Starting phenix.real_space_refine on Thu Mar 13 22:58:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ki0_22882/03_2025/7ki0_22882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki0_22882/03_2025/7ki0_22882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2025/7ki0_22882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2025/7ki0_22882.map" model { file = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2025/7ki0_22882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki0_22882/03_2025/7ki0_22882.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 54 5.16 5 C 5838 2.51 5 N 1588 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9242 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1742 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 236 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3175 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'WF1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'WF1:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 5.98, per 1000 atoms: 0.65 Number of scatterers: 9242 At special positions: 0 Unit cell: (92.13, 98.77, 170.98, 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 54 16.00 O 1762 8.00 N 1588 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.543A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.507A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.730A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.559A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.532A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.541A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.610A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 34 removed outlier: 3.907A pdb=" N ILE P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.800A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 169 removed outlier: 3.989A pdb=" N ILE R 165 " --> pdb=" O ILE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 204 Processing helix chain 'R' and resid 206 through 215 removed outlier: 3.624A pdb=" N GLN R 211 " --> pdb=" O THR R 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.902A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.587A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.356A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 375 Processing helix chain 'R' and resid 376 through 403 removed outlier: 3.542A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.386A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.428A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.606A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.861A 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: 6.813A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.733A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.615A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.255A 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: 6.376A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.678A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.143A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AB3, first strand: chain 'R' and resid 80 through 84 459 hydrogen bonds defined for protein. 1299 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: 2.93 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1489 1.31 - 1.44: 2679 1.44 - 1.56: 5131 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 9371 Sorted by residual: bond pdb=" C17 WF1 P 101 " pdb=" N16 WF1 P 101 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C PRO R 137 " pdb=" N GLU R 138 " ideal model delta sigma weight residual 1.334 1.385 -0.051 1.27e-02 6.20e+03 1.60e+01 bond pdb=" CA PRO R 55 " pdb=" C PRO R 55 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.20e+01 bond pdb=" C LEU R 118 " pdb=" N PRO R 119 " ideal model delta sigma weight residual 1.332 1.369 -0.037 1.12e-02 7.97e+03 1.11e+01 bond pdb=" CA SER R 219 " pdb=" CB SER R 219 " ideal model delta sigma weight residual 1.534 1.488 0.046 1.45e-02 4.76e+03 1.02e+01 ... (remaining 9366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12029 1.89 - 3.78: 602 3.78 - 5.68: 47 5.68 - 7.57: 15 7.57 - 9.46: 2 Bond angle restraints: 12695 Sorted by residual: angle pdb=" N ALA R 256 " pdb=" CA ALA R 256 " pdb=" C ALA R 256 " ideal model delta sigma weight residual 113.02 106.40 6.62 1.20e+00 6.94e-01 3.05e+01 angle pdb=" C LEU R 118 " pdb=" N PRO R 119 " pdb=" CA PRO R 119 " ideal model delta sigma weight residual 119.98 126.34 -6.36 1.16e+00 7.43e-01 3.01e+01 angle pdb=" N LYS P 26 " pdb=" CA LYS P 26 " pdb=" C LYS P 26 " ideal model delta sigma weight residual 112.41 105.40 7.01 1.30e+00 5.92e-01 2.91e+01 angle pdb=" N THR A 364 " pdb=" CA THR A 364 " pdb=" C THR A 364 " ideal model delta sigma weight residual 113.16 106.73 6.43 1.24e+00 6.50e-01 2.69e+01 angle pdb=" N ASP R 215 " pdb=" CA ASP R 