Starting phenix.real_space_refine on Thu Feb 13 06:23:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihb_35442/02_2025/8ihb_35442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihb_35442/02_2025/8ihb_35442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihb_35442/02_2025/8ihb_35442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihb_35442/02_2025/8ihb_35442.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihb_35442/02_2025/8ihb_35442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihb_35442/02_2025/8ihb_35442.cif" } resolution = 2.85 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= -0.001 sd= 0.044 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: 5 Type Number sf(0) Gaussians S 62 5.16 5 Cl 1 4.86 5 C 5568 2.51 5 N 1480 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2385 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1706 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2491 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 386 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'NAG': 1, 'OKL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.54, per 1000 atoms: 0.64 Number of scatterers: 8708 At special positions: 0 Unit cell: (86.32, 116.2, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 62 16.00 O 1597 8.00 N 1480 7.00 C 5568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 37.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'R' and resid 23 through 28 removed outlier: 4.340A pdb=" N VAL R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 23 through 28' Processing helix chain 'R' and resid 29 through 55 Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 88 Processing helix chain 'R' and resid 97 through 130 removed outlier: 3.537A pdb=" N LEU R 104 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN R 110 " --> pdb=" O MET R 106 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.648A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 Processing helix chain 'R' and resid 160 through 165 removed outlier: 3.635A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 196 Processing helix chain 'R' and resid 197 through 218 removed outlier: 3.560A pdb=" N ILE R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 261 removed outlier: 3.527A pdb=" N THR R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.595A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 295 removed outlier: 3.714A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.580A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.577A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.354A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.153A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.713A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.566A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.863A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.189A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.682A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 4.037A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'R' and resid 11 through 13 removed outlier: 4.089A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 170 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.638A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AA5, first strand: chain 'S' and resid 58 through 60 removed outlier: 4.248A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'S' and resid 156 through 160 Processing sheet with id=AA8, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.473A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.508A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.903A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.828A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.629A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.514A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.424A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1146 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: 2.53 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1902 1.33 - 1.46: 2600 1.46 - 1.58: 4313 1.58 - 1.71: 1 1.71 - 1.84: 88 Bond restraints: 8904 Sorted by residual: bond pdb=" C SER B 331 " pdb=" O SER B 331 " ideal model delta sigma weight residual 1.233 1.201 0.032 1.17e-02 7.31e+03 7.55e+00 bond pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.37e-02 5.33e+03 7.18e+00 bond pdb=" C15 OKL R 602 " pdb=" N16 OKL R 602 " ideal model delta sigma weight residual 1.335 1.383 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C SER B 316 " pdb=" O SER B 316 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.29e-02 6.01e+03 4.97e+00 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.529 1.494 0.036 1.63e-02 3.76e+03 4.76e+00 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 11792 1.39 - 2.78: 224 2.78 - 4.17: 42 4.17 - 5.56: 22 5.56 - 6.95: 4 Bond angle restraints: 12084 Sorted by residual: angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 112.23 117.57 -5.34 1.26e+00 6.30e-01 1.80e+01 angle pdb=" N SER B 316 " pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 110.30 105.45 4.85 1.54e+00 4.22e-01 9.92e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 113.17 -4.57 1.46e+00 4.69e-01 9.80e+00 angle pdb=" C ASP R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta sigma weight residual 120.33 122.57 -2.24 8.00e-01 1.56e+00 7.81e+00 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 109.47 4.43 1.80e+00 3.09e-01 6.06e+00 ... (remaining 12079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 4733 23.42 - 46.85: 430 46.85 - 70.27: 56 70.27 - 93.69: 7 93.69 - 117.11: 1 Dihedral angle restraints: 5227 sinusoidal: 1951 harmonic: 3276 Sorted by residual: dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -127.37 41.37 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 800 0.029 - 0.058: 370 0.058 - 0.087: 119 0.087 - 0.116: 69 0.116 - 0.145: 19 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA ASP S 90 " pdb=" N ASP S 90 " pdb=" C ASP S 90 " pdb=" CB ASP S 90 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA GLU S 42 " pdb=" N GLU S 42 " pdb=" C GLU S 42 " pdb=" CB GLU S 42 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1374 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 OKL R 602 " -0.012 2.00e-02 2.50e+03 4.05e-02 5.34e+01 pdb=" C07 OKL R 602 " -0.020 2.00e-02 2.50e+03 pdb=" C10 OKL R 602 " 0.006 2.00e-02 2.50e+03 pdb=" C12 OKL R 602 " 0.040 2.00e-02 2.50e+03 pdb=" C13 OKL R 602 " 0.052 2.00e-02 2.50e+03 pdb=" C15 OKL R 602 " 0.019 2.00e-02 2.50e+03 pdb=" N06 OKL R 602 " 0.018 2.00e-02 2.50e+03 pdb=" N09 OKL R 602 " -0.020 2.00e-02 2.50e+03 pdb=" N14 OKL R 602 " 0.052 2.00e-02 2.50e+03 pdb=" N16 OKL R 602 " 0.023 2.00e-02 2.50e+03 pdb=" O08 OKL R 602 " -0.040 2.00e-02 2.50e+03 pdb=" O11 OKL R 602 " -0.016 2.00e-02 2.50e+03 pdb="CL17 OKL R 602 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " 0.029 2.00e-02 2.50e+03 1.74e-02 6.04e+00 pdb=" CG TYR S 235 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO R 32 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.031 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 799 2.74 - 3.28: 8284 3.28 - 3.82: 14358 3.82 - 4.36: 17565 4.36 - 4.90: 31056 Nonbonded interactions: 72062 Sorted by model distance: nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.202 3.120 nonbonded pdb=" O ASP S 223 " pdb=" OH TYR S 227 " model vdw 2.230 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 2.238 3.120 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.240 3.120 ... (remaining 72057 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.100 Find NCS groups from input model: 0.120 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.004 0.059 8904 Z= 0.262 Angle : 0.536 6.950 12084 Z= 0.286 Chirality : 0.042 0.145 1377 Planarity : 0.004 0.054 1524 Dihedral : 17.040 117.112 3100 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.44 % Allowed : 28.24 % Favored : 71.32 % 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: -0.70 (0.24), residues: 1115 helix: -0.01 (0.26), residues: 358 sheet: 0.17 (0.32), residues: 263 loop : -1.08 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.002 0.001 HIS A 188 PHE 0.016 0.001 PHE A 334 TYR 0.039 0.001 TYR S 235 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7619 (ptpt) REVERT: R 63 ARG cc_start: 0.8369 (mtp85) cc_final: 0.8168 (mmt90) REVERT: R 170 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6666 (tm130) REVERT: A 263 SER cc_start: 0.8696 (m) cc_final: 0.8295 (p) REVERT: S 83 MET cc_start: 0.9136 (mtm) cc_final: 0.8857 (mtp) REVERT: B 197 ARG cc_start: 0.7465 (mmm160) cc_final: 0.7256 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 1.2103 time to fit residues: 186.5698 Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 39 GLN S 179 GLN S 183 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125564 restraints weight = 10111.223| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.00 r_work: 0.3202 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8904 Z= 0.367 Angle : 0.624 7.609 12084 Z= 0.337 Chirality : 0.045 0.212 1377 Planarity : 0.005 0.049 1524 Dihedral : 6.490 113.128 1241 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.95 % Allowed : 25.82 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1115 helix: 1.09 (0.26), residues: 362 sheet: 0.23 (0.31), residues: 272 loop : -1.06 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 63 HIS 0.005 0.001 HIS B 91 PHE 0.015 0.002 PHE S 27 TYR 0.035 0.002 TYR S 235 ARG 0.004 0.000 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7574 (ptpt) REVERT: R 227 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7284 (ptpt) REVERT: R 298 SER cc_start: 0.8952 (m) cc_final: 0.8747 (t) REVERT: A 263 SER cc_start: 0.8727 (m) cc_final: 0.8344 (p) REVERT: A 276 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: A 313 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.5610 (pmm-80) REVERT: S 42 GLU cc_start: 0.7092 (pp20) cc_final: 0.6791 (pp20) REVERT: S 43 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8623 (mmmt) REVERT: S 77 ASN cc_start: 0.8219 (m-40) cc_final: 0.7997 (m-40) REVERT: S 83 MET cc_start: 0.9291 (mtm) cc_final: 0.9013 (mtp) REVERT: B 195 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7610 (p0) REVERT: B 197 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7843 (mmt-90) REVERT: B 219 ARG cc_start: 0.8457 (mmt90) cc_final: 0.8224 (mmt180) REVERT: B 293 ASN cc_start: 0.8522 (m-40) cc_final: 0.8193 (m-40) REVERT: B 336 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8996 (mp) outliers start: 45 outliers final: 15 residues processed: 161 average time/residue: 1.1789 time to fit residues: 202.9988 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 0.0030 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126982 restraints weight = 10205.683| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.99 r_work: 0.3246 