Starting phenix.real_space_refine on Thu Jul 2 12:06:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbx_23749/07_2026/7mbx_23749.cif" } resolution = 1.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 63 5.16 5 C 5326 2.51 5 N 1444 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1959 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2589 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 431 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 985 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2304 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER N 127 " occ=0.50 ... (8 atoms not shown) pdb=" CB BSER N 127 " occ=0.50 Time building chain proxies: 2.47, per 1000 atoms: 0.29 Number of scatterers: 8433 At special positions: 0 Unit cell: (79.4444, 97.7166, 139.028, 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 63 16.00 O 1600 8.00 N 1444 7.00 C 5326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " 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: 0.72 Conformation dependent library (CDL) restraints added in 590.9 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2014 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 44.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.733A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.713A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.819A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.152A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.877A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.590A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.589A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.632A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.520A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.734A 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 Processing helix chain 'R' and resid 39 through 69 Processing helix chain 'R' and resid 70 through 73 removed outlier: 3.745A pdb=" N ARG R 73 " --> pdb=" O LYS R 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 70 through 73' Processing helix chain 'R' and resid 74 through 105 removed outlier: 3.731A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Proline residue: R 96 - end of helix Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 110 through 145 Processing helix chain 'R' and resid 145 through 153 removed outlier: 3.851A pdb=" N ARG R 150 " --> pdb=" O PRO R 146 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TRP R 152 " --> pdb=" O GLN R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 removed outlier: 3.617A pdb=" N ALA R 158 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.792A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 218 Processing helix chain 'R' and resid 218 through 243 Processing helix chain 'R' and resid 303 through 339 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 339 through 348 removed outlier: 3.644A pdb=" N SER R 348 " --> pdb=" O GLU R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 361 Processing helix chain 'R' and resid 361 through 371 Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 382 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.421A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.719A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.550A 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: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.856A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.080A 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: 3.501A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.025A 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: 3.515A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.212A 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: 6.597A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.693A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.133A 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 12 removed outlier: 6.215A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 180 through 186 455 hydrogen bonds defined for protein. 