215 " pdb=" C ASP R 215 " ideal model delta sigma weight residual 112.87 106.82 6.05 1.20e+00 6.94e-01 2.54e+01 ... (remaining 12690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.00: 5097 19.00 - 38.00: 374 38.00 - 57.00: 50 57.00 - 76.00: 13 76.00 - 95.00: 8 Dihedral angle restraints: 5542 sinusoidal: 2214 harmonic: 3328 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 1.61 -87.61 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 179.48 -86.48 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CA THR R 105 " pdb=" C THR R 105 " pdb=" N ALA R 106 " pdb=" CA ALA R 106 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 5539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1128 0.069 - 0.137: 218 0.137 - 0.205: 38 0.205 - 0.274: 5 0.274 - 0.342: 4 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA TYR R 220 " pdb=" N TYR R 220 " pdb=" C TYR R 220 " pdb=" CB TYR R 220 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA VAL R 370 " pdb=" N VAL R 370 " pdb=" C VAL R 370 " pdb=" CB VAL R 370 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA GLU R 292 " pdb=" N GLU R 292 " pdb=" C GLU R 292 " pdb=" CB GLU R 292 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1390 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.039 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR B 59 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 218 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU R 218 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU R 218 " -0.022 2.00e-02 2.50e+03 pdb=" N SER R 219 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 198 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ASP R 198 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP R 198 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA R 199 " 0.019 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1379 2.75 - 3.29: 8992 3.29 - 3.83: 15822 3.83 - 4.36: 20259 4.36 - 4.90: 33235 Nonbonded interactions: 79687 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.251 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.255 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR R 235 " pdb=" O TRP R 274 " model vdw 2.304 3.040 ... (remaining 79682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.180 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.007 0.108 9371 Z= 0.450 Angle : 0.872 9.462 12695 Z= 0.606 Chirality : 0.059 0.342 1393 Planarity : 0.004 0.052 1614 Dihedral : 13.735 94.998 3372 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.06 % 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: -0.60 (0.24), residues: 1119 helix: -0.53 (0.24), residues: 433 sheet: 0.38 (0.34), residues: 238 loop : -0.50 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 31 HIS 0.017 0.002 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.075 0.002 TYR B 59 ARG 0.007 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 1.896 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6924 (tp30) cc_final: 0.6662 (tp30) REVERT: A 311 TYR cc_start: 0.8499 (m-80) cc_final: 0.8236 (m-80) REVERT: B 10 GLU cc_start: 0.7470 (tt0) cc_final: 0.7150 (tp30) REVERT: B 23 LYS cc_start: 0.8521 (tptm) cc_final: 0.8151 (tppt) REVERT: B 217 MET cc_start: 0.7469 (ppp) cc_final: 0.7159 (ppp) REVERT: B 266 HIS cc_start: 0.7803 (t-170) cc_final: 0.7578 (t70) REVERT: G 17 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7561 (mm-30) REVERT: N 50 ASP cc_start: 0.8333 (p0) cc_final: 0.8049 (p0) REVERT: N 105 ARG cc_start: 0.7534 (mmm-85) cc_final: 0.7128 (mtp85) REVERT: R 139 GLU cc_start: 0.4411 (tt0) cc_final: 0.3562 (mt-10) REVERT: R 140 GLN cc_start: 0.5438 (mt0) cc_final: 0.5042 (tp-100) outliers start: 1 outliers final: 2 residues processed: 149 average time/residue: 1.9512 time to fit residues: 306.6799 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain P residue 26 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 213 GLN A 239 ASN B 9 GLN B 17 GLN B 268 ASN N 1 GLN R 82 ASN R 234 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN R 374 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104002 restraints weight = 9151.833| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.63 r_work: 0.2971 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9371 Z= 0.173 Angle : 0.543 6.674 12695 Z= 0.301 Chirality : 0.042 0.146 1393 Planarity : 0.004 0.051 1614 Dihedral : 6.184 73.681 1272 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.02 % Allowed : 7.65 % Favored : 91.34 % 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: 0.66 (0.25), residues: 1119 helix: 1.41 (0.24), residues: 432 sheet: 0.36 (0.33), residues: 247 loop : -0.41 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.021 0.001 PHE A 212 TYR 0.033 0.001 TYR R 148 ARG 0.004 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.171 