Starting phenix.real_space_refine on Tue Jan 21 03:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zr5_60392/01_2025/8zr5_60392_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zr5_60392/01_2025/8zr5_60392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zr5_60392/01_2025/8zr5_60392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zr5_60392/01_2025/8zr5_60392.map" model { file = "/net/cci-nas-00/data/ceres_data/8zr5_60392/01_2025/8zr5_60392_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zr5_60392/01_2025/8zr5_60392_trim.cif" } resolution = 3.31 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= 0.027 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: 6 Type Number sf(0) Gaussians S 55 5.16 5 C 5171 2.51 5 N 1417 2.21 5 O 1508 1.98 5 F 1 1.80 5 H 8043 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16195 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3903 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5098 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1910 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "C" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4365 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'A1D8M': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.99, per 1000 atoms: 0.49 Number of scatterers: 16195 At special positions: 0 Unit cell: (82.45, 102.85, 134.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 F 1 9.00 O 1508 8.00 N 1417 7.00 C 5171 6.00 H 8043 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 78 " - pdb=" SG CYS C 155 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 44.2% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.890A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.616A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.626A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.551A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.032A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.185A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.724A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.615A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.620A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.944A 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 removed outlier: 3.560A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for '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 'C' and resid 7 through 36 removed outlier: 3.552A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 66 removed outlier: 3.960A pdb=" N CYS C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 109 removed outlier: 3.851A pdb=" N LEU C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 101 " --> pdb=" O MET C 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 118 through 138 removed outlier: 3.938A pdb=" N GLY C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.526A pdb=" N VAL C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 removed outlier: 3.979A pdb=" N VAL C 166 " --> pdb=" O HIS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 210 removed outlier: 3.514A pdb=" N LEU C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 190 " --> pdb=" O CYS C 186 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.624A pdb=" N SER C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.901A pdb=" N PHE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 265 removed outlier: 4.195A pdb=" N LEU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.619A pdb=" N VAL C 269 " --> pdb=" O TRP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 Processing helix chain 'C' and resid 283 through 298 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.294A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.804A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.675A 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: 6.743A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.977A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.558A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.567A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.131A 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: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.704A 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: 6.636A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.692A 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: 7.042A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1164 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: 5.36 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 1856 1.05 - 1.24: 7281 1.24 - 1.43: 2437 1.43 - 1.62: 4704 1.62 - 1.81: 79 Bond restraints: 16357 Sorted by residual: bond pdb=" CE2 PHE C 165 " pdb=" HE2 PHE C 165 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" CZ PHE A 238 " pdb=" HZ PHE A 238 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" CZ2 TRP A 234 " pdb=" HZ2 TRP A 234 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" CZ PHE C 161 " pdb=" HZ PHE C 161 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" CD2 HIS C 195 " pdb=" HD2 HIS C 195 " ideal model delta sigma weight residual 0.930 1.101 -0.171 2.00e-02 2.50e+03 7.27e+01 ... (remaining 16352 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 28718 1.90 - 3.79: 639 3.79 - 5.69: 61 5.69 - 7.58: 8 7.58 - 9.48: 5 Bond angle restraints: 29431 Sorted by residual: angle pdb=" CB HIS C 34 " pdb=" CG HIS C 34 " pdb=" CD2 HIS C 34 " ideal model delta