Starting phenix.real_space_refine on Thu Mar 14 22:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfd_33786/03_2024/7yfd_33786_updated.pdb" } resolution = 3.1 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6348 2.51 5 N 1686 2.21 5 O 1840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 348": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 61": "OD1" <-> "OD2" Residue "R ASP 111": "OD1" <-> "OD2" Residue "R PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9934 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1912 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "R" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2132 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'CLR': 2, 'ITF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.12, per 1000 atoms: 0.52 Number of scatterers: 9934 At special positions: 0 Unit cell: (85.36, 128.48, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1840 8.00 N 1686 7.00 C 6348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.6 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 30.9% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.647A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.972A pdb=" N TYR A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.641A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 357 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'R' and resid 13 through 43 Processing helix chain 'R' and resid 49 through 76 removed outlier: 4.624A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 85 through 117 Processing helix chain 'R' and resid 120 through 123 No H-bonds generated for 'chain 'R' and resid 120 through 123' Processing helix chain 'R' and resid 130 through 157 removed outlier: 4.136A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 168 through 170 No H-bonds generated for 'chain 'R' and resid 168 through 170' Processing helix chain 'R' and resid 172 through 203 Proline residue: R 186 - end of helix Processing helix chain 'R' and resid 299 through 328 removed outlier: 3.711A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 339 through 357 removed outlier: 4.017A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 363 through 372 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.710A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 41 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 7.020A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.051A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.865A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.773A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.046A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.735A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.437A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.512A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 155 through 160 removed outlier: 3.648A pdb=" N ALA C 211 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 243 through 245 removed outlier: 6.336A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= N, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.110A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1254 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: 2.94 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3179 1.35 - 1.48: 2672 1.48 - 1.60: 4221 1.60 - 1.73: 0 1.73 - 1.86: 87 Bond restraints: 10159 Sorted by residual: bond pdb=" C01 ITF R 601 " pdb=" N05 ITF R 601 " ideal model delta sigma weight residual 1.314 1.393 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C09 ITF R 601 " pdb=" N11 ITF R 601 " ideal model delta sigma weight residual 1.452 1.384 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C02 ITF R 601 " pdb=" N03 ITF R 601 " ideal model delta sigma weight residual 1.314 1.379 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C02 ITF R 601 " pdb=" C06 ITF R 601 " ideal model delta sigma weight residual 1.527 1.480 0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" C07 ITF R 601 " pdb=" S08 ITF R 601 " ideal model delta sigma weight residual 1.816 1.858 -0.042 2.00e-02 2.50e+03 4.32e+00 ... (remaining 10154 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.82: 244 106.82 - 113.63: 5564 113.63 - 120.45: 3831 120.45 - 127.26: 4032 127.26 - 134.08: 112 Bond angle restraints: 13783 Sorted by residual: angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 103.39 8.61 1.40e+00 5.10e-01 3.78e+01 angle pdb=" CA LEU R 35 " pdb=" CB LEU R 35 " pdb=" CG LEU R 35 " ideal model delta sigma weight residual 116.30 125.17 -8.87 3.50e+00 8.16e-02 6.42e+00 angle pdb=" N ALA N 92 " pdb=" CA ALA N 92 " pdb=" C ALA N 92 " ideal model delta sigma weight residual 107.88 111.22 -3.34 1.41e+00 5.03e-01 5.61e+00 angle pdb=" CB LEU R 35 " pdb=" CG LEU R 35 " pdb=" CD1 LEU R 35 " ideal model delta sigma weight residual 110.70 117.61 -6.91 3.00e+00 1.11e-01 5.31e+00 angle pdb=" C VAL R 184 " pdb=" N ILE R 185 " pdb=" CA ILE R 185 " ideal model delta sigma weight residual 122.13 118.01 4.12 1.85e+00 2.92e-01 4.96e+00 ... (remaining 13778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5340 17.76 - 35.53: 583 35.53 - 53.29: 131 53.29 - 71.05: 21 71.05 - 88.82: 7 Dihedral angle restraints: 6082 sinusoidal: 2430 harmonic: 3652 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -145.81 59.81 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG C 191 " pdb=" C ARG C 191 " pdb=" N MET C 192 " pdb=" CA MET C 192 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1168 0.046 - 0.092: 298 0.092 - 0.138: 79 0.138 - 0.184: 2 0.184 - 0.230: 1 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CG LEU R 35 " pdb=" CB LEU R 35 " pdb=" CD1 LEU R 35 " pdb=" CD2 LEU R 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA TYR A 306 " pdb=" N TYR A 306 " pdb=" C TYR A 306 " pdb=" CB TYR A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA GLU G 42 " pdb=" N GLU G 42 " pdb=" C GLU G 42 " pdb=" CB GLU G 42 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 1545 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.088 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO R 355 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 181 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C LEU R 181 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU R 181 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU R 182 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 236 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.026 5.00e-02 4.00e+02 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 491 2.73 - 3.27: 9413 3.27 - 3.81: 15838 3.81 - 4.36: 19972 4.36 - 4.90: 35806 Nonbonded interactions: 81520 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.184 2.440 nonbonded pdb=" OD2 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.198 2.440 nonbonded pdb=" OG SER R 154 " pdb=" O PRO R 166 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.252 2.440 nonbonded pdb=" OE1 GLU C 6 " pdb=" N GLY C 114 " model vdw 2.288 2.520 ... (remaining 81515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.560 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: 0.000 Extract box with map and model: 7.370 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.760 Find NCS groups from input model: 0.310 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.003 0.090 10159 Z= 0.221 Angle : 0.547 8.868 13783 Z= 0.296 Chirality : 0.043 0.230 1548 Planarity : 0.005 0.129 1734 Dihedral : 15.429 88.817 3715 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.09 % Allowed : 13.48 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1238 helix: 1.12 (0.25), residues: 413 sheet: 0.01 (0.27), residues: 341 loop : -1.02 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 211 HIS 0.003 0.001 HIS R 126 PHE 0.015 0.001 PHE A 189 TYR 0.018 0.001 TYR A 306 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.066 Fit side-chains REVERT: B 32 GLN cc_start: 0.8720 (mt0) cc_final: 0.8482 (mt0) REVERT: B 219 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7632 (mmp80) REVERT: R 35 LEU cc_start: 0.6685 (mp) cc_final: 0.6484 (mt) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.2306 time to fit residues: 40.6360 Evaluate side-chains 121 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10159 Z= 0.192 Angle : 0.509 7.179 13783 Z= 0.272 Chirality : 0.041 0.137 1548 Planarity : 0.004 0.073 1734 Dihedral : 5.160 46.425 1505 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.97 % Allowed : 13.67 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1238 helix: 1.35 (0.25), residues: 413 sheet: 0.06 (0.27), residues: 341 loop : -1.03 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.004 0.001 HIS R 126 PHE 0.016 0.001 PHE A 189 TYR 0.014 0.001 TYR A 306 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.042 Fit side-chains REVERT: B 9 GLN cc_start: 0.4699 (OUTLIER) cc_final: 0.4393 (mp10) REVERT: B 32 GLN cc_start: 0.8708 (mt0) cc_final: 0.8492 (mt0) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 0.2234 time to fit residues: 43.2197 Evaluate side-chains 137 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.0040 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10159 Z= 0.223 Angle : 0.529 7.763 13783 Z= 0.281 Chirality : 0.042 0.143 1548 Planarity : 0.004 0.057 1734 Dihedral : 5.249 52.628 1505 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.72 % Allowed : 15.36 % Favored : 81.93 % 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: 0.16 (0.24), residues: 1238 helix: 1.51 (0.25), residues: 407 sheet: 0.04 (0.27), residues: 343 loop : -1.01 