Starting phenix.real_space_refine on Thu Mar 13 05:02:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mbx_23749/03_2025/7mbx_23749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mbx_23749/03_2025/7mbx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mbx_23749/03_2025/7mbx_23749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mbx_23749/03_2025/7mbx_23749.map" model { file = "/net/cci-nas-00/data/ceres_data/7mbx_23749/03_2025/7mbx_23749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mbx_23749/03_2025/7mbx_23749.cif" } resolution = 1.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLU:plan': 1, 'ASN:plan1': 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, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 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: 6.15, per 1000 atoms: 0.73 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.88 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: 2.41 Time building geometry restraints manager: 2.53 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: 4988 24.18 - 48.37: 142 48.37 - 72.55: 17 72.55 - 96.74: 5 96.74 - 120.92: 2 Dihedral angle restraints: 5154 sinusoidal: 2048 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 5151 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: 2.030 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.120 Process input model: 23.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 0.081 8543 Z= 0.341 Angle : 0.884 12.300 11582 Z= 0.504 Chirality : 0.059 0.415 1319 Planarity : 0.007 0.117 1466 Dihedral : 12.161 120.919 3131 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (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 TRP 0.022 0.002 TRP A 234 HIS 0.007 0.002 HIS A 357 PHE 0.025 0.002 PHE R 185 TYR 0.015 0.002 TYR B 105 ARG 0.003 0.000 ARG N 67 *********************** 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 : 0.892 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: 1.6386 time to fit residues: 301.7417 Evaluate side-chains 144 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 86 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3878 r_free = 0.3878 target = 0.132252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092514 restraints weight = 10940.477| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.88 r_work: 0.3168 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 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 = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8543 Z= 0.249 Angle : 0.567 5.703 11582 Z= 0.308 Chirality : 0.043 0.148 1319 Planarity : 0.005 0.052 1466 Dihedral : 6.018 57.703 1231 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.01 % Allowed : 8.37 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1047 helix: 1.92 (0.25), residues: 415 sheet: 0.64 (0.35), residues: 228 loop : -0.14 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS B 311 PHE 0.016 0.002 PHE A 238 TYR 0.013 0.002 TYR B 105 ARG 0.007 0.001 ARG A 347 *********************** 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 166 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7493 (mptt) REVERT: A 389 ARG cc_start: 0.8205 (mmt180) cc_final: 0.7579 (tpp-160) REVERT: B 214 ARG cc_start: 0.8366 (mtt90) cc_final: 0.8014 (mtm180) REVERT: R 57 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5896 (tp) REVERT: R 70 LYS cc_start: 0.7814 (mptt) cc_final: 0.7453 (mptt) REVERT: R 98 ASN cc_start: 0.6019 (m-40) cc_final: 0.5660 (m110) REVERT: R 195 MET cc_start: 0.5082 (mtm) cc_final: 0.4790 (mtm) REVERT: R 237 TYR cc_start: 0.8103 (t80) cc_final: 0.7652 (t80) outliers start: 18 outliers final: 4 residues processed: 158 average time/residue: 1.7617 time to fit residues: 290.9651 Evaluate side-chains 143 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094152 restraints weight = 11009.635| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.89 r_work: 0.3195 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 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 = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8543 Z= 0.171 Angle : 0.517 10.071 11582 Z= 0.272 Chirality : 0.042 0.201 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.709 58.948 1231 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.45 % Allowed : 11.05 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1047 helix: 2.53 (0.25), residues: 419 sheet: 0.59 (0.33), residues: 236 loop : -0.05 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.010 0.001 PHE A 212 TYR 0.022 0.001 TYR R 179 ARG 0.008 0.001 ARG B 96 *********************** 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 164 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7453 (mptt) REVERT: A 389 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7588 (ttm110) REVERT: B 136 SER cc_start: 0.8976 (t) cc_final: 0.8776 (p) REVERT: G 32 LYS cc_start: 0.8328 (tptm) cc_final: 0.7950 (tptp) REVERT: R 70 LYS cc_start: 0.7758 (mptt) cc_final: 0.7446 (mptt) REVERT: R 98 ASN cc_start: 0.6041 (m-40) cc_final: 0.5666 (m110) REVERT: R 237 TYR cc_start: 0.8129 (t80) cc_final: 0.7696 (t80) REVERT: R 309 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7597 (mttm) REVERT: R 338 TYR cc_start: 0.7885 (m-80) cc_final: 0.7600 (m-80) outliers