASN R 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.139282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114728 restraints weight = 12969.291| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.69 r_work: 0.3407 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9600 Z= 0.278 Angle : 0.571 6.810 13002 Z= 0.302 Chirality : 0.043 0.203 1438 Planarity : 0.005 0.096 1626 Dihedral : 8.628 58.900 1618 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.09 % Favored : 96.56 % Rotamer: Outliers : 4.73 % Allowed : 15.11 % Favored : 80.16 % 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: 1.07 (0.25), residues: 1133 helix: 2.67 (0.24), residues: 448 sheet: 0.30 (0.33), residues: 219 loop : -1.09 (0.28), residues: 466 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 0.022 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 220 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7905 (mtpm) REVERT: A 26 ASP cc_start: 0.7884 (m-30) cc_final: 0.7622 (m-30) REVERT: A 39 LEU cc_start: 0.8324 (mt) cc_final: 0.8053 (mp) REVERT: A 230 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: A 276 ILE cc_start: 0.8599 (mt) cc_final: 0.8395 (mp) REVERT: A 344 GLU cc_start: 0.8135 (tp30) cc_final: 0.7802 (tp30) REVERT: A 370 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: B 22 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8176 (mtt180) REVERT: B 74 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 76 ASP cc_start: 0.8378 (p0) cc_final: 0.7915 (p0) REVERT: B 325 MET cc_start: 0.8454 (mmm) cc_final: 0.8129 (mmt) REVERT: R 36 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4997 (mt-10) REVERT: R 112 TRP cc_start: -0.0552 (OUTLIER) cc_final: -0.4308 (m100) REVERT: R 154 TRP cc_start: 0.5492 (OUTLIER) cc_final: 0.5211 (m100) outliers start: 47 outliers final: 27 residues processed: 207 average time/residue: 1.7747 time to fit residues: 387.1788 Evaluate side-chains 200 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 A residue 370 GLU 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 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 154 TRP 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: 0.5980 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: 0.9980 chunk 84 optimal weight: 0.0060 chunk 109 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 220 GLN N 31 ASN N 77 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 = 0.3862 r_free = 0.3862 target = 0.140047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115546 restraints weight = 12844.142| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.67 r_work: 0.3419 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9600 Z= 0.237 Angle : 0.537 6.051 13002 Z= 0.285 Chirality : 0.041 0.171 1438 Planarity : 0.005 0.094 1626 Dihedral : 8.110 59.323 1611 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 4.33 % Allowed : 16.01 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1133 helix: 2.86 (0.24), residues: 449 sheet: 0.37 (0.34), residues: 221 loop : -0.99 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.006 0.000 ARG A 35 *********************** 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 208 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7812 (m-30) cc_final: 0.7602 (m-30) REVERT: A 39 LEU cc_start: 0.8355 (mt) cc_final: 0.8114 (mp) REVERT: A 230 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: A 344 GLU cc_start: 0.8141 (tp30) cc_final: 0.7810 (tp30) REVERT: A 370 GLU cc_start: 0.6736 (tt0) cc_final: 0.6447 (tm-30) REVERT: B 22 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8183 (mtt-85) REVERT: B 137 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.7620 (tpp-160) REVERT: B 325 MET cc_start: 0.8375 (mmm) cc_final: 0.7985 (mmt) REVERT: R 36 GLU cc_start: 0.5469 (OUTLIER) cc_final: 0.5078 (mt-10) REVERT: R 112 TRP cc_start: -0.0236 (OUTLIER) cc_final: -0.4295 (m100) REVERT: R 147 ARG cc_start: 0.2738 (OUTLIER) cc_final: 0.2377 (mtt180) REVERT: R 214 ARG cc_start: 0.7705 (ttt180) cc_final: 0.7500 (ttt180) outliers start: 43 outliers final: 30 residues processed: 196 average time/residue: 1.6820 time to fit residues: 347.6740 Evaluate side-chains 197 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 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 292 LEU 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: 0.0970 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 88 ASN B 