1302 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: 1.24 Time building geometry restraints manager: 0.91 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: 1352 1.31 - 1.44: 2328 1.44 - 1.56: 4766 1.56 - 1.69: 5 1.69 - 1.82: 92 Bond restraints: 8543 Sorted by residual: bond pdb=" C LEU A 291 " pdb=" O LEU A 291 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.28e-02 6.10e+03 1.77e+01 bond pdb=" CAI Y01 R 501 " pdb=" CAK Y01 R 501 " ideal model delta sigma weight residual 1.492 1.573 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" CAY Y01 R 501 " pdb=" OAW Y01 R 501 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.64e-02 3.72e+03 1.24e+01 bond pdb=" C PHE A 363 " pdb=" N THR A 364 " ideal model delta sigma weight residual 1.331 1.286 0.045 1.30e-02 5.92e+03 1.21e+01 ... (remaining 8538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11291 2.46 - 4.92: 236 4.92 - 7.38: 47 7.38 - 9.84: 7 9.84 - 12.30: 1 Bond angle restraints: 11582 Sorted by residual: angle pdb=" CA ASN A 292 " pdb=" CB ASN A 292 " pdb=" CG ASN A 292 " ideal model delta sigma weight residual 112.60 117.83 -5.23 1.00e+00 1.00e+00 2.74e+01 angle pdb=" C ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta sigma weight residual 110.79 119.26 -8.47 1.66e+00 3.63e-01 2.61e+01 angle pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" O LEU A 291 " ideal model delta sigma weight residual 120.98 115.55 5.43 1.08e+00 8.57e-01 2.53e+01 angle pdb=" N LYS A 58 " pdb=" CA LYS A 58 " pdb=" C LYS A 58 " ideal model delta sigma weight residual 111.28 105.85 5.43 1.09e+00 8.42e-01 2.48e+01 angle pdb=" CA LYS A 53 " pdb=" C LYS A 53 " pdb=" O LYS A 53 " ideal model delta sigma weight residual 120.55 115.41 5.14 1.06e+00 8.90e-01 2.36e+01 ... (remaining 11577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 4940 24.18 - 48.37: 139 48.37 - 72.55: 12 72.55 - 96.74: 4 96.74 - 120.92: 1 Dihedral angle restraints: 5096 sinusoidal: 1990 harmonic: 3106 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" C ASN A 371 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta harmonic sigma weight residual -122.60 -133.51 10.91 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1158 0.083 - 0.166: 140 0.166 - 0.249: 14 0.249 - 0.332: 4 0.332 - 0.415: 3 Chirality restraints: 1319 Sorted by residual: chirality pdb=" CB VAL A 57 " pdb=" CA VAL A 57 " pdb=" CG1 VAL A 57 " pdb=" CG2 VAL A 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CBD Y01 R 501 " pdb=" CAK Y01 R 501 " pdb=" CBF Y01 R 501 " pdb=" CBG Y01 R 501 " both_signs ideal model delta sigma weight residual False 2.70 3.08 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CBH Y01 R 501 " pdb=" CAT Y01 R 501 " pdb=" CAZ Y01 R 501 " pdb=" CBF Y01 R 501 " both_signs ideal model delta sigma weight residual False -2.85 -2.50 -0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1316 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO B 39 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 19 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C GLN A 19 " -0.051 2.00e-02 2.50e+03 pdb=" O GLN A 19 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 20 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 379 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C CYS A 379 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS A 379 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 380 " -0.017 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2212 2.81 - 3.33: 7561 3.33 - 3.85: 14649 3.85 - 4.38: 17459 4.38 - 4.90: 29652 Nonbonded interactions: 71533 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" O HOH B 401 " model vdw 2.347 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.349 3.040 nonbonded pdb=" O ALA B 248 " pdb=" O HOH B 402 " model vdw 2.350 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.356 3.040 ... (remaining 71528 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=0.00 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: 2.140 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 8547 Z= 0.311 Angle : 0.885 12.300 11588 Z= 0.504 Chirality : 0.059 0.415 1319 Planarity : 0.007 0.117 1466 Dihedral : 11.679 120.919 3073 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.45 % Allowed : 1.12 % Favored : 98.44 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1047 helix: -0.03 (0.24), residues: 408 sheet: 0.46 (0.34), residues: 232 loop : -0.23 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 67 TYR 0.015 0.002 TYR B 105 PHE 0.025 0.002 PHE R 185 TRP 0.022 0.002 TRP A 234 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.29 ( 8543) covalent geometry : angle 0.88404 / 0.50 (11582) SS BOND : bond 0.00351 / 0.18 ( 3) SS BOND : angle 1.93246 / 1.06 ( 6) hydrogen bonds : bond 0.13473 / 8.89 ( 455) hydrogen bonds : angle 6.31943 / 4.56 ( 1302) Misc. bond : bond 0.10163 / 5.