start: 13 outliers final: 6 residues processed: 157 average time/residue: 1.7550 time to fit residues: 289.9182 Evaluate side-chains 151 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 N residue 12 VAL Chi-restraints excluded: chain P residue 3 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 86 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3902 r_free = 0.3902 target = 0.134252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094716 restraints weight = 10882.889| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.88 r_work: 0.3204 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8543 Z= 0.158 Angle : 0.497 6.249 11582 Z= 0.264 Chirality : 0.041 0.139 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.589 59.991 1231 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.67 % Allowed : 12.05 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.26), residues: 1047 helix: 2.75 (0.25), residues: 419 sheet: 0.68 (0.33), residues: 230 loop : -0.06 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.010 0.001 PHE B 199 TYR 0.019 0.001 TYR R 179 ARG 0.008 0.000 ARG B 96 *********************** 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 168 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7435 (tptt) REVERT: A 389 ARG cc_start: 0.8120 (mmt180) cc_final: 0.7526 (ttm110) REVERT: B 197 ARG cc_start: 0.8513 (mmp80) cc_final: 0.7745 (mmp80) REVERT: B 214 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7694 (mtt90) REVERT: G 32 LYS cc_start: 0.8288 (tptm) cc_final: 0.7970 (tptp) REVERT: R 70 LYS cc_start: 0.7818 (mptt) cc_final: 0.7472 (mptt) REVERT: R 98 ASN cc_start: 0.6057 (m-40) cc_final: 0.5673 (m110) REVERT: R 205 MET cc_start: 0.6843 (ptm) cc_final: 0.6426 (ptt) REVERT: R 237 TYR cc_start: 0.8128 (t80) cc_final: 0.7705 (t80) REVERT: R 338 TYR cc_start: 0.7837 (m-80) cc_final: 0.7599 (m-80) outliers start: 15 outliers final: 7 residues processed: 162 average time/residue: 1.6516 time to fit residues: 280.0545 Evaluate side-chains 152 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 58 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN N 1 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 = 0.3924 r_free = 0.3924 target = 0.135809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096657 restraints weight = 10848.272| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.87 r_work: 0.3243 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8543 Z= 0.138 Angle : 0.482 6.402 11582 Z= 0.255 Chirality : 0.040 0.147 1319 Planarity : 0.003 0.047 1466 Dihedral : 5.374 59.600 1231 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.79 % Allowed : 12.61 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1047 helix: 2.89 (0.25), residues: 419 sheet: 0.72 (0.34), residues: 220 loop : -0.06 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR R 179 ARG 0.008 0.000 ARG B 96 *********************** 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 171 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7452 (mptt) REVERT: A 389 ARG cc_start: 0.8082 (mmt180) cc_final: 0.7531 (ttm110) REVERT: G 32 LYS cc_start: 0.8226 (tptm) cc_final: 0.7973 (tptp) REVERT: N 5 GLN cc_start: 0.8670 (mm-40) cc_final: 0.7943 (tm-30) REVERT: R 70 LYS cc_start: 0.7791 (mptt) cc_final: 0.7462 (mptt) REVERT: R 98 ASN cc_start: 0.6063 (m-40) cc_final: 0.5661 (m110) REVERT: R 205 MET cc_start: 0.6964 (ptm) cc_final: 0.6569 (ptt) REVERT: R 219 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8214 (mm) REVERT: R 237 TYR cc_start: 0.8106 (t80) cc_final: 0.7698 (t80) REVERT: R 309 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7878 (mtmm) outliers start: 16 outliers final: 6 residues processed: 163 average time/residue: 1.9867 time to fit residues: 338.5246 Evaluate side-chains 153 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 101 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3888 r_free = 0.3888 target = 0.133032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093156 restraints weight = 10837.211| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.89 r_work: 0.3179 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 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 = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8543 Z= 0.210 Angle : 0.528 7.316 11582 Z= 0.282 Chirality : 0.042 0.156 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.545 59.123 1231 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.90 % Allowed : 13.