340 ASN N 31 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.141142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116254 restraints weight = 12761.329| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.70 r_work: 0.3428 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9600 Z= 0.197 Angle : 0.516 5.865 13002 Z= 0.273 Chirality : 0.040 0.168 1438 Planarity : 0.005 0.096 1626 Dihedral : 7.829 58.575 1609 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.82 % Rotamer: Outliers : 4.33 % Allowed : 17.02 % Favored : 78.65 % 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: 1.46 (0.26), residues: 1133 helix: 3.01 (0.24), residues: 450 sheet: 0.43 (0.34), residues: 221 loop : -0.88 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS P 14 PHE 0.023 0.002 PHE R 335 TYR 0.022 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 203 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8027 (ttt-90) cc_final: 0.7768 (ttt-90) REVERT: A 39 LEU cc_start: 0.8345 (mt) cc_final: 0.8091 (mp) REVERT: A 230 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: A 231 ARG cc_start: 0.8602 (ptp-170) cc_final: 0.8187 (ptt180) REVERT: A 344 GLU cc_start: 0.8059 (tp30) cc_final: 0.7709 (tp30) REVERT: A 370 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: B 22 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8144 (mtt-85) REVERT: B 137 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7624 (tpp-160) REVERT: B 325 MET cc_start: 0.8426 (mmm) cc_final: 0.8115 (mmt) REVERT: R 112 TRP cc_start: -0.0083 (OUTLIER) cc_final: -0.4497 (m100) REVERT: R 214 ARG cc_start: 0.7754 (ttt180) cc_final: 0.7546 (ttt180) outliers start: 43 outliers final: 30 residues processed: 190 average time/residue: 1.6091 time to fit residues: 322.3991 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 : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP 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 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 65 LYS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 0.0570 chunk 84 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN N 31 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.138582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113684 restraints weight = 12788.037| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.68 r_work: 0.3386 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9600 Z= 0.365 Angle : 0.588 6.931 13002 Z= 0.311 Chirality : 0.044 0.185 1438 Planarity : 0.005 0.097 1626 Dihedral : 7.846 59.493 1607 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.71 % Favored : 95.94 % Rotamer: Outliers : 4.43 % Allowed : 17.22 % Favored : 78.35 % 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: 1.33 (0.25), residues: 1133 helix: 2.80 (0.24), residues: 449 sheet: 0.47 (0.34), residues: 221 loop : -0.90 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.025 0.002 PHE R 335 TYR 0.024 0.002 TYR R 191 ARG 0.007 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 : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7862 (ttt-90) REVERT: A 39 LEU cc_start: 0.8484 (mt) cc_final: 0.8257 (mp) REVERT: A 230 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: A 293 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8396 (mtpt) REVERT: A 344 GLU cc_start: 0.8122 (tp30) cc_final: 0.7839 (tp30) REVERT: A 370 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: B 22 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8169 (mtt180) REVERT: B 325 MET cc_start: 0.8466 (mmm) cc_final: 0.8121 (mmt) REVERT: R 40 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7238 (tt) REVERT: R 112 TRP cc_start: -0.0053 (OUTLIER) cc_final: -0.4358 (m100) REVERT: R 214 ARG cc_start: 0.7785 (ttt180) cc_final: 0.7581 (ttt180) outliers start: 44 outliers final: 27 residues processed: 198 average time/residue: 1.5702 time to fit residues: 327.2009 Evaluate side-chains 196 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 65 LYS 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 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 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: 0.5980 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 96 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116290 restraints weight = 12817.566| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.69 r_work: 0.3418 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.003 0.079 