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.004 0.001 HIS R 126 PHE 0.017 0.001 PHE A 189 TYR 0.011 0.001 TYR C 102 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.159 Fit side-chains REVERT: B 9 GLN cc_start: 0.4717 (OUTLIER) cc_final: 0.4406 (mp10) REVERT: R 126 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5355 (p-80) outliers start: 29 outliers final: 20 residues processed: 141 average time/residue: 0.2100 time to fit residues: 42.2050 Evaluate side-chains 143 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 53 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 99 optimal weight: 10.0000 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10159 Z= 0.126 Angle : 0.458 5.985 13783 Z= 0.246 Chirality : 0.040 0.135 1548 Planarity : 0.003 0.051 1734 Dihedral : 4.947 54.255 1505 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.56 % Allowed : 15.17 % Favored : 81.27 % 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: 0.40 (0.24), residues: 1238 helix: 1.80 (0.26), residues: 405 sheet: 0.20 (0.27), residues: 334 loop : -0.96 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.001 0.000 HIS R 126 PHE 0.015 0.001 PHE A 189 TYR 0.010 0.001 TYR R 192 ARG 0.001 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 0.979 Fit side-chains REVERT: B 9 GLN cc_start: 0.4729 (OUTLIER) cc_final: 0.4446 (mp10) REVERT: B 261 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8299 (mp) REVERT: R 126 HIS cc_start: 0.6089 (OUTLIER) cc_final: 0.5301 (p-80) outliers start: 38 outliers final: 24 residues processed: 158 average time/residue: 0.1974 time to fit residues: 44.9228 Evaluate side-chains 157 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10159 Z= 0.294 Angle : 0.576 8.811 13783 Z= 0.303 Chirality : 0.044 0.165 1548 Planarity : 0.004 0.073 1734 Dihedral : 5.403 59.260 1505 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.31 % Allowed : 15.82 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1238 helix: 1.54 (0.25), residues: 414 sheet: 0.05 (0.27), residues: 345 loop : -1.01 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.005 0.001 HIS R 126 PHE 0.018 0.002 PHE A 189 TYR 0.011 0.001 TYR C 102 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 125 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: B 9 GLN cc_start: 0.4754 (OUTLIER) cc_final: 0.4471 (mp10) REVERT: B 261 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8316 (mp) REVERT: R 126 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5477 (p-80) outliers start: 46 outliers final: 33 residues processed: 156 average time/residue: 0.2234 time to fit residues: 49.1444 Evaluate side-chains 159 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10159 Z= 0.178 Angle : 0.500 7.042 13783 Z= 0.266 Chirality : 0.041 0.142 1548 Planarity : 0.003 0.046 1734 Dihedral : 5.203 56.854 1505 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.31 % Allowed : 16.20 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1238 helix: 1.67 (0.25), residues: 411 sheet: 0.13 (0.27), residues: 341 loop : -0.97 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.002 0.001 HIS R 126 PHE 0.016 0.001 PHE A 189 TYR 0.011 0.001 TYR C 102 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: B 9 GLN cc_start: 0.4730 (OUTLIER) cc_final: 0.4449 (mp10) REVERT: B 261 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8281 (mp) REVERT: C 178 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8528 (tp) REVERT: R 126 HIS cc_start: 0.6169 (OUTLIER) cc_final: 0.5523 (p-80) outliers start: 46 outliers final: 31 residues processed: 161 average time/residue: 0.2020 time to fit residues: 46.7370 Evaluate side-chains 164 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 45 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10159 Z= 0.190 Angle : 0.510 7.206 13783 Z= 0.270 Chirality : 0.041 0.143 1548 Planarity : 0.004 0.046 1734 Dihedral : 5.181 54.814 1505 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.12 % Allowed : 17.04 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1238 helix: 1.65 (0.25), residues: 412 sheet: 0.12 (0.27), residues: 341 loop : -0.96 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.003 0.001 HIS R 126 PHE 0.016 0.001 PHE A 189 TYR 0.011 0.001 TYR C 102 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 127 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: B 9 GLN cc_start: 0.4797 (OUTLIER) cc_final: 0.4546 (mp10) REVERT: B 261 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 178 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8519 (tp) REVERT: R 126 HIS cc_start: 0.6206 (OUTLIER) cc_final: 0.5532 (p-80) REVERT: R 195 MET cc_start: 0.6127 (OUTLIER) cc_final: 0.4147 (ptt) outliers start: 44 outliers final: 34 residues processed: 158 average time/residue: 0.2140 time to fit residues: 