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.26), residues: 1047 helix: 2.83 (0.25), residues: 420 sheet: 0.66 (0.34), residues: 224 loop : 0.01 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.012 0.001 PHE A 238 TYR 0.015 0.001 TYR R 179 ARG 0.009 0.001 ARG G 13 *********************** 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 : 0.927 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7458 (tptt) REVERT: A 370 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: A 389 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7504 (ttm110) REVERT: B 197 ARG cc_start: 0.8734 (mmp80) cc_final: 0.8502 (mmp80) REVERT: G 32 LYS cc_start: 0.8299 (tptm) cc_final: 0.7986 (tptp) REVERT: N 11 LEU cc_start: 0.9111 (tp) cc_final: 0.8873 (tm) REVERT: R 57 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5828 (tp) REVERT: R 70 LYS cc_start: 0.7768 (mptt) cc_final: 0.7434 (mptt) REVERT: R 98 ASN cc_start: 0.6135 (m-40) cc_final: 0.5713 (m110) REVERT: R 205 MET cc_start: 0.7017 (ptm) cc_final: 0.6728 (ptp) REVERT: R 237 TYR cc_start: 0.8125 (t80) cc_final: 0.7702 (t80) outliers start: 17 outliers final: 9 residues processed: 157 average time/residue: 1.6629 time to fit residues: 273.2715 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 : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 0.0170 chunk 100 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3912 r_free = 0.3912 target = 0.134867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095456 restraints weight = 10946.945| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.88 r_work: 0.3222 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8543 Z= 0.147 Angle : 0.498 7.405 11582 Z= 0.264 Chirality : 0.040 0.161 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.385 59.920 1231 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.79 % Allowed : 13.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.27), residues: 1047 helix: 2.92 (0.25), residues: 420 sheet: 0.66 (0.34), residues: 223 loop : 0.00 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS B 54 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.001 ARG B 96 *********************** 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 167 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7438 (tptt) REVERT: A 356 ARG cc_start: 0.8472 (mtt180) cc_final: 0.8117 (mtt180) REVERT: A 370 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7174 (pp20) REVERT: A 389 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7420 (ttm110) REVERT: B 197 ARG cc_start: 0.8659 (mmp80) cc_final: 0.8355 (mmp80) REVERT: G 13 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7477 (mtm110) REVERT: G 20 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8658 (mtmm) REVERT: G 32 LYS cc_start: 0.8245 (tptm) cc_final: 0.7977 (tptp) REVERT: N 5 GLN cc_start: 0.8637 (mm-40) cc_final: 0.7922 (tm-30) REVERT: N 11 LEU cc_start: 0.9071 (tp) cc_final: 0.8831 (tm) REVERT: R 70 LYS cc_start: 0.7775 (mptt) cc_final: 0.7450 (mptt) REVERT: R 98 ASN cc_start: 0.6149 (m-40) cc_final: 0.5728 (m110) REVERT: R 237 TYR cc_start: 0.8110 (t80) cc_final: 0.7691 (t80) REVERT: R 309 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7880 (mtmm) outliers start: 16 outliers final: 8 residues processed: 161 average time/residue: 1.6448 time to fit residues: 277.1459 Evaluate side-chains 153 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 114 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3881 r_free = 0.3881 target = 0.132558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.092756 restraints weight = 10973.413| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.89 r_work: 0.3171 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 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 = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8543 Z= 0.213 Angle : 0.538 7.493 11582 Z= 0.288 Chirality : 0.042 0.163 1319 Planarity : 0.004 0.046 1466 Dihedral : 5.544 59.050 1231 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.01 % Allowed : 14.06 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1047 helix: 2.85 (0.25), residues: 420 sheet: 0.58 (0.34), residues: 224 loop : -0.00 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.012 0.001 PHE A 238 TYR 0.014 0.001 TYR R 179 ARG 0.008 0.001 ARG B 96 *********************** 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 168 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7461 (tptt) REVERT: A 356 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8212 (mtt180) REVERT: A 370 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: A 389 ARG cc_start: 0.8109 (mmt180) cc_final: 0.7419 (ttm110) REVERT: B 197 ARG cc_start: 0.8640 (mmp80) cc_final: 0.8278 (mmp80) REVERT: G 13 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7349 (mtm110) REVERT: G 32 LYS cc_start: 0.8292 (tptm) cc_final: 0.8021 (tptp) REVERT: N 11 LEU cc_start: 0.9075 (tp) cc_final: 0.8844 (tm) REVERT: R 70 LYS cc_start: 0.7772 (mptt) cc_final: 0.7445 (mptt) REVERT: R 98 ASN cc_start: 0.6139 (m-40) cc_final: 0.5717 (m110) REVERT: R 145 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8447 (mtpm) REVERT: R 205 MET cc_start: 0.7533 (ptp) cc_final: 0.7286 (ptt) REVERT: R 219 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8279 (mm) REVERT: R 237 TYR cc_start: 0.8120 (t80) cc_final: 0.7702 (t80) outliers start: 18 outliers final: 8 residues processed: 160 average time/residue: 1.9246 time to fit residues: 323.1686 Evaluate side-chains 158 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 219 LEU Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 GLN N 1 GLN R 44 GLN R 148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.132583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.092797 restraints weight = 11061.782| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.93 r_work: 0.3173 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 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 = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8543 