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7960 (mmt180) cc_final: 0.7650 (mtt90) REVERT: R 195 MET cc_start: 0.5437 (mtm) cc_final: 0.5005 (mtm) REVERT: R 237 TYR cc_start: 0.7736 (t80) cc_final: 0.7437 (t80) outliers start: 4 outliers final: 2 residues processed: 176 average time/residue: 0.7013 time to fit residues: 129.1121 Evaluate side-chains 145 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0270 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 390 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.136344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097452 restraints weight = 11081.188| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.89 r_work: 0.3251 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8547 Z= 0.101 Angle : 0.498 5.597 11588 Z= 0.268 Chirality : 0.040 0.140 1319 Planarity : 0.004 0.053 1466 Dihedral : 6.109 114.968 1173 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.67 % Allowed : 9.15 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1047 helix: 2.04 (0.25), residues: 414 sheet: 0.71 (0.33), residues: 242 loop : -0.05 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.012 0.001 TYR R 179 PHE 0.015 0.001 PHE R 212 TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 8543) covalent geometry : angle 0.49749 / 0.27 (11582) SS BOND : bond 0.00081 / 0.04 ( 3) SS BOND : angle 1.28916 / 0.73 ( 6) hydrogen bonds : bond 0.03853 / 2.63 ( 455) hydrogen bonds : angle 4.59799 / 3.35 ( 1302) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 389 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7654 (ttm110) REVERT: B 6 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 197 ARG cc_start: 0.8422 (mmp80) cc_final: 0.8215 (mmp80) REVERT: B 214 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7891 (mtm180) REVERT: G 32 LYS cc_start: 0.8190 (tptm) cc_final: 0.7665 (tptp) REVERT: R 57 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5733 (tp) REVERT: R 68 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.7093 (ptm-80) REVERT: R 70 LYS cc_start: 0.7742 (mptt) cc_final: 0.7400 (mptt) REVERT: R 195 MET cc_start: 0.4903 (mtm) cc_final: 0.4571 (mtm) REVERT: R 237 TYR cc_start: 0.8092 (t80) cc_final: 0.7647 (t80) REVERT: R 309 LYS cc_start: 0.8022 (mtmp) cc_final: 0.7795 (mtmm) outliers start: 15 outliers final: 3 residues processed: 162 average time/residue: 0.7917 time to fit residues: 134.0387 Evaluate side-chains 145 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 68 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN R 148 GLN R 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094250 restraints weight = 10896.665| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.88 r_work: 0.3194 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8547 Z= 0.131 Angle : 0.522 5.963 11588 Z= 0.277 Chirality : 0.041 0.146 1319 Planarity : 0.004 0.046 1466 Dihedral : 6.092 115.615 1173 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.79 % Allowed : 10.83 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.26), residues: 1047 helix: 2.62 (0.25), residues: 418 sheet: 0.58 (0.33), residues: 236 loop : -0.07 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.015 0.001 TYR R 179 PHE 0.013 0.001 PHE A 238 TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8543) covalent geometry : angle 0.52104 / 0.28 (11582) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 1.21051 / 0.68 ( 6) hydrogen bonds : bond 0.03968 / 2.71 ( 455) hydrogen bonds : angle 4.47282 / 3.26 ( 1302) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7462 (mptt) REVERT: A 389 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7570 (ttm110) REVERT: B 6 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 197 ARG cc_start: 0.8453 (mmp80) cc_final: 0.8097 (mmp80) REVERT: B 214 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7984 (mtm-85) REVERT: G 32 LYS cc_start: 0.8234 (tptm) cc_final: 0.7795 (tptp) REVERT: R 70 LYS cc_start: 0.7790 (mptt) cc_final: 0.7492 (mptt) REVERT: R 98 ASN cc_start: 0.6035 (m-40) cc_final: 0.5684 (m110) REVERT: R 155 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7470 (tptt) REVERT: R 195 MET cc_start: 0.4792 (mtm) cc_final: 0.4562 (mtm) REVERT: R 237 TYR cc_start: 0.8101 (t80) cc_final: 0.7659 (t80) REVERT: R 309 LYS cc_start: 0.8057 (mtmp) cc_final: 0.7841 (mtpp) REVERT: R 338 TYR cc_start: 0.7873 (m-80) cc_final: 0.7538 (m-80) outliers start: 16 outliers final: 6 residues processed: 160 average time/residue: 0.8059 time to fit residues: 134.8634 Evaluate side-chains 149 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 145 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 84 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 390 GLN N 1 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.094824 restraints weight = 11137.435| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.92 r_work: 0.3205 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8547 Z= 0.115 Angle : 0.496 6.311 11588 Z= 0.265 Chirality : 0.041 0.149 1319 Planarity : 0.004 0.046 1466 Dihedral : 5.967 115.716 1173 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.56 % Allowed : 12.05 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.26), residues: 1047 helix: 2.83 (0.25), residues: 419 sheet: 0.66 (0.33), residues: 232 loop : -0.02 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.020 0.001 TYR R 179 PHE 0.010 0.001 PHE B 199 TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8543) covalent geometry : angle 0.49504 / 0.27 (11582) SS BOND : bond 0.00191 / 0.10 ( 3) SS BOND : angle 1.06656 / 0.59 ( 6) hydrogen bonds : bond 0.03686 / 2.53 ( 455) hydrogen bonds : angle 4.36060 / 3.18 ( 1302) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7437 (tptt) REVERT: A 389 ARG cc_start: 0.8130 (mmt180) cc_final: 0.7541 (ttm110) REVERT: G 32 LYS cc_start: 0.8212 (tptm) cc_final: 0.7724 (tptp) REVERT: R 98 ASN cc_start: 0.6003 (m-40) cc_final: 0.5623 (m110) REVERT: R 205 MET cc_start: 0.6969 (ptm) cc_final: 0.6384 (ptp) REVERT: R 219 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8196 (mm) REVERT: R 237 TYR cc_start: 0.8110 (t80) cc_final: 0.7676 (t80) REVERT: R 309 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7847 (mtpp) REVERT: R 338 TYR cc_start: 0.7799 (m-80) cc_final: 0.7540 (m-80) outliers start: 14 outliers final: 5 residues processed: 157 average time/residue: 0.8259 time to fit residues: 135.5429 Evaluate side-chains 148 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 81 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 390 GLN N 1 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.133842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.094176 restraints weight = 10903.727| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.88 r_work: 0.3194 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8547 Z= 0.125 Angle : 0.511 6.565 11588 Z= 0.272 Chirality : 0.041 0.153 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.958 116.081 1173 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.45 % Allowed : 12.83 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.26), residues: 1047 helix: 2.87 (0.25), residues: 420 sheet: 0.68 (0.33), residues: 230 loop : 0.01 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.017 0.001 TYR R 179 PHE 0.011 0.001 PHE B 199 TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8543) covalent geometry : angle 0.51073 / 0.27 (11582) SS BOND : bond 0.00214 / 0.11 ( 3) SS BOND : angle 0.95246 / 0.53 ( 6) hydrogen bonds : bond 0.03735 / 2.56 ( 455) hydrogen bonds : angle 4.33773 / 3.16 ( 1302) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7467 (tptt) REVERT: A 389 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7521 (ttm110) REVERT: B 197 ARG cc_start: 0.8540 (mmp80) cc_final: 0.7961 (mmp80) REVERT: G 32 LYS cc_start: 0.8198 (tptm) cc_final: 0.7760 (tptp) REVERT: R 70 LYS cc_start: 0.7735 (mptt) cc_final: 0.7414 (mptt) REVERT: R 98 ASN cc_start: 0.6107 (m-40) cc_final: 0.5730 (m110) REVERT: R 205 MET cc_start: 0.7007 (ptm) cc_final: 0.6656 (ptp) REVERT: R 207 GLN cc_start: 0.6927 (mt0) cc_final: 0.6726 (mt0) REVERT: R 219 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8203 (mm) REVERT: R 237 TYR cc_start: 0.8111 (t80) cc_final: 0.7707 (t80) REVERT: R 309 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7867 (mtpp) outliers start: 13 outliers final: 5 residues processed: 153 average time/residue: 0.7930 time to fit residues: 126.9135 Evaluate