sigma weight residual 131.20 122.61 8.59 1.30e+00 5.92e-01 4.37e+01 angle pdb=" CB HIS C 34 " pdb=" CG HIS C 34 " pdb=" ND1 HIS C 34 " ideal model delta sigma weight residual 122.70 131.27 -8.57 1.50e+00 4.44e-01 3.26e+01 angle pdb=" C ILE C 143 " pdb=" N PRO C 144 " pdb=" CA PRO C 144 " ideal model delta sigma weight residual 120.47 114.57 5.90 1.07e+00 8.73e-01 3.04e+01 angle pdb=" N SER B 84 " pdb=" CA SER B 84 " pdb=" C SER B 84 " ideal model delta sigma weight residual 111.33 117.09 -5.76 1.21e+00 6.83e-01 2.27e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.80 120.28 -9.48 2.13e+00 2.20e-01 1.98e+01 ... (remaining 29426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6752 17.65 - 35.31: 676 35.31 - 52.96: 220 52.96 - 70.62: 55 70.62 - 88.27: 15 Dihedral angle restraints: 7718 sinusoidal: 4147 harmonic: 3571 Sorted by residual: dihedral pdb=" CB CYS C 78 " pdb=" SG CYS C 78 " pdb=" SG CYS C 155 " pdb=" CB CYS C 155 " ideal model delta sinusoidal sigma weight residual 93.00 161.84 -68.84 1 1.00e+01 1.00e-02 6.13e+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 -160.93 -19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB GLU C 261 " pdb=" CG GLU C 261 " pdb=" CD GLU C 261 " pdb=" OE1 GLU C 261 " ideal model delta sinusoidal sigma weight residual 0.00 -87.37 87.37 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 7715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 995 0.045 - 0.090: 210 0.090 - 0.135: 67 0.135 - 0.180: 4 0.180 - 0.224: 5 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA LEU C 258 " pdb=" N LEU C 258 " pdb=" C LEU C 258 " pdb=" CB LEU C 258 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE C 143 " pdb=" N ILE C 143 " pdb=" C ILE C 143 " pdb=" CB ILE C 143 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1278 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 237 " 0.327 2.00e-02 2.50e+03 4.22e-01 2.67e+03 pdb=" CG ASN B 237 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 237 " -0.317 2.00e-02 2.50e+03 pdb=" ND2 ASN B 237 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 237 " 0.666 2.00e-02 2.50e+03 pdb="HD22 ASN B 237 " -0.645 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 283 " 0.273 2.00e-02 2.50e+03 2.80e-01 1.18e+03 pdb=" CD GLN C 283 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN C 283 " -0.260 2.00e-02 2.50e+03 pdb=" NE2 GLN C 283 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN C 283 " -0.401 2.00e-02 2.50e+03 pdb="HE22 GLN C 283 " 0.409 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 154 " 0.226 2.00e-02 2.50e+03 2.25e-01 7.57e+02 pdb=" CD GLN C 154 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN C 154 " -0.212 2.00e-02 2.50e+03 pdb=" NE2 GLN C 154 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 154 " 0.327 2.00e-02 2.50e+03 pdb="HE22 GLN C 154 " -0.315 2.00e-02 2.50e+03 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 194 1.94 - 2.60: 16681 2.60 - 3.27: 47196 3.27 - 3.93: 60747 3.93 - 4.60: 93046 Nonbonded interactions: 217864 Sorted by model distance: nonbonded pdb=" HG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 1.272 2.450 nonbonded pdb=" O VAL C 56 " pdb=" HG SER C 59 " model vdw 1.290 2.450 nonbonded pdb=" OD1 ASP C 51 " pdb=" HG SER C 92 " model vdw 1.309 2.450 nonbonded pdb=" O THR B 86 " pdb=" HG1 THR B 87 " model vdw 1.338 2.450 nonbonded pdb=" O ASP B 195 " pdb=" HG1 THR B 196 " model vdw 1.355 2.450 ... (remaining 217859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.170 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: 0.280 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 0.100 8314 Z= 0.344 Angle : 0.710 9.477 11263 Z= 0.438 Chirality : 0.043 0.224 1281 Planarity : 0.005 0.051 1435 Dihedral : 15.902 88.273 2999 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.23 % Allowed : 17.24 % Favored : 82.53 % 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: -0.42 (0.26), residues: 1028 helix: 0.34 (0.27), residues: 414 sheet: 0.04 (0.35), residues: 200 loop : -0.98 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS C 162 PHE 0.011 0.001 PHE C 158 TYR 0.016 0.001 TYR C 134 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 ASP cc_start: 0.7030 (t70) cc_final: 0.6826 (m-30) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.5045 time to fit residues: 85.4495 Evaluate side-chains 111 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.143630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107092 restraints weight = 27396.088| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.40 r_work: 0.3083 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8314 Z= 0.197 Angle : 0.511 5.800 11263 Z= 0.279 Chirality : 0.040 0.146 1281 Planarity : 0.004 0.053 1435 Dihedral : 4.541 55.448 1158 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.26 % Allowed : 17.59 % Favored : 81.15 % 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: 0.07 (0.27), residues: 1028 helix: 1.22 (0.27), residues: 417 sheet: -0.05 (0.35), residues: 197 loop : -1.08 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS C 292 PHE 0.011 0.001 PHE C 181 TYR 0.016 0.001 TYR C 281 ARG 0.004 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8484 (t0) cc_final: 0.7794 (p0) REVERT: B 234 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8263 (t80) REVERT: C 37 ASP cc_start: 0.7113 (t70) cc_final: 0.6827 (m-30) outliers start: 11 outliers final: 7 residues processed: 128 average