Z= 0.206 Angle : 0.542 7.876 11582 Z= 0.289 Chirality : 0.042 0.179 1319 Planarity : 0.004 0.047 1466 Dihedral : 5.543 59.021 1231 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.56 % Allowed : 14.62 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.26), residues: 1047 helix: 2.84 (0.25), residues: 419 sheet: 0.54 (0.34), residues: 229 loop : 0.02 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS B 311 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR A 339 ARG 0.009 0.001 ARG B 96 *********************** 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 165 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7439 (tptt) REVERT: A 356 ARG cc_start: 0.8514 (mtt180) cc_final: 0.8206 (mtt180) REVERT: A 370 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: A 389 ARG cc_start: 0.8094 (mmt180) cc_final: 0.7407 (ttm110) REVERT: B 197 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8170 (mmp80) REVERT: B 214 ARG cc_start: 0.8387 (mtt90) cc_final: 0.8078 (mtt90) REVERT: G 13 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7349 (mtm110) REVERT: G 20 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8685 (mtmm) REVERT: G 32 LYS cc_start: 0.8289 (tptm) cc_final: 0.8031 (tptp) REVERT: N 11 LEU cc_start: 0.9060 (tp) cc_final: 0.8833 (tm) REVERT: R 70 LYS cc_start: 0.7759 (mptt) cc_final: 0.7428 (mptt) REVERT: R 98 ASN cc_start: 0.6167 (m-40) cc_final: 0.5759 (m110) REVERT: R 145 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8444 (mtpm) REVERT: R 205 MET cc_start: 0.7508 (ptp) cc_final: 0.7299 (ptt) REVERT: R 237 TYR cc_start: 0.8122 (t80) cc_final: 0.7707 (t80) REVERT: R 309 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7749 (mtmm) outliers start: 14 outliers final: 9 residues processed: 158 average time/residue: 1.8048 time to fit residues: 298.9373 Evaluate side-chains 159 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 226 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 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 = 0.3909 r_free = 0.3909 target = 0.134603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095478 restraints weight = 10934.010| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.88 r_work: 0.3220 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 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 = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8543 Z= 0.152 Angle : 0.521 8.964 11582 Z= 0.275 Chirality : 0.041 0.189 1319 Planarity : 0.004 0.048 1466 Dihedral : 5.373 59.992 1231 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.00 % Allowed : 15.18 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1047 helix: 2.92 (0.25), residues: 418 sheet: 0.60 (0.34), residues: 228 loop : 0.04 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS B 54 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.001 ARG B 96 ********************** 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 159 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7416 (mptt) REVERT: A 370 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: A 389 ARG cc_start: 0.8039 (mmt180) cc_final: 0.7382 (ttm110) REVERT: B 217 MET cc_start: 0.9216 (pmt) cc_final: 0.8913 (pmt) REVERT: G 13 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7337 (mtm110) REVERT: G 20 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8676 (mtmm) REVERT: G 32 LYS cc_start: 0.8208 (tptm) cc_final: 0.7969 (tptp) REVERT: N 5 GLN cc_start: 0.8620 (mm-40) cc_final: 0.7905 (tm-30) REVERT: N 11 LEU cc_start: 0.9035 (tp) cc_final: 0.8807 (tm) REVERT: R 70 LYS cc_start: 0.7821 (mptt) cc_final: 0.7430 (mptt) REVERT: R 98 ASN cc_start: 0.6230 (m-40) cc_final: 0.5817 (m110) REVERT: R 145 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8394 (mtpm) REVERT: R 205 MET cc_start: 0.7668 (ptp) cc_final: 0.7430 (ptt) REVERT: R 237 TYR cc_start: 0.8103 (t80) cc_final: 0.7695 (t80) outliers start: 9 outliers final: 7 residues processed: 156 average time/residue: 1.7371 time to fit residues: 283.5169 Evaluate side-chains 152 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 83 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 0.0040 chunk 81 optimal weight: 10.0000 overall best weight: 0.9574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 390 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 = 0.3893 r_free = 0.3893 target = 0.133348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093865 restraints weight = 11047.659| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.89 r_work: 0.3195 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 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 = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8543 Z= 0.181 Angle : 0.543 8.345 11582 Z= 0.286 Chirality : 0.042 0.184 1319 Planarity : 0.004 0.049 1466 Dihedral : 5.463 59.508 1231 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.45 % Allowed : 14.96 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.26), residues: 1047 helix: 2.85 (0.25), residues: 419 sheet: 0.53 (0.34), residues: 224 loop : 0.02 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.001 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18316.74 seconds wall clock time: 316 minutes 38.04 seconds (18998.04 seconds total)