Starting phenix.real_space_refine on Wed Apr 30 14:14:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ha0_34585/04_2025/8ha0_34585_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ha0_34585/04_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_34585/04_2025/8ha0_34585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ha0_34585/04_2025/8ha0_34585.map" model { file = "/net/cci-nas-00/data/ceres_data/8ha0_34585/04_2025/8ha0_34585_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ha0_34585/04_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-5669/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: 5.85, per 1000 atoms: 0.62 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: 2.52 Conformation dependent library (CDL) restraints added in 1.0 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: 1.01 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: 2.70 Time building geometry restraints manager: 2.95 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: 2.050 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- 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 : 0.009 0.683 9607 Z= 0.862 Angle : 0.789 24.015 13010 Z= 0.491 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 Details of bonding type rmsd hydrogen bonds : bond 0.17319 ( 468) hydrogen bonds : angle 6.57953 ( 1344) SS BOND : bond 0.02887 ( 4) SS BOND : angle 3.98544 ( 8) covalent geometry : bond 0.00502 ( 9600) covalent geometry : angle 0.78337 (13002) Misc. bond : bond 0.44568 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 1.041 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: 1.5083 time to fit residues: 451.4776 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 : 1.172 ------------------------------------------------------------------------------- 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 9607 Z= 0.161 Angle : 0.593 7.194 13010 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 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 468) hydrogen bonds : angle 4.25188 ( 1344) SS BOND : bond 0.00696 ( 4) SS BOND : angle 1.18541 ( 8) covalent geometry : bond 0.00383 ( 9600) covalent geometry : angle 0.59275 (13002) Misc. bond : bond 0.00332 ( 3) *********************** 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 : 1.149 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: 1.2862 time to fit residues: 303.5551 Evaluate side-chains 209 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.139374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114904 restraints weight = 13009.172| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.69 r_work: 0.3408 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9607 Z= 0.174 Angle : 0.571 6.797 13010 Z= 0.302 Chirality : 0.043 0.192 1438 Planarity : 0.005 0.097 1626 Dihedral : 8.693 59.621 1618 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.82 % Favored : 96.82 % Rotamer: Outliers : 4.63 % Allowed : 15.31 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1133 helix: 2.65 (0.24), residues: 448 sheet: 0.29 (0.33), residues: 219 loop : -1.10 (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 0.007 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 468) hydrogen bonds : angle 4.14951 ( 1344) SS BOND : bond 0.00445 ( 4) SS BOND : angle 0.68488 ( 8) covalent geometry : bond 0.00419 ( 9600) covalent geometry : angle 0.57113 (13002) Misc. bond : bond 0.00261 ( 3) *********************** 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 217 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7894 (m-30) cc_final: 0.7635 (m-30) REVERT: A 39 LEU cc_start: 0.8323 (mt) cc_final: 0.8059 (mp) REVERT: A 230 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: A 275 SER cc_start: 0.8679 (t) cc_final: 0.8472 (m) REVERT: A 276 ILE cc_start: 0.8595 (mt) cc_final: 0.8387 (mp) REVERT: A 344 GLU cc_start: 0.8143 (tp30) cc_final: 0.7800 (tp30) REVERT: A 370 GLU cc_start: 0.6781 (tt0) cc_final: 0.6448 (tm-30) REVERT: B 22 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8191 (mtt180) REVERT: B 74 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 76 ASP cc_start: 0.8375 (p0) cc_final: 0.7917 (p0) REVERT: B 197 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7162 (mpp80) REVERT: R 36 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.4984 (mt-10) REVERT: R 112 TRP cc_start: -0.0521 (OUTLIER) cc_final: -0.4355 (m100) REVERT: R 154 TRP cc_start: 0.5476 (OUTLIER) cc_final: 0.5191 (m100) outliers start: 46 outliers final: 26 residues processed: 204 average time/residue: 1.5303 time to fit residues: 