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8904 Z= 0.234 Angle : 0.551 6.143 12084 Z= 0.295 Chirality : 0.043 0.217 1377 Planarity : 0.004 0.045 1524 Dihedral : 5.982 104.880 1237 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.62 % Allowed : 27.25 % Favored : 68.13 % 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: 0.17 (0.25), residues: 1115 helix: 1.57 (0.27), residues: 364 sheet: 0.07 (0.30), residues: 291 loop : -1.03 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE A 334 TYR 0.028 0.001 TYR S 235 ARG 0.003 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7372 (ptpt) REVERT: R 227 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7288 (ptpt) REVERT: R 298 SER cc_start: 0.8992 (m) cc_final: 0.8781 (t) REVERT: A 276 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: A 313 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5562 (pmm-80) REVERT: S 43 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8852 (mmmt) REVERT: S 83 MET cc_start: 0.9223 (mtm) cc_final: 0.8975 (mtp) REVERT: S 235 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6831 (t80) REVERT: B 52 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8332 (mtt90) REVERT: B 195 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7628 (p0) REVERT: B 197 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7786 (mmt-90) REVERT: B 293 ASN cc_start: 0.8352 (m-40) cc_final: 0.8035 (m-40) outliers start: 42 outliers final: 20 residues processed: 155 average time/residue: 1.1400 time to fit residues: 189.4905 Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 105 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.165859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127446 restraints weight = 10079.956| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.96 r_work: 0.3234 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8904 Z= 0.263 Angle : 0.568 8.110 12084 Z= 0.301 Chirality : 0.043 0.205 1377 Planarity : 0.004 0.048 1524 Dihedral : 5.751 95.598 1237 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.71 % Allowed : 27.03 % Favored : 67.25 % 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: 0.22 (0.25), residues: 1115 helix: 1.77 (0.27), residues: 363 sheet: -0.01 (0.30), residues: 294 loop : -1.05 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.015 0.001 PHE A 334 TYR 0.025 0.001 TYR S 235 ARG 0.003 0.000 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7276 (ptpt) REVERT: R 112 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8585 (mt0) REVERT: R 227 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7269 (ptpt) REVERT: R 288 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8265 (ptt) REVERT: R 298 SER cc_start: 0.9003 (m) cc_final: 0.8789 (t) REVERT: A 257 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.7929 (ptmt) REVERT: A 276 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: A 313 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5575 (pmm-80) REVERT: S 83 MET cc_start: 0.9218 (mtm) cc_final: 0.8962 (mtp) REVERT: S 235 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7013 (t80) REVERT: B 52 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8327 (mtt90) REVERT: B 195 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7644 (p0) REVERT: B 197 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7791 (mmt-90) REVERT: B 336 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8992 (mp) outliers start: 52 outliers final: 26 residues processed: 153 average time/residue: 1.1345 time to fit residues: 186.2224 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.165777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125802 restraints weight = 10015.648| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.99 r_work: 0.3236 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8904 Z= 0.270 Angle : 0.570 8.313 12084 Z= 0.301 Chirality : 0.044 0.215 1377 Planarity : 0.004 0.045 1524 Dihedral : 5.729 94.008 1237 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.04 % Allowed : 26.70 % Favored : 67.25 % 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: 0.23 (0.25), residues: 1115 helix: 1.87 (0.27), residues: 363 sheet: -0.07 (0.29), residues: 295 loop : -1.09 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE A 334 TYR 0.026 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7239 (ptpt) REVERT: R 112 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8547 (mt0) REVERT: R 227 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7266 (ptpt) REVERT: R 298 SER cc_start: 0.9015 (m) cc_final: 0.8794 (t) REVERT: A 21 ARG cc_start: 0.8315 (ptm-80) cc_final: 0.7931 (ptp90) REVERT: A 207 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: A 257 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7880 (ptmt) REVERT: A 276 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 313 ARG cc_start: 0.6238 (OUTLIER) cc_final: 0.5544 (pmm-80) REVERT: S 83 MET cc_start: 0.9196 (mtm) cc_final: 0.8955 (mtp) REVERT: S 235 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 52 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8423 (mtt90) REVERT: B 195 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7615 (p0) REVERT: B 197 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7737 (mmt-90) REVERT: B 336 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9007 (mp) outliers start: 55 outliers final: 28 residues processed: 157 average time/residue: 1.1958 time to fit residues: 200.3591 Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.166058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126011 restraints weight = 10001.227| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.01 r_work: 0.3243 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8904 Z= 0.250 Angle : 0.555 6.880 12084 Z= 0.295 Chirality : 0.043 0.204 1377 Planarity : 0.004 0.048 1524 Dihedral : 5.634 92.079 1237 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.15 % Allowed : 26.59 % Favored : 67.25 % 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 (0.25), residues: 1115 helix: 1.98 (0.27), residues: 363 sheet: -0.07 (0.29), residues: 298 loop : -1.05 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.016 0.001 PHE A 334 TYR 0.025 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 122 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7169 (ptpt) REVERT: R 101 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7449 (mtt-85) REVERT: R 106 MET cc_start: 0.8708 (tpp) cc_final: 0.8231 (mmp) REVERT: R 112 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8630 (mt0) REVERT: R 227 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7265 (ptpt) REVERT: R 298 SER cc_start: 0.9007 (m) cc_final: 0.8798 (t) REVERT: A 21 ARG cc_start: 0.8324 (ptm-80) cc_final: 0.7934 (ptp90) REVERT: A 207 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: A 257 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7892 (ptmt) REVERT: A 276 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 313 ARG cc_start: 0.6237 (OUTLIER) cc_final: 0.5550 (pmm-80) REVERT: S 87 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7021 (mtm180) REVERT: S 235 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.7002 (t80) REVERT: B 52 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8416 (mtt90) REVERT: B 195 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7629 (p0) REVERT: B 197 ARG cc_start: 0.7997 (mmm160) cc_final: 0.7754 (mmt-90) REVERT: B 336 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8986 (mp) outliers start: 56 outliers final: 29 residues processed: 159 average time/residue: 1.2435 time to fit residues: 211.2280 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.166028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127260 restraints weight = 10188.887| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.00 r_work: 0.3232 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8904 Z= 0.254 Angle : 0.562 7.072 12084 Z= 0.299 Chirality : 0.043 0.209 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.600 90.071 1237 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.82 % Allowed : 26.48 % Favored : 67.69 % 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: 0.32 (0.25), residues: 1115 helix: 2.01 (0.27), residues: 363 sheet: -0.08 (0.29), residues: 297 loop : -1.06 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 PHE 0.017 0.001 PHE A 334 TYR 0.025 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7163 (ptpt) REVERT: R 101 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7460 (mtt-85) REVERT: R 112 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8589 (mt0) REVERT: R 227 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7289 (ptpt) REVERT: R 298 SER cc_start: 0.9002 (m) cc_final: 0.8798 (t) REVERT: A 21 ARG cc_start: 0.8345 (ptm-80) cc_final: 0.7933 (ptp90) REVERT: A 207 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: A 257 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7897 (ptmt) REVERT: A 276 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: A 313 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5573 (pmm-80) REVERT: S 235 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7008 (t80) REVERT: B 52 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8437 (mtt90) REVERT: B 195 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7662 (p0) REVERT: B 197 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7782 (mmt-90) REVERT: B 336 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8997 (mp) outliers start: 53 outliers final: 32 residues processed: 161 average time/residue: 1.2696 time to fit residues: 217.4858 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126317 restraints weight = 10168.315| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.00 r_work: 0.3219 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8904 Z= 0.296 Angle : 0.585 7.603 12084 Z= 0.310 Chirality : 0.044 0.216 1377 Planarity : 0.004 0.047 1524 Dihedral : 5.690 90.180 1237 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 6.04 % Allowed : 26.81 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1115 helix: 1.94 (0.27), residues: 363 sheet: 0.03 (0.30), residues: 282 loop : -1.12 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.002 PHE A 334 TYR 0.025 0.002 TYR S 235 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7156 (ptpt) REVERT: R 101 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7482 (mtt-85) REVERT: R 112 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8636 (mt0) REVERT: R 227 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7319 (ptpt) REVERT: A 21 ARG cc_start: 0.8328 (ptm-80) cc_final: 0.7919 (ptp90) REVERT: A 207 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: A 257 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7905 (ptmt) REVERT: A 276 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 312 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8361 (mptt) REVERT: A 313 