Fit side-chains REVERT: A 17 LYS cc_start: 0.6893 (tptp) cc_final: 0.6606 (pptt) REVERT: A 265 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8199 (mtt90) REVERT: A 311 TYR cc_start: 0.8455 (m-80) cc_final: 0.8101 (m-80) REVERT: B 10 GLU cc_start: 0.7305 (tt0) cc_final: 0.6795 (tp30) REVERT: B 23 LYS cc_start: 0.8586 (tptm) cc_final: 0.8041 (ttmt) REVERT: B 134 ARG cc_start: 0.7219 (ptm-80) cc_final: 0.6844 (ppt170) REVERT: B 197 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8113 (mtp-110) REVERT: B 217 MET cc_start: 0.8620 (ppp) cc_final: 0.8114 (ppp) REVERT: B 266 HIS cc_start: 0.8156 (t-170) cc_final: 0.7842 (t70) REVERT: G 17 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7524 (mm-30) REVERT: N 50 ASP cc_start: 0.8678 (p0) cc_final: 0.8425 (p0) REVERT: N 105 ARG cc_start: 0.7636 (mmm-85) cc_final: 0.6953 (mtp85) REVERT: R 140 GLN cc_start: 0.4953 (mt0) cc_final: 0.4457 (tp-100) outliers start: 10 outliers final: 2 residues processed: 129 average time/residue: 1.6242 time to fit residues: 220.9624 Evaluate side-chains 117 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN B 340 ASN N 1 GLN R 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.179610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104882 restraints weight = 9256.777| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.04 r_work: 0.2898 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9371 Z= 0.209 Angle : 0.527 5.963 12695 Z= 0.289 Chirality : 0.042 0.147 1393 Planarity : 0.004 0.053 1614 Dihedral : 5.664 62.698 1265 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.83 % Allowed : 10.30 % Favored : 87.87 % 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: 1.00 (0.25), residues: 1119 helix: 1.85 (0.24), residues: 434 sheet: 0.35 (0.33), residues: 249 loop : -0.30 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 120 HIS 0.009 0.001 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.025 0.002 TYR R 148 ARG 0.003 0.000 ARG P 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6579 (pptt) REVERT: A 265 ARG cc_start: 0.8729 (mtp180) cc_final: 0.8218 (mtt90) REVERT: A 311 TYR cc_start: 0.8444 (m-80) cc_final: 0.8115 (m-80) REVERT: B 23 LYS cc_start: 0.8604 (tptm) cc_final: 0.8023 (ttmt) REVERT: B 134 ARG cc_start: 0.7285 (ptm-80) cc_final: 0.6877 (ppt170) REVERT: B 197 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8092 (mtp-110) REVERT: G 17 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7459 (mm-30) REVERT: G 42 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: N 50 ASP cc_start: 0.8770 (p0) cc_final: 0.8515 (p0) REVERT: N 105 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.6894 (mtp85) REVERT: R 140 GLN cc_start: 0.5001 (mt0) cc_final: 0.4527 (tp40) REVERT: R 161 ILE cc_start: 0.7181 (pt) cc_final: 0.6891 (mt) REVERT: R 221 GLN cc_start: 0.5068 (tm130) cc_final: 0.4686 (mp10) REVERT: R 336 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6932 (mtmp) outliers start: 18 outliers final: 6 residues processed: 117 average time/residue: 1.6542 time to fit residues: 203.7603 Evaluate side-chains 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 336 LYS Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107859 restraints weight = 9218.274| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.00 r_work: 0.2945 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9371 Z= 0.148 Angle : 0.473 5.298 12695 Z= 0.260 Chirality : 0.040 0.144 1393 Planarity : 0.003 0.052 1614 Dihedral : 5.214 56.211 1265 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.33 % Allowed : 11.11 % Favored : 87.56 % 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: 1.25 (0.25), residues: 1119 helix: 2.21 (0.24), residues: 435 sheet: 0.46 (0.32), residues: 246 loop : -0.32 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 120 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.025 0.001 TYR R 148 ARG 0.002 0.000 ARG P 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6583 (pptt) REVERT: A 265 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8150 (mtt90) REVERT: A 311 TYR cc_start: 0.8400 (m-80) cc_final: 0.8123 (m-80) REVERT: B 23 LYS cc_start: 0.8531 (tptm) cc_final: 0.7968 (ttmt) REVERT: B 134 ARG cc_start: 0.7294 (ptm-80) cc_final: 0.6895 (ppt170) REVERT: B 197 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8066 (mmm-85) REVERT: G 17 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7420 (mm-30) REVERT: G 32 LYS cc_start: 0.8170 (tptp) cc_final: 0.7923 (tmtm) REVERT: N 50 ASP cc_start: 0.8748 (p0) cc_final: 0.8478 (p0) REVERT: N 105 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.6903 (mtm180) REVERT: R 140 GLN cc_start: 0.4979 (mt0) cc_final: 0.4522 (tp40) REVERT: R 221 GLN cc_start: 0.5183 (tm130) cc_final: 0.4790 (mp10) REVERT: R 271 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7912 (m) REVERT: R 292 GLU cc_start: 0.6315 (tt0) cc_final: 0.5921 (pp20) REVERT: R 347 CYS cc_start: 0.5695 (m) cc_final: 0.5108 (t) REVERT: R 415 LYS cc_start: 0.6185 (mtpt) cc_final: 0.5975 (mppt) outliers start: 13 outliers final: 4 residues processed: 118 average time/residue: 1.8178 time to fit residues: 225.9329 Evaluate side-chains 116 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 271 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.0030 chunk 33 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 106 optimal weight: 0.0970 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN N 35 ASN N 77 ASN R 234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103741 restraints weight = 9252.991| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.64 r_work: 0.2957 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9371 Z= 0.175 Angle : 0.486 5.287 12695 Z= 0.267 Chirality : 0.041 0.140 1393 Planarity : 0.003 0.050 1614 Dihedral : 5.109 50.247 1265 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.24 % Allowed : 11.31 % Favored : 86.44 % 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: 1.35 (0.25), residues: 1119 helix: 2.34 (0.24), residues: 435 sheet: 0.44 (0.33), residues: 241 loop : -0.26 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 120 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR R 148 ARG 0.002 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6467 (pptt) REVERT: A 265 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8155 (mtt90) REVERT: A 311 TYR cc_start: 0.8401 (m-80) cc_final: 0.8111 (m-80) REVERT: B 23 LYS cc_start: 0.8555 (tptm) cc_final: 0.7983 (ttmt) REVERT: B 134 ARG cc_start: 0.7276 (ptm-80) cc_final: 0.6881 (ppt170) REVERT: B 197 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8062 (mmm-85) REVERT: G 17 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7344 (mm-30) REVERT: G 32 LYS cc_start: 0.8111 (tptp) cc_final: 0.7884 (tmtm) REVERT: G 42 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: N 50 ASP cc_start: 0.8715 (p0) cc_final: 0.8446 (p0) REVERT: N 105 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.6958 (mtm180) REVERT: R 140 GLN cc_start: 0.4973 (mt0) cc_final: 0.4521 (tp40) REVERT: R 221 GLN cc_start: 0.5104 (tm130) cc_final: 0.4785 (mp10) REVERT: R 271 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7914 (m) REVERT: R 292 GLU cc_start: 0.6464 (tt0) cc_final: 0.5984 (pp20) REVERT: R 336 LYS cc_start: 0.7650 (mtmp) cc_final: 0.7164 (mttp) REVERT: R 415 LYS cc_start: 0.6196 (mtpt) cc_final: 0.5966 (mppt) outliers start: 22 outliers final: 7 residues processed: 122 average time/residue: 2.1253 time to fit residues: 275.4561 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN N 35 ASN N 77 ASN R 234 GLN ** R 338 ASN ** 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 = 0.4058 r_free = 0.4058 target = 0.182056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108857 restraints weight = 9225.243| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.03 r_work: 0.2960 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9371 Z= 0.132 Angle : 0.451 5.203 12695 Z= 0.247 Chirality : 0.040 0.142 1393 Planarity : 0.003 0.051 1614 Dihedral : 4.781 46.333 1265 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.63 % Allowed : 12.23 % Favored : 86.14 % 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 (0.25), residues: 1119 helix: 2.48 (0.24), residues: 438 sheet: 0.52 (0.32), residues: 240 loop : -0.19 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 120 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.022 0.001 TYR R 148 ARG 0.002 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6526 (pptt) REVERT: A 265 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8132 (mtt90) REVERT: A 311 TYR cc_start: 0.8392 (m-80) cc_final: 0.8128 (m-80) REVERT: A 386 MET cc_start: 0.8993 (ttp) cc_final: 0.8715 (tmm) REVERT: B 23 LYS cc_start: 0.8553 (tptm) cc_final: 0.7979 (ttmt) REVERT: B 134 ARG cc_start: 0.7245 (ptm-80) cc_final: 0.6844 (ppt170) REVERT: B 146 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8537 (mt) REVERT: B 172 GLU cc_start: 0.8439 (tp30) cc_final: 0.8238 (tt0) REVERT: B 197 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8047 (mmm-85) REVERT: G 17 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7360 (mm-30) REVERT: G 32 LYS cc_start: 0.8104 (tptp) cc_final: 0.7854 (tptp) REVERT: N 50 ASP cc_start: 0.8709 (p0) cc_final: 0.8426 (p0) REVERT: N 105 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.6925 (mtm180) REVERT: R 140 GLN cc_start: 0.4874 (mt0) cc_final: 0.4479 (tp40) REVERT: R 221 GLN cc_start: 0.5206 (tm130) cc_final: 0.4777 (mp10) REVERT: R 271 SER cc_start: 0.8145 (OUTLIER) cc_final: 0.7854 (m) REVERT: R 336 LYS cc_start: 0.7597 (mtmp) cc_final: 0.7212 (mttp) REVERT: R 415 