47.8132 Evaluate side-chains 164 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 45 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.0060 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10159 Z= 0.173 Angle : 0.499 6.982 13783 Z= 0.264 Chirality : 0.041 0.149 1548 Planarity : 0.003 0.046 1734 Dihedral : 5.111 52.279 1505 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.40 % Allowed : 16.95 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1238 helix: 1.71 (0.26), residues: 411 sheet: 0.15 (0.27), residues: 341 loop : -0.93 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 211 HIS 0.003 0.001 HIS R 126 PHE 0.016 0.001 PHE A 189 TYR 0.010 0.001 TYR C 190 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7363 (mp0) REVERT: B 9 GLN cc_start: 0.4824 (OUTLIER) cc_final: 0.4575 (mp10) REVERT: B 261 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 140 MET cc_start: 0.8587 (mtp) cc_final: 0.8304 (mtp) REVERT: C 178 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8510 (tp) REVERT: R 126 HIS cc_start: 0.6268 (OUTLIER) cc_final: 0.5593 (p-80) REVERT: R 195 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.4142 (ptt) outliers start: 47 outliers final: 35 residues processed: 160 average time/residue: 0.1888 time to fit residues: 43.5229 Evaluate side-chains 169 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10159 Z= 0.200 Angle : 0.511 7.389 13783 Z= 0.271 Chirality : 0.041 0.144 1548 Planarity : 0.004 0.046 1734 Dihedral : 5.154 49.761 1505 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.03 % Allowed : 17.13 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1238 helix: 1.70 (0.25), residues: 414 sheet: 0.14 (0.27), residues: 335 loop : -0.90 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.003 0.001 HIS R 126 PHE 0.016 0.001 PHE A 189 TYR 0.011 0.001 TYR C 102 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 266 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7370 (mp0) REVERT: B 9 GLN cc_start: 0.4823 (OUTLIER) cc_final: 0.4580 (mp10) REVERT: B 261 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8289 (mp) REVERT: C 178 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8493 (tp) REVERT: R 126 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5593 (p-80) REVERT: R 195 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.4170 (ptt) outliers start: 43 outliers final: 36 residues processed: 159 average time/residue: 0.2041 time to fit residues: 46.4443 Evaluate side-chains 167 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 126 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 126 HIS Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 0.0030 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 350 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10159 Z= 0.258 Angle : 0.551 8.348 13783 Z= 0.291 Chirality : 0.043 0.149 1548 Planarity : 0.004 0.046 1734 Dihedral : 5.311 46.155 1505 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.93 % Allowed : 17.42 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1238 helix: 1.58 (0.25), residues: 414 sheet: 0.08 (0.27), residues: 337 loop : -0.96 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 316 HIS 0.004 0.001 HIS R 126 PHE 0.017 0.001 PHE A 189 TYR 0.012 0.001 TYR C 102 ARG 0.004 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: B 9 GLN cc_start: 0.4816 (OUTLIER) cc_final: 0.4562 (mp10) REVERT: B 261 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8262 (mp) REVERT: C 178 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8524 (tp) REVERT: R 175 LEU cc_start: 0.6700 (mp) cc_final: 0.6397 (mp) REVERT: R 195 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.4166 (ptt) outliers start: 42 outliers final: 34 residues processed: 155 average time/residue: 0.2077 time to fit residues: 45.9610 Evaluate side-chains 160 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 87 CYS Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.201733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.187963 restraints weight = 9920.380| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 0.67 r_work: 0.4008 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10159 Z= 0.205 Angle : 0.527 8.572 13783 Z= 0.278 Chirality : 0.042 0.170 1548 Planarity : 0.004 0.046 1734 Dihedral : 5.231 43.430 1505 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.65 % Allowed : 17.98 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1238 helix: 1.62 (0.25), residues: 412 sheet: 0.10 (0.27), residues: 335 loop : -0.92 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.005 0.001 HIS R 126 PHE 0.016 0.001 PHE A 189 TYR 0.011 0.001 TYR C 102 ARG 0.004 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.15 seconds wall clock time: 40 minutes 1.69 seconds (2401.69 seconds total)