time/residue: 0.5076 time to fit residues: 86.4478 Evaluate side-chains 119 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.141697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104849 restraints weight = 27451.322| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.38 r_work: 0.3161 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8314 Z= 0.239 Angle : 0.502 6.041 11263 Z= 0.272 Chirality : 0.040 0.143 1281 Planarity : 0.003 0.050 1435 Dihedral : 4.398 52.838 1158 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.26 % Allowed : 18.16 % Favored : 80.57 % 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: 0.28 (0.27), residues: 1028 helix: 1.62 (0.28), residues: 417 sheet: -0.17 (0.35), residues: 199 loop : -1.10 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS C 292 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR A 37 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8527 (t0) cc_final: 0.7783 (p0) REVERT: C 37 ASP cc_start: 0.7091 (t70) cc_final: 0.6778 (m-30) outliers start: 11 outliers final: 7 residues processed: 121 average time/residue: 0.5309 time to fit residues: 84.6634 Evaluate side-chains 114 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.143732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106998 restraints weight = 27183.978| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.38 r_work: 0.3206 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8314 Z= 0.154 Angle : 0.462 5.034 11263 Z= 0.248 Chirality : 0.039 0.144 1281 Planarity : 0.003 0.049 1435 Dihedral : 3.852 17.698 1156 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.61 % Allowed : 18.28 % Favored : 80.11 % 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: 0.69 (0.27), residues: 1028 helix: 2.05 (0.28), residues: 412 sheet: 0.07 (0.36), residues: 195 loop : -0.97 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS C 292 PHE 0.010 0.001 PHE A 212 TYR 0.011 0.001 TYR A 37 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8463 (t0) cc_final: 0.7830 (p0) REVERT: C 37 ASP cc_start: 0.7128 (t70) cc_final: 0.6817 (m-30) outliers start: 14 outliers final: 10 residues processed: 127 average time/residue: 0.5128 time to fit residues: 86.0856 Evaluate side-chains 121 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.143424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106530 restraints weight = 27555.698| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.39 r_work: 0.3197 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8314 Z= 0.169 Angle : 0.461 5.288 11263 Z= 0.247 Chirality : 0.039 0.143 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.839 18.465 1156 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.72 % Allowed : 17.59 % Favored : 80.69 % 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: 0.72 (0.27), residues: 1028 helix: 2.10 (0.28), residues: 412 sheet: 0.05 (0.36), residues: 197 loop : -0.98 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS C 292 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR A 37 ARG 0.001 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8472 (t0) cc_final: 0.7898 (p0) REVERT: B 215 GLU cc_start: 0.7607 (tt0) cc_final: 0.7357 (tt0) REVERT: C 37 ASP cc_start: 0.7025 (t70) cc_final: 0.6699 (m-30) REVERT: C 105 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8435 (mp) outliers start: 15 outliers final: 12 residues processed: 125 average time/residue: 0.5105 time to fit residues: 84.4451 Evaluate side-chains 123 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.143361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106407 restraints weight = 27298.100| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.38 r_work: 0.3083 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8314 Z= 0.174 Angle : 0.458 5.351 11263 Z= 0.245 Chirality : 0.039 0.144 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.849 18.795 1156 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.84 % Allowed : 17.24 % Favored : 80.92 % 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: 0.76 (0.27), residues: 1028 helix: 2.15 (0.28), residues: 412 sheet: 0.07 (0.36), residues: 202 loop : -0.98 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS C 292 PHE 0.011 0.001 PHE B 199 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8452 (t0) cc_final: 0.7871 (p0) REVERT: G 22 GLU cc_start: 0.7378 (tt0) cc_final: 0.6515 (mt-10) REVERT: C 37 ASP cc_start: 0.7111 (t70) cc_final: 0.6750 (m-30) REVERT: C 105 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8447 (mp) outliers start: 16 outliers final: 13 residues processed: 125 average time/residue: 0.5185 time to fit residues: 86.5769 Evaluate side-chains 125 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.142780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105769 restraints weight = 27374.207| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.38 r_work: 0.3094 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8314 Z= 0.195 Angle : 0.469 5.477 11263 Z= 0.250 Chirality : 0.039 0.143 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.912 19.974 1156 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.18 % Allowed : 17.13 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1028 helix: 2.14 (0.28), residues: 412 sheet: 0.02 (0.36), residues: 199 loop : -0.99 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS C 292 PHE 0.012 0.001 PHE B 199 TYR 0.013 0.001 TYR