LYS cc_start: 0.6134 (mtpt) cc_final: 0.5928 (mppt) outliers start: 16 outliers final: 5 residues processed: 126 average time/residue: 1.5236 time to fit residues: 202.8537 Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 390 GLN N 1 GLN N 35 ASN R 234 GLN R 338 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.178202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103772 restraints weight = 9233.786| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.01 r_work: 0.2871 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9371 Z= 0.327 Angle : 0.566 6.347 12695 Z= 0.308 Chirality : 0.044 0.142 1393 Planarity : 0.004 0.049 1614 Dihedral : 5.181 39.962 1265 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.75 % Allowed : 12.54 % Favored : 84.71 % 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: 1.39 (0.25), residues: 1119 helix: 2.24 (0.24), residues: 435 sheet: 0.57 (0.33), residues: 241 loop : -0.16 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 120 HIS 0.010 0.002 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.027 0.002 TYR A 358 ARG 0.003 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6545 (pptt) REVERT: A 265 ARG cc_start: 0.8715 (mtp180) cc_final: 0.8200 (mtt90) REVERT: A 311 TYR cc_start: 0.8455 (m-80) cc_final: 0.8243 (m-80) REVERT: B 23 LYS cc_start: 0.8566 (tptm) cc_final: 0.7938 (ttmt) REVERT: B 59 TYR cc_start: 0.9352 (OUTLIER) cc_final: 0.8449 (t80) REVERT: B 134 ARG cc_start: 0.7282 (ptm-80) cc_final: 0.6859 (ppt170) REVERT: B 146 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 197 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8019 (mtp-110) REVERT: G 17 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7354 (mm-30) REVERT: G 42 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: N 50 ASP cc_start: 0.8820 (p0) cc_final: 0.8540 (p0) REVERT: N 105 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6909 (mtm180) REVERT: R 140 GLN cc_start: 0.5009 (mt0) cc_final: 0.4560 (tp40) REVERT: R 221 GLN cc_start: 0.5183 (tm130) cc_final: 0.4710 (mp10) REVERT: R 271 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7947 (m) REVERT: R 336 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7192 (mttp) REVERT: R 415 LYS cc_start: 0.6197 (mtpt) cc_final: 0.5960 (mppt) outliers start: 27 outliers final: 8 residues processed: 129 average time/residue: 1.5555 time to fit residues: 211.9386 Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 336 LYS Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.178720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104186 restraints weight = 9346.807| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.02 r_work: 0.2887 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9371 Z= 0.257 Angle : 0.534 7.092 12695 Z= 0.292 Chirality : 0.042 0.145 1393 Planarity : 0.004 0.050 1614 Dihedral : 5.055 35.802 1265 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 13.86 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1119 helix: 2.21 (0.24), residues: 438 sheet: 0.50 (0.33), residues: 240 loop : -0.24 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 120 HIS 0.004 0.001 HIS R 180 PHE 0.016 0.002 PHE A 212 TYR 0.027 0.002 TYR A 358 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.084 Fit side-chains REVERT: A 17 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6548 (pptt) REVERT: A 21 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 265 ARG cc_start: 0.8692 (mtp180) cc_final: 0.8182 (mtt90) REVERT: B 23 LYS cc_start: 0.8576 (tptm) cc_final: 0.7923 (ttmt) REVERT: B 59 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8432 (t80) REVERT: B 134 ARG cc_start: 0.7256 (ptm-80) cc_final: 0.6840 (ppt170) REVERT: B 146 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 197 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8054 (mtp-110) REVERT: G 17 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7368 (mm-30) REVERT: N 50 ASP cc_start: 0.8786 (p0) cc_final: 0.8505 (p0) REVERT: N 105 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.6908 (mtm180) REVERT: R 140 GLN cc_start: 0.4929 (mt0) cc_final: 0.4474 (tp40) REVERT: R 221 GLN cc_start: 0.5105 (tm130) cc_final: 0.4604 (mp10) REVERT: R 271 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7936 (m) REVERT: R 336 LYS cc_start: 0.7507 (mtmp) cc_final: 0.7212 (mttp) REVERT: R 415 LYS cc_start: 0.6195 (mtpt) cc_final: 0.5968 (mppt) outliers start: 17 outliers final: 7 residues processed: 121 average time/residue: 1.6168 time to fit residues: 206.5748 Evaluate side-chains 123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 347 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108221 restraints weight = 9235.459| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.00 r_work: 0.2949 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9371 Z= 