329.6267 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 : 1.051 ------------------------------------------------------------------------------- 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 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 27 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: 0.9990 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 0.0010 chunk 109 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.139596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114981 restraints weight = 12841.806| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.68 r_work: 0.3411 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9607 Z= 0.157 Angle : 0.546 6.145 13010 Z= 0.290 Chirality : 0.042 0.172 1438 Planarity : 0.005 0.094 1626 Dihedral : 8.302 58.245 1615 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.09 % Favored : 96.56 % Rotamer: Outliers : 4.63 % Allowed : 15.31 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1133 helix: 2.82 (0.24), residues: 449 sheet: 0.37 (0.34), residues: 221 loop : -1.00 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 34 PHE 0.023 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 468) hydrogen bonds : angle 4.04550 ( 1344) SS BOND : bond 0.00260 ( 4) SS BOND : angle 0.55394 ( 8) covalent geometry : bond 0.00375 ( 9600) covalent geometry : angle 0.54638 (13002) Misc. bond : bond 0.00215 ( 3) *********************** 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 209 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7835 (m-30) cc_final: 0.7620 (m-30) REVERT: A 39 LEU cc_start: 0.8365 (mt) cc_final: 0.8107 (mp) REVERT: A 230 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: A 274 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8295 (ttpp) REVERT: A 275 SER cc_start: 0.8688 (t) cc_final: 0.8455 (m) REVERT: A 344 GLU cc_start: 0.8139 (tp30) cc_final: 0.7781 (tp30) REVERT: A 370 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6490 (tm-30) REVERT: B 22 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8160 (mtt-85) REVERT: B 137 ARG cc_start: 0.7925 (tpp-160) cc_final: 0.7633 (tpp-160) REVERT: B 325 MET cc_start: 0.8344 (mmm) cc_final: 0.8056 (mmt) REVERT: R 36 GLU cc_start: 0.5452 (OUTLIER) cc_final: 0.5066 (mt-10) REVERT: R 112 TRP cc_start: -0.0196 (OUTLIER) cc_final: -0.4193 (m100) REVERT: R 147 ARG cc_start: 0.2709 (OUTLIER) cc_final: 0.2345 (mtt180) REVERT: R 214 ARG cc_start: 0.7703 (ttt180) cc_final: 0.7462 (ttt180) outliers start: 46 outliers final: 32 residues processed: 194 average time/residue: 1.5899 time to fit residues: 324.5517 Evaluate side-chains 200 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 34 LYS Chi-restraints excluded: chain R residue 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: 0.3980 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 N 31 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115770 restraints weight = 12709.030| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.70 r_work: 0.3415 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9607 Z= 0.145 Angle : 0.533 5.973 13010 Z= 0.282 Chirality : 0.041 0.172 1438 Planarity : 0.005 0.098 1626 Dihedral : 7.906 58.054 1609 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.91 % Favored : 96.73 % Rotamer: Outliers : 4.43 % Allowed : 16.82 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1133 helix: 2.93 (0.24), residues: 450 sheet: 0.43 (0.34), residues: 221 loop : -0.89 (0.29), residues: 462 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 0.007 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 468) hydrogen bonds : angle 3.96271 ( 1344) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.46177 ( 8) covalent geometry : bond 0.00348 ( 9600) covalent geometry : angle 0.53330 (13002) Misc. bond : bond 0.00193 ( 3) *********************** 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 208 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8039 (ttt-90) cc_final: 0.7790 (ttt-90) REVERT: A 39 LEU cc_start: 0.8393 (mt) cc_final: 0.8120 (mp) REVERT: A 230 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: A 275 SER cc_start: 0.8696 (t) cc_final: 0.8454 (m) REVERT: A 344 GLU cc_start: 0.8091 (tp30) cc_final: 0.7758 (tp30) REVERT: A 370 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: B 22 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8181 (mtt180) REVERT: B 137 ARG cc_start: 0.7917 (tpp-160) cc_final: 0.7699 (tpp-160) REVERT: B 325 MET cc_start: 0.8353 (mmm) cc_final: 0.7959 (mmt) REVERT: R 112 TRP cc_start: -0.0105 (OUTLIER) cc_final: -0.4482 (m100) REVERT: R 214 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7455 (ttt180) outliers start: 44 outliers final: 30 residues processed: 196 average time/residue: 1.5430 time to fit residues: 318.8793 Evaluate side-chains 199 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS 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 370 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 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 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: 0.1980 chunk 84 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 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: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 N 77 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114405 restraints weight = 12743.479| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.68 r_work: 0.3404 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9607 Z= 0.181 Angle : 0.556 6.615 13010 Z= 0.294 Chirality : 0.042 0.178 1438 Planarity : 0.005 0.096 1626 Dihedral : 7.766 59.765 1607 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.44 % Favored : 96.20 % Rotamer: Outliers : 4.53 % Allowed : 16.82 % 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: 1.40 (0.26), residues: 1133 helix: 2.88 (0.24), residues: 450 sheet: 0.48 (0.34), residues: 220 loop : -0.88 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 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 0.007 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 468) hydrogen bonds : angle 4.03771 ( 1344) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.53846 ( 8) covalent geometry : bond 0.00439 ( 9600) covalent geometry : angle 0.55571 (13002) Misc. bond : bond 0.00216 ( 3) *********************** 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 218 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7810 (ttt-90) REVERT: A 39 LEU cc_start: 0.8440 (mt) cc_final: 0.8191 (mp) REVERT: A 230 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: A 275 SER cc_start: 0.8700 (t) cc_final: 0.8480 (m) REVERT: A 344 GLU cc_start: 0.8075 (tp30) cc_final: 0.7773 (tp30) REVERT: A 370 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: B 22 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8150 (mtt180) REVERT: B 137 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7696 (tpp-160) REVERT: B 325 MET cc_start: 0.8424 (mmm) cc_final: 0.8144 (mmt) REVERT: R 40 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7254 (tt) REVERT: R 112 TRP cc_start: -0.0157 (OUTLIER) cc_final: -0.4414 (m100) outliers start: 45 outliers final: 30 residues processed: 204 average time/residue: 1.6151 time to fit residues: 347.5013 Evaluate side-chains 203 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS 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 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 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: 0.9990 chunk 89 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 218 ASN A 220 HIS A 236 GLN A 294 GLN A 390 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.115730 restraints weight = 12829.144| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.69 r_work: 0.3417 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9607 Z= 0.136 Angle : 0.522 6.120 13010 Z= 0.277 Chirality : 0.041 0.171 1438 Planarity : 0.005 0.096 1626 Dihedral : 7.287 56.394 1603 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.91 % Favored : 96.73 % Rotamer: Outliers : 3.93 % Allowed : 17.82 % Favored : 78.25 % 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: 1.51 (0.26), residues: 1133 helix: 3.03 (0.24), residues: 450 sheet: 0.50 (0.34), residues: 220 loop : -0.86 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS P 14 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 468) hydrogen bonds : angle 3.92116 ( 1344) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.56497 ( 8) covalent geometry : bond 0.00321 ( 9600) covalent geometry : angle 0.52190 (13002) Misc. bond : bond 0.00170 ( 3) *********************** 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 204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8027 (ttt-90) cc_final: 0.7746 (ttt-90) REVERT: A 39 LEU cc_start: 0.8376 (mt) cc_final: 0.8131 (mp) REVERT: A 230 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: A 231 ARG cc_start: 0.8551 (ptp-170) cc_final: 0.8243 (ptt180) REVERT: A 275 SER cc_start: 0.8700 (t) cc_final: 0.8455 (m) REVERT: A 344 GLU cc_start: 0.8080 (tp30) cc_final: 0.7764 (tp30) REVERT: A 370 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: B 137 ARG cc_start: 0.7924 (tpp-160) cc_final: 0.7647 (tpp-160) REVERT: B 325 MET cc_start: 0.8359 (mmm) cc_final: 0.8029 (mmt) REVERT: R 40 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7306 (tt) REVERT: R 112 TRP cc_start: -0.0211 (OUTLIER) cc_final: -0.4423 (m100) REVERT: R 348 ASN cc_start: 0.7730 (t0) cc_final: 0.7464 (t160) outliers start: 39 outliers final: 28 residues processed: 194 average time/residue: 1.6083 time to fit residues: 328.4756 Evaluate side-chains 197 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 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: 0.0980 chunk 70 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115748 restraints weight = 12915.560| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.71 r_work: 0.3420 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9607 Z= 0.132 Angle : 0.522 6.110 13010 Z= 0.276 Chirality : 0.041 0.175 1438 Planarity : 0.005 0.096 1626 Dihedral : 7.096 56.504 1602 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 4.03 % Allowed : 18.33 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1133 helix: 3.03 (0.24), residues: 453 sheet: 0.51 (0.34), residues: 220 loop : -0.80 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS A 357 PHE 0.024 0.002 PHE R 335 TYR 0.022 0.001 TYR R 191 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 468) hydrogen bonds : angle 3.88446 ( 1344) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.52713 ( 8) covalent geometry : bond 0.00313 ( 9600) covalent geometry : angle 0.52207 (13002) Misc. bond : bond 0.00157 ( 3) *********************** 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 205 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8001 (ttt-90) cc_final: 0.7759 (ttt-90) REVERT: A 21 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7908 (mtpm) REVERT: A 39 LEU cc_start: 0.8392 (mt) cc_final: 0.8145 (mp) REVERT: A 230 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: A 231 ARG cc_start: 0.8492 (ptp-170) cc_final: 0.8106 (ptt90) REVERT: A 275 SER cc_start: 0.8696 (t) cc_final: 0.8464 (m) REVERT: A 280 ARG cc_start: 0.7980 (tpt170) cc_final: 0.7779 (tpt170) REVERT: A 344 GLU cc_start: 0.8075 (tp30) cc_final: 0.7770 (tp30) REVERT: A 370 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6434 (tm-30) REVERT: B 137 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7653 (tpp-160) REVERT: B 325 MET cc_start: 0.8366 (mmm) cc_final: 0.8112 (mmt) REVERT: R 40 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7294 (tt) REVERT: R 112 TRP cc_start: -0.0256 (OUTLIER) cc_final: -0.4337 (m100) outliers start: 40 outliers final: 30 residues processed: 194 average time/residue: 1.8479 time to fit residues: 377.9987 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 : 0.959 ------------------------------------------------------------------------------- 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 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 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 308 SER Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS B 125 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 HIS R 380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115137 restraints weight = 12719.750| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.69 r_work: 0.3405 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9607 Z= 0.159 Angle : 0.547 6.999 13010 Z= 0.289 Chirality : 0.042 0.179 1438 Planarity : 0.005 0.096 1626 Dihedral : 6.989 57.030 1598 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 3.73 % Allowed : 18.93 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1133 helix: 3.05 (0.24), residues: 449 sheet: 0.48 (0.34), residues: 220 loop : -0.84 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.025 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 468) hydrogen bonds : angle 3.95933 ( 1344) SS BOND : bond 0.00256 ( 4) SS BOND : angle 0.47954 ( 8) covalent geometry : bond 0.00384 ( 9600) covalent geometry : angle 0.54703 (13002) Misc. bond : bond 0.00178 ( 3) *********************** 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 201 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.8024 (ttt-90) cc_final: 0.7757 (ttt-90) REVERT: A 21 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7913 (mtpm) REVERT: A 39 LEU cc_start: 0.8429 (mt) cc_final: 0.8198 (mp) REVERT: A 230 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: A 231 ARG cc_start: 0.8509 (ptp-170) cc_final: 0.8245 (ptt180) REVERT: A 275 SER cc_start: 0.8681 (t) cc_final: 0.8474 (m) REVERT: A 344 