9600 Z= 0.213 Angle : 0.526 6.119 13002 Z= 0.279 Chirality : 0.041 0.171 1438 Planarity : 0.005 0.096 1626 Dihedral : 7.250 56.187 1603 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.91 % Favored : 96.73 % Rotamer: Outliers : 3.63 % Allowed : 18.33 % Favored : 78.05 % 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: 1.48 (0.26), residues: 1133 helix: 2.99 (0.24), residues: 450 sheet: 0.49 (0.34), residues: 220 loop : -0.85 (0.29), residues: 463 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 0.010 0.000 ARG A 356 *********************** 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 201 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8023 (ttt-90) cc_final: 0.7746 (ttt-90) REVERT: A 39 LEU cc_start: 0.8378 (mt) cc_final: 0.8134 (mp) REVERT: A 230 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: A 231 ARG cc_start: 0.8561 (ptp-170) cc_final: 0.8298 (ptt180) REVERT: A 344 GLU cc_start: 0.8088 (tp30) cc_final: 0.7773 (tp30) REVERT: A 370 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6399 (tm-30) REVERT: B 22 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8169 (mtt180) REVERT: B 325 MET cc_start: 0.8409 (mmm) cc_final: 0.8093 (mmt) REVERT: R 40 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7300 (tt) REVERT: R 112 TRP cc_start: -0.0205 (OUTLIER) cc_final: -0.4416 (m100) REVERT: R 348 ASN cc_start: 0.7707 (t0) cc_final: 0.7442 (t160) outliers start: 36 outliers final: 27 residues processed: 193 average time/residue: 1.6827 time to fit residues: 342.1721 Evaluate side-chains 199 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP 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 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 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 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 414 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 25 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS B 340 ASN N 31 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118077 restraints weight = 12953.376| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.72 r_work: 0.3457 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 9600 Z= 0.154 Angle : 0.492 6.311 13002 Z= 0.260 Chirality : 0.039 0.176 1438 Planarity : 0.004 0.096 1626 Dihedral : 6.911 55.897 1602 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 3.52 % Allowed : 18.73 % 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: 1.70 (0.26), residues: 1133 helix: 3.18 (0.24), residues: 449 sheet: 0.53 (0.34), residues: 225 loop : -0.70 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS P 14 PHE 0.023 0.001 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.009 0.000 ARG A 356 *********************** 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 204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.7717 (ttt-90) REVERT: A 21 LYS cc_start: 0.8102 (mtmm) cc_final: 0.7887 (mtpm) REVERT: A 39 LEU cc_start: 0.8281 (mt) cc_final: 0.8008 (mp) REVERT: A 230 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: A 344 GLU cc_start: 0.8038 (tp30) cc_final: 0.7701 (tp30) REVERT: A 356 ARG cc_start: 0.7585 (ptt-90) cc_final: 0.7333 (ptt-90) REVERT: A 370 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6365 (tm-30) REVERT: P 19 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: R 112 TRP cc_start: -0.0336 (OUTLIER) cc_final: -0.4367 (m100) REVERT: R 189 MET cc_start: 0.7646 (ttp) cc_final: 0.7264 (ttp) outliers start: 35 outliers final: 21 residues processed: 196 average time/residue: 1.6096 time to fit residues: 332.5470 Evaluate side-chains 190 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 N residue 114 THR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN N 31 ASN N 77 ASN R 37 GLN R 220 ASN R 380 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.140112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115203 restraints weight = 12760.926| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.69 r_work: 0.3407 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9600 Z= 0.277 Angle : 0.557 8.618 13002 Z= 0.294 Chirality : 0.042 0.178 1438 Planarity : 0.005 0.096 1626 Dihedral : 6.972 56.465 1598 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 3.12 % Allowed : 19.94 % Favored : 76.94 % 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: 1.59 (0.26), residues: 1133 helix: 3.11 (0.24), residues: 449 sheet: 0.54 (0.35), residues: 