0.136 Angle : 0.463 6.048 12695 Z= 0.254 Chirality : 0.040 0.148 1393 Planarity : 0.003 0.052 1614 Dihedral : 4.577 33.467 1265 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.63 % Allowed : 14.17 % Favored : 84.20 % 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 (0.25), residues: 1119 helix: 2.53 (0.24), residues: 435 sheet: 0.59 (0.32), residues: 243 loop : -0.21 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 120 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.003 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.056 Fit side-chains REVERT: A 17 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6518 (pptt) REVERT: A 265 ARG cc_start: 0.8664 (mtp180) cc_final: 0.8138 (mtt90) REVERT: B 23 LYS cc_start: 0.8566 (tptm) cc_final: 0.7981 (ttmt) REVERT: B 59 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 134 ARG cc_start: 0.7198 (ptm-80) cc_final: 0.6792 (ppt170) REVERT: B 172 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: B 197 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8041 (mmm-85) REVERT: B 215 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7858 (mm-30) REVERT: G 17 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7366 (mm-30) REVERT: N 50 ASP cc_start: 0.8703 (p0) cc_final: 0.8430 (p0) REVERT: N 105 ARG cc_start: 0.7580 (mmm-85) cc_final: 0.6934 (mtm180) REVERT: R 140 GLN cc_start: 0.4900 (mt0) cc_final: 0.4461 (tp40) REVERT: R 221 GLN cc_start: 0.5109 (tm130) cc_final: 0.4597 (mp10) REVERT: R 336 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7216 (mttp) REVERT: R 376 ARG cc_start: 0.4877 (mpt180) cc_final: 0.4548 (mmt180) outliers start: 16 outliers final: 6 residues processed: 125 average time/residue: 1.5905 time to fit residues: 209.6670 Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 336 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.0040 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108538 restraints weight = 9367.083| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.03 r_work: 0.2954 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9371 Z= 0.132 Angle : 0.466 6.279 12695 Z= 0.253 Chirality : 0.040 0.142 1393 Planarity : 0.003 0.052 1614 Dihedral : 4.405 32.487 1265 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.33 % Allowed : 14.78 % Favored : 83.89 % 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: 1.63 (0.25), residues: 1119 helix: 2.56 (0.24), residues: 438 sheet: 0.62 (0.32), residues: 243 loop : -0.14 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 120 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.002 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.715 Fit side-chains REVERT: A 17 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6484 (pptt) REVERT: A 265 ARG cc_start: 0.8695 (mtp180) cc_final: 0.8162 (mtt90) REVERT: B 23 LYS cc_start: 0.8568 (tptm) cc_final: 0.7997 (ttmt) REVERT: B 59 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8464 (t80) REVERT: B 134 ARG cc_start: 0.7230 (ptm-80) cc_final: 0.6826 (ppt170) REVERT: B 172 GLU cc_start: 0.8484 (tp30) cc_final: 0.8264 (tt0) REVERT: B 197 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8033 (mmm-85) REVERT: B 215 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7842 (mm-30) REVERT: G 17 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7362 (mm-30) REVERT: G 42 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: N 50 ASP cc_start: 0.8680 (p0) cc_final: 0.8385 (p0) REVERT: N 105 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.6924 (mtm180) REVERT: R 140 GLN cc_start: 0.4833 (mt0) cc_final: 0.4423 (tp40) REVERT: R 221 GLN cc_start: 0.5066 (tm130) cc_final: 0.4566 (mp10) REVERT: R 411 LEU cc_start: 0.6606 (tp) cc_final: 0.6117 (mt) outliers start: 13 outliers final: 5 residues processed: 122 average time/residue: 1.6787 time to fit residues: 217.4267 Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 35 ASN N 77 ASN R 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.180068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106378 restraints weight = 9251.951| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.98 r_work: 0.2919 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9371 Z= 0.187 Angle : 0.498 5.863 12695 Z= 0.271 Chirality : 0.041 0.139 1393 Planarity : 0.003 0.052 1614 Dihedral : 4.566 30.794 1265 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.53 % Allowed : 14.58 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1119 helix: 2.47 (0.24), residues: 441 sheet: 0.49 (0.33), residues: 247 loop : -0.08 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 120 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.018 0.001 TYR R 148 ARG 0.002 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10744.91 seconds wall clock time: 187 minutes 12.62 seconds (11232.62 seconds total)