GLU cc_start: 0.8081 (tp30) cc_final: 0.7778 (tp30) REVERT: A 370 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: B 137 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7628 (tpp-160) REVERT: B 239 ASN cc_start: 0.8683 (m110) cc_final: 0.8468 (m110) REVERT: R 40 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7310 (tt) REVERT: R 112 TRP cc_start: -0.0334 (OUTLIER) cc_final: -0.4311 (m100) outliers start: 37 outliers final: 29 residues processed: 194 average time/residue: 1.5092 time to fit residues: 308.9072 Evaluate side-chains 197 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 327 VAL 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 P residue 13 LYS Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 220 HIS B 340 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115744 restraints weight = 12984.954| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.72 r_work: 0.3413 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9607 Z= 0.142 Angle : 0.530 7.050 13010 Z= 0.281 Chirality : 0.041 0.182 1438 Planarity : 0.005 0.097 1626 Dihedral : 6.864 59.943 1598 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.27 % Favored : 96.38 % Rotamer: Outliers : 3.93 % Allowed : 18.63 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1133 helix: 3.08 (0.24), residues: 450 sheet: 0.49 (0.35), residues: 217 loop : -0.75 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 468) hydrogen bonds : angle 3.88395 ( 1344) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.51944 ( 8) covalent geometry : bond 0.00339 ( 9600) covalent geometry : angle 0.52994 (13002) Misc. bond : bond 0.00160 ( 3) ********************** 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 205 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ARG cc_start: 0.7991 (ttt-90) cc_final: 0.7746 (ttt-90) REVERT: A 21 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7898 (mtpm) REVERT: A 39 LEU cc_start: 0.8416 (mt) cc_final: 0.8167 (mp) REVERT: A 227 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8069 (tp40) REVERT: A 230 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 275 SER cc_start: 0.8691 (t) cc_final: 0.8475 (m) REVERT: A 344 GLU cc_start: 0.8077 (tp30) cc_final: 0.7769 (tp30) REVERT: A 370 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: B 137 ARG cc_start: 0.7912 (tpp-160) cc_final: 0.7646 (tpp-160) REVERT: B 325 MET cc_start: 0.8300 (mmm) cc_final: 0.7854 (mmt) REVERT: P 19 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: R 40 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7342 (tt) REVERT: R 112 TRP cc_start: -0.0488 (OUTLIER) cc_final: -0.4223 (m100) outliers start: 39 outliers final: 30 residues processed: 197 average time/residue: 1.5491 time to fit residues: 321.5152 Evaluate side-chains 199 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 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 19 GLU Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain R residue 112 TRP Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 191 TYR Chi-restraints excluded: chain R residue 307 HIS Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 LYS Chi-restraints excluded: chain R residue 319 LYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 0.0050 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 75 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 380 ASN 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 = 0.140350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115593 restraints weight = 12785.918| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.68 r_work: 0.3413 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9607 Z= 0.149 Angle : 0.539 6.920 13010 Z= 0.286 Chirality : 0.041 0.178 1438 Planarity : 0.005 0.099 1626 Dihedral : 6.837 58.132 1598 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.18 % Favored : 96.56 % Rotamer: Outliers : 3.32 % Allowed : 19.13 % Favored : 77.54 % 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: 1.56 (0.26), residues: 1133 helix: 3.07 (0.24), residues: 449 sheet: 0.52 (0.35), residues: 220 loop : -0.81 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP R 118 HIS 0.005 0.001 HIS A 357 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 468) hydrogen bonds : angle 3.88656 ( 1344) SS BOND : bond 0.00273 ( 4) SS BOND : angle 1.04573 ( 8) covalent geometry : bond 0.00356 ( 9600) covalent geometry : angle 0.53858 (13002) Misc. bond : bond 0.00163 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10238.62 seconds wall clock time: 176 minutes 3.59 seconds (10563.59 seconds total)