220 loop : -0.82 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.002 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 191 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8031 (ttt-90) cc_final: 0.7732 (ttt-90) REVERT: A 21 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7899 (mtpm) REVERT: A 39 LEU cc_start: 0.8388 (mt) cc_final: 0.8135 (mp) REVERT: A 227 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8149 (tp40) REVERT: A 230 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: A 344 GLU cc_start: 0.8100 (tp30) cc_final: 0.7796 (tp30) REVERT: A 356 ARG cc_start: 0.7601 (ptt-90) cc_final: 0.7384 (ptt-90) REVERT: A 370 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6413 (tm-30) REVERT: B 325 MET cc_start: 0.8390 (tpp) cc_final: 0.8108 (mmt) REVERT: P 19 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: R 112 TRP cc_start: -0.0383 (OUTLIER) cc_final: -0.4351 (m100) REVERT: R 212 PHE cc_start: 0.8001 (m-10) cc_final: 0.7744 (m-80) REVERT: R 414 MET cc_start: 0.8427 (ttp) cc_final: 0.8202 (mtt) outliers start: 31 outliers final: 25 residues processed: 185 average time/residue: 1.5366 time to fit residues: 301.3506 Evaluate side-chains 193 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 262 MET 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 N residue 114 THR 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 37 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS B 340 ASN R 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115613 restraints weight = 13050.259| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.71 r_work: 0.3408 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9600 Z= 0.251 Angle : 0.552 8.349 13002 Z= 0.290 Chirality : 0.042 0.180 1438 Planarity : 0.005 0.097 1626 Dihedral : 6.936 56.853 1598 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.44 % Favored : 96.20 % Rotamer: Outliers : 3.32 % Allowed : 19.84 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1133 helix: 3.08 (0.24), residues: 449 sheet: 0.59 (0.35), residues: 220 loop : -0.85 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 PHE 0.025 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.013 0.001 ARG A 317 ********************** 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 198 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8024 (ttt-90) cc_final: 0.7758 (ttt-90) REVERT: A 39 LEU cc_start: 0.8371 (mt) cc_final: 0.8127 (mp) REVERT: A 227 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: A 230 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: A 231 ARG cc_start: 0.8604 (ptp90) cc_final: 0.8262 (ptt180) REVERT: A 344 GLU cc_start: 0.8097 (tp30) cc_final: 0.7793 (tp30) REVERT: A 370 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: B 325 MET cc_start: 0.8398 (tpp) cc_final: 0.8144 (mmt) REVERT: P 19 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: R 39 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5396 (t80) REVERT: R 112 TRP cc_start: -0.0399 (OUTLIER) cc_final: -0.4288 (m100) REVERT: R 212 PHE cc_start: 0.7864 (m-10) cc_final: 0.7511 (m-80) REVERT: R 414 MET cc_start: 0.8446 (ttp) cc_final: 0.8225 (mtt) outliers start: 33 outliers final: 25 residues processed: 191 average time/residue: 1.5661 time to fit residues: 315.1674 Evaluate side-chains 197 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS A 227 GLN A 292 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 = 0.3842 r_free = 0.3842 target = 0.138252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113332 restraints weight = 12833.971| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.68 r_work: 0.3392 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 9600 Z= 0.341 Angle : 0.594 7.973 13002 Z= 0.313 Chirality : 0.044 0.183 1438 Planarity : 0.005 0.098 1626 Dihedral : 7.047 59.125 1598 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.88 % Favored : 95.85 % Rotamer: Outliers : 3.02 % Allowed : 20.44 % Favored : 76.54 % 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: 1.45 (0.26), residues: 1133 helix: 2.92 (0.24), residues: 449 sheet: 0.57 (0.35), residues: 217 loop : -0.86 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP R 118 HIS 0.006 0.001 HIS A 357 PHE 0.025 0.002 PHE R 335 TYR 0.024 0.002 TYR R 191 ARG 0.013 0.001 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9939.81 seconds wall clock time: 172 minutes 20.47 seconds (10340.47 seconds total)