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5662 (pmm-80) REVERT: S 87 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7146 (mtm180) REVERT: S 235 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7035 (t80) REVERT: B 52 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8435 (mtt90) REVERT: B 195 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7666 (p0) REVERT: B 197 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7781 (mmt-90) REVERT: B 336 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8999 (mp) outliers start: 55 outliers final: 33 residues processed: 161 average time/residue: 1.2361 time to fit residues: 212.0742 Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 206 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN B 32 GLN B 88 ASN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.167310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127377 restraints weight = 10145.419| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.02 r_work: 0.3261 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8904 Z= 0.199 Angle : 0.545 6.254 12084 Z= 0.290 Chirality : 0.043 0.193 1377 Planarity : 0.004 0.045 1524 Dihedral : 5.484 88.288 1237 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.29 % Allowed : 28.46 % Favored : 67.25 % 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: 0.41 (0.25), residues: 1115 helix: 2.12 (0.27), residues: 363 sheet: 0.02 (0.29), residues: 286 loop : -1.05 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.018 0.001 PHE A 334 TYR 0.024 0.001 TYR S 235 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7511 (mtmm) cc_final: 0.7113 (ptpt) REVERT: R 101 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7468 (mtt-85) REVERT: R 112 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: A 21 ARG cc_start: 0.8249 (ptm-80) cc_final: 0.7855 (ptp90) REVERT: A 207 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: A 276 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 313 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5530 (pmm-80) REVERT: S 87 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7087 (mtm180) REVERT: S 235 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6929 (t80) REVERT: B 52 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8380 (mtt90) REVERT: B 195 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7658 (p0) REVERT: B 197 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7740 (mmt-90) REVERT: B 336 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8966 (mp) outliers start: 39 outliers final: 23 residues processed: 150 average time/residue: 1.2739 time to fit residues: 203.2671 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 105 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.166290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127623 restraints weight = 10151.904| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.00 r_work: 0.3237 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8904 Z= 0.251 Angle : 0.575 8.804 12084 Z= 0.303 Chirality : 0.043 0.201 1377 Planarity : 0.004 0.048 1524 Dihedral : 5.544 88.670 1237 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.07 % Allowed : 28.90 % Favored : 67.03 % 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 (0.25), residues: 1115 helix: 2.07 (0.27), residues: 363 sheet: 0.01 (0.29), residues: 286 loop : -1.05 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.019 0.001 PHE A 334 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7527 (mtmm) cc_final: 0.7114 (ptpt) REVERT: R 101 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7458 (mtt-85) REVERT: R 112 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: A 21 ARG cc_start: 0.8287 (ptm-80) cc_final: 0.7902 (ptp90) REVERT: A 207 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: A 276 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: A 313 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5627 (pmm-80) REVERT: S 87 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7103 (mtm180) REVERT: S 235 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 52 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8421 (mtt90) REVERT: B 195 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7660 (p0) REVERT: B 197 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7770 (mmt-90) REVERT: B 336 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8974 (mp) outliers start: 37 outliers final: 26 residues processed: 142 average time/residue: 1.2605 time to fit residues: 192.0035 Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 165 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126140 restraints weight = 10211.203| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.02 r_work: 0.3215 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8904 Z= 0.311 Angle : 0.620 11.394 12084 Z= 0.322 Chirality : 0.045 0.219 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.726 89.478 1237 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.29 % Allowed : 28.90 % Favored : 66.81 % 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: 0.29 (0.25), residues: 1115 helix: 1.90 (0.27), residues: 363 sheet: 0.05 (0.30), residues: 282 loop : -1.08 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.005 0.001 HIS A 322 PHE 0.018 0.002 PHE A 334 TYR 0.025 0.002 TYR S 235 ARG 0.003 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7154.54 seconds wall clock time: 126 minutes 54.27 seconds (7614.27 seconds total)