A 37 ARG 0.001 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8457 (t0) cc_final: 0.7861 (p0) REVERT: G 22 GLU cc_start: 0.7376 (tt0) cc_final: 0.6571 (mt-10) REVERT: C 105 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8453 (mp) outliers start: 19 outliers final: 15 residues processed: 126 average time/residue: 0.4892 time to fit residues: 82.1827 Evaluate side-chains 126 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.142517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.105544 restraints weight = 27261.768| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.37 r_work: 0.3083 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8314 Z= 0.192 Angle : 0.465 5.511 11263 Z= 0.249 Chirality : 0.039 0.144 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.934 20.376 1156 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.95 % Allowed : 17.47 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1028 helix: 2.15 (0.28), residues: 412 sheet: 0.04 (0.37), residues: 199 loop : -1.01 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS C 292 PHE 0.012 0.001 PHE B 199 TYR 0.013 0.001 TYR A 37 ARG 0.001 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8421 (t0) cc_final: 0.7821 (p0) REVERT: G 14 LYS cc_start: 0.7268 (tptt) cc_final: 0.6728 (mtmt) REVERT: G 22 GLU cc_start: 0.7375 (tt0) cc_final: 0.6559 (mt-10) REVERT: C 77 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6899 (mp) REVERT: C 105 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8437 (mp) outliers start: 17 outliers final: 15 residues processed: 125 average time/residue: 0.4778 time to fit residues: 80.2551 Evaluate side-chains 125 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.144325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107186 restraints weight = 27127.576| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.38 r_work: 0.3107 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8314 Z= 0.140 Angle : 0.447 5.080 11263 Z= 0.237 Chirality : 0.038 0.145 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.799 19.550 1156 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.84 % Allowed : 17.36 % Favored : 80.80 % 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: 0.95 (0.27), residues: 1028 helix: 2.42 (0.28), residues: 406 sheet: 0.03 (0.36), residues: 200 loop : -0.86 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS C 292 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR A 37 ARG 0.001 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8377 (t0) cc_final: 0.7910 (p0) REVERT: G 14 LYS cc_start: 0.7231 (tptt) cc_final: 0.6693 (mtmt) REVERT: G 22 GLU cc_start: 0.7366 (tt0) cc_final: 0.6563 (mt-10) REVERT: C 77 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6802 (mp) REVERT: C 105 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8445 (mp) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 0.4706 time to fit residues: 81.7439 Evaluate side-chains 125 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.144529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107435 restraints weight = 27218.654| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.38 r_work: 0.3114 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8314 Z= 0.144 Angle : 0.449 5.514 11263 Z= 0.238 Chirality : 0.038 0.144 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.769 19.760 1156 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.61 % Allowed : 17.93 % Favored : 80.46 % 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: 1.01 (0.27), residues: 1028 helix: 2.49 (0.28), residues: 406 sheet: 0.04 (0.36), residues: 200 loop : -0.86 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS B 54 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR A 37 ARG 0.001 0.000 ARG G 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 366 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue THR 73 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue TYR 257 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8360 (t0) cc_final: 0.7911 (p0) REVERT: G 14 LYS cc_start: 0.7286 (tptt) cc_final: 0.6747 (mtmt) REVERT: G 22 GLU cc_start: 0.7363 (tt0) cc_final: 0.6580 (mt-10) REVERT: C 77 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6819 (mp) REVERT: C 105 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8455 (mp) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 0.4723 time to fit residues: 82.6152 Evaluate side-chains 123 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 33 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.144671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107609 restraints weight = 27094.689| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.38 r_work: 0.3096 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8314 Z= 0.136 Angle : 0.443 5.458 11263 Z= 0.235 Chirality : 0.038 0.143 1281 Planarity : 0.003 0.048 1435 Dihedral : 3.710 19.284 1156 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.72 % Allowed : 18.05 % Favored : 80.23 % 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: 1.07 (0.28), residues: 1028 helix: 2.56 (0.28), residues: 407 sheet: 0.10 (0.36), residues: 205 loop : -0.87 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS C 292 PHE 0.010 0.001 PHE B 199 TYR 0.009 0.001 TYR A 37 ARG 0.001 0.000 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 8197.90 seconds wall clock time: 144 minutes 48.77 seconds (8688.77 seconds total)