side-chains 150 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.0470 chunk 21 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN N 1 GLN R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.135552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096171 restraints weight = 10860.096| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.89 r_work: 0.3231 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8547 Z= 0.098 Angle : 0.485 7.205 11588 Z= 0.257 Chirality : 0.040 0.157 1319 Planarity : 0.004 0.046 1466 Dihedral : 5.800 116.057 1173 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.90 % Allowed : 12.72 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.26), residues: 1047 helix: 3.00 (0.25), residues: 419 sheet: 0.68 (0.33), residues: 229 loop : 0.01 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 13 TYR 0.014 0.001 TYR R 179 PHE 0.011 0.001 PHE B 199 TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 8543) covalent geometry : angle 0.48473 / 0.26 (11582) SS BOND : bond 0.00162 / 0.08 ( 3) SS BOND : angle 0.86008 / 0.47 ( 6) hydrogen bonds : bond 0.03381 / 2.33 ( 455) hydrogen bonds : angle 4.21798 / 3.08 ( 1302) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7424 (mptt) REVERT: A 356 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8142 (mtt180) REVERT: A 389 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7461 (ttm110) REVERT: B 197 ARG cc_start: 0.8511 (mmp80) cc_final: 0.7505 (mmp80) REVERT: B 214 ARG cc_start: 0.8258 (mtt90) cc_final: 0.7746 (mtt90) REVERT: G 13 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7341 (mtm110) REVERT: G 14 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8034 (mtmt) REVERT: G 32 LYS cc_start: 0.8161 (tptm) cc_final: 0.7783 (tptp) REVERT: N 5 GLN cc_start: 0.8649 (mm-40) cc_final: 0.7932 (tm-30) REVERT: R 70 LYS cc_start: 0.7738 (mptt) cc_final: 0.7423 (mptt) REVERT: R 98 ASN cc_start: 0.6123 (m-40) cc_final: 0.5716 (m110) REVERT: R 205 MET cc_start: 0.7137 (ptm) cc_final: 0.6874 (ptp) REVERT: R 237 TYR cc_start: 0.8104 (t80) cc_final: 0.7704 (t80) REVERT: R 373 MET cc_start: 0.8572 (mtp) cc_final: 0.8361 (mtm) outliers start: 17 outliers final: 7 residues processed: 157 average time/residue: 0.7801 time to fit residues: 128.2210 Evaluate side-chains 155 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 114 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 84 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 390 GLN N 1 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093975 restraints weight = 10916.227| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.89 r_work: 0.3193 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8547 Z= 0.129 Angle : 0.520 7.286 11588 Z= 0.276 Chirality : 0.042 0.166 1319 Planarity : 0.004 0.046 1466 Dihedral : 5.918 116.597 1173 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.67 % Allowed : 12.61 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.26), residues: 1047 helix: 2.92 (0.25), residues: 420 sheet: 0.65 (0.34), residues: 224 loop : 0.02 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.014 0.001 TYR R 179 PHE 0.011 0.001 PHE B 151 TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 8543) covalent geometry : angle 0.51965 / 0.28 (11582) SS BOND : bond 0.00244 / 0.13 ( 3) SS BOND : angle 0.94185 / 0.52 ( 6) hydrogen bonds : bond 0.03773 / 2.59 ( 455) hydrogen bonds : angle 4.33482 / 3.15 ( 1302) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7434 (tptt) REVERT: A 356 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8170 (mtt180) REVERT: A 389 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7400 (ttm110) REVERT: B 197 ARG cc_start: 0.8545 (mmp80) cc_final: 0.7448 (mmp80) REVERT: B 214 ARG cc_start: 0.8311 (mtt90) cc_final: 0.7843 (mtt90) REVERT: G 14 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8043 (mtmt) REVERT: G 32 LYS cc_start: 0.8194 (tptm) cc_final: 0.7818 (tptp) REVERT: N 11 LEU cc_start: 0.9123 (tp) cc_final: 0.8882 (tm) REVERT: R 45 ILE cc_start: 0.6659 (mt) cc_final: 0.6422 (tp) REVERT: R 70 LYS cc_start: 0.7750 (mptt) cc_final: 0.7433 (mptt) REVERT: R 98 ASN cc_start: 0.6144 (m-40) cc_final: 0.5708 (m110) REVERT: R 145 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8413 (mtpm) REVERT: R 205 MET cc_start: 0.7150 (ptm) cc_final: 0.6936 (ptp) REVERT: R 237 TYR cc_start: 0.8116 (t80) cc_final: 0.7717 (t80) REVERT: R 309 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7778 (mttm) outliers start: 15 outliers final: 8 residues processed: 156 average time/residue: 0.7123 time to fit residues: 116.3980 Evaluate side-chains 152 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 0.0170 chunk 45 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 390 GLN N 1 GLN R 148 GLN R 207 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.135866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096793 restraints weight = 10964.875| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.88 r_work: 0.3241 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8547 Z= 0.097 Angle : 0.489 7.904 11588 Z= 0.259 Chirality : 0.040 0.169 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.727 116.138 1173 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.12 % Allowed : 13.28 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.26), residues: 1047 helix: 3.02 (0.25), residues: 419 sheet: 0.71 (0.34), residues: 218 loop : 0.01 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 13 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE B 199 TRP 0.014 0.001 TRP B 297 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 8543) covalent geometry : angle 0.48906 / 0.26 (11582) SS BOND : bond 0.00145 / 0.07 ( 3) SS BOND : angle 0.83937 / 0.45 ( 6) hydrogen bonds : bond 0.03316 / 2.29 ( 455) hydrogen bonds : angle 4.20020 / 3.06 ( 1302) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8085 (mtt180) REVERT: A 389 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7350 (ttm110) REVERT: B 217 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8907 (pmt) REVERT: G 13 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7343 (mtm110) REVERT: G 14 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8033 (mtmt) REVERT: G 20 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8626 (mtmm) REVERT: G 32 LYS cc_start: 0.8124 (tptm) cc_final: 0.7744 (tptp) REVERT: N 5 GLN cc_start: 0.8616 (mm-40) cc_final: 0.7895 (tm-30) REVERT: N 11 LEU cc_start: 0.9057 (tp) cc_final: 0.8807 (tm) REVERT: R 45 ILE cc_start: 0.6699 (mt) cc_final: 0.6454 (tp) REVERT: R 70 LYS cc_start: 0.7765 (mptt) cc_final: 0.7460 (mptt) REVERT: R 98 ASN cc_start: 0.6185 (m-40) cc_final: 0.5764 (m110) REVERT: R 145 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8379 (mtpm) REVERT: R 237 TYR cc_start: 0.8080 (t80) cc_final: 0.7657 (t80) REVERT: R 309 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7773 (mttm) outliers start: 19 outliers final: 9 residues processed: 154 average time/residue: 0.7206 time to fit residues: 116.3082 Evaluate side-chains 155 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN N 1 GLN R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.133165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093467 restraints weight = 10882.999| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.88 r_work: 0.3182 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8547 Z= 0.141 Angle : 0.548 8.242 11588 Z= 0.291 Chirality : 0.042 0.166 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.951 116.887 1173 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.56 % Allowed : 13.84 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.26), residues: 1047 helix: 2.92 (0.25), residues: 419 sheet: 0.62 (0.34), residues: 222 loop : 0.01 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.013 0.001 TYR R 179 PHE 0.012 0.001 PHE B 151 TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8543) covalent geometry : angle 0.54734 / 0.29 (11582) SS BOND : bond 0.00267 / 0.14 ( 3) SS BOND : angle 0.99192 / 0.54 ( 6) hydrogen bonds : bond 0.03845 / 2.63 ( 455) hydrogen bonds : angle 4.37189 / 3.18 ( 1302) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7460 (tptt) REVERT: A 356 ARG cc_start: 0.8485 (mtt180) cc_final: 0.8207 (mtt180) REVERT: A 389 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7399 (ttm110) REVERT: B 217 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8913 (pmt) REVERT: G 13 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7445 (mtm110) REVERT: G 14 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8027 (mtmt) REVERT: G 32 LYS cc_start: 0.8186 (tptm) cc_final: 0.7817 (tptp) REVERT: N 11 LEU cc_start: 0.9072 (tp) cc_final: 0.8839 (tm) REVERT: R 45 ILE cc_start: 0.6617 (mt) cc_final: 0.6350 (tp) REVERT: R 70 LYS cc_start: 0.7759 (mptt) cc_final: 0.7441 (mptt) REVERT: R 98 ASN cc_start: 0.6222 (m-40) cc_final: 0.5778 (m110) REVERT: R 145 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8422 (mtpm) REVERT: R 237 TYR cc_start: 0.8107 (t80) cc_final: 0.7702 (t80) REVERT: R 309 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7702 (mttm) outliers start: 14 outliers final: 7 residues processed: 153 average time/residue: 0.6867 time to fit residues: 110.2703 Evaluate side-chains 155 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 390 GLN N 1 GLN R 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.133916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094529 restraints weight = 10932.612| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.88 r_work: 0.3203 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8547 Z= 0.118 Angle : 0.530 7.640 11588 Z= 0.279 Chirality : 0.042 0.176 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.882 116.466 1173 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.67 % Allowed : 13.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.26), residues: 1047 helix: 2.94 (0.25), residues: 419 sheet: 0.59 (0.34), residues: 224 loop : 0.05 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.012 0.001 TYR A 339 PHE 0.010 0.001 PHE B 199 TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8543) covalent geometry : angle 0.53022 / 0.28 (11582) SS BOND : bond 0.00224 / 0.12 ( 3) SS BOND : angle 0.90879 / 0.50 ( 6) hydrogen bonds : bond 0.03656 / 2.52 ( 455) hydrogen bonds : angle 4.34732 / 3.16 ( 1302) Misc. bond : bond 0.00021 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7418 (tptt) REVERT: A 389 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7350 (ttm110) REVERT: B 217 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8922 (pmt) REVERT: G 13 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7433 (mtm110) REVERT: G 14 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8030 (mtmt) REVERT: G 32 LYS cc_start: 0.8152 (tptm) cc_final: 0.7783 (tptp) REVERT: N 5 GLN cc_start: 0.8639 (mm-40) cc_final: 0.7910 (tm-30) REVERT: N 11 LEU cc_start: 0.9054 (tp) cc_final: 0.8823 (tm) REVERT: R 45 ILE cc_start: 0.6617 (mt) cc_final: 0.6361 (tp) REVERT: R 70 LYS cc_start: 0.7792 (mptt) cc_final: 0.7465 (mptt) REVERT: R 98 ASN cc_start: 0.6232 (m-40) cc_final: 0.5793 (m110) REVERT: R 145 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (mtpm) REVERT: R 205 MET cc_start: 0.7359 (ptp) cc_final: 0.7094 (ptp) REVERT: R 237 TYR cc_start: 0.8098 (t80) cc_final: 0.7696 (t80) REVERT: R 309 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7837 (mttm) outliers start: 15 outliers final: 9 residues processed: 156 average time/residue: 0.7114 time to fit residues: 116.3603 Evaluate side-chains 157 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 309 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 0.0470 chunk 89 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 0.0570 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 390 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN R 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.135049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095994 restraints weight = 10958.590| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.87 r_work: 0.3228 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8547 Z= 0.105 Angle : 0.525 9.178 11588 Z= 0.274 Chirality : 0.041 0.180 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.783 116.666 1173 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.67 % Allowed : 13.95 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.26), residues: 1047 helix: 2.97 (0.25), residues: 418 sheet: 0.62 (0.34), residues: 223 loop : 0.04 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.011 0.001 TYR A 339 PHE 0.010 0.001 PHE B 199 TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 8543) covalent geometry : angle 0.52517 / 0.27 (11582) SS BOND : bond 0.00137 / 0.07 ( 3) SS BOND : angle 0.80674 / 0.44 ( 6) hydrogen bonds : bond 0.03412 / 2.35 ( 455) hydrogen bonds : angle 4.25933 / 3.09 ( 1302) Misc. bond : bond 0.00012 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8345.70 seconds wall clock time: 141 minutes 53.90 seconds (8513.90 seconds total)