Starting phenix.real_space_refine on Mon May 12 05:17:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihb_35442/05_2025/8ihb_35442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihb_35442/05_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_35442/05_2025/8ihb_35442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihb_35442/05_2025/8ihb_35442.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihb_35442/05_2025/8ihb_35442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihb_35442/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.19, per 1000 atoms: 0.60 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: 1.95 Conformation dependent library (CDL) restraints added in 964.2 milliseconds 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: 0.97 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: 2.37 Time building geometry restraints manager: 2.30 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: 2.990 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.050 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- 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 8908 Z= 0.172 Angle : 0.540 6.950 12093 Z= 0.287 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 3.55407 ( 3) hydrogen bonds : bond 0.26251 ( 413) hydrogen bonds : angle 8.29448 ( 1146) SS BOND : bond 0.00694 ( 3) SS BOND : angle 1.48510 ( 6) covalent geometry : bond 0.00385 ( 8904) covalent geometry : angle 0.53642 (12084) *********************** 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 : 1.001 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: 1.1482 time to fit residues: 176.8296 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 : 0.976 ------------------------------------------------------------------------------- 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 8908 Z= 0.235 Angle : 0.628 7.609 12093 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 1) link_NAG-ASN : angle 4.05084 ( 3) hydrogen bonds : bond 0.06164 ( 413) hydrogen bonds : angle 5.20273 ( 1146) SS BOND : bond 0.00584 ( 3) SS BOND : angle 1.26008 ( 6) covalent geometry : bond 0.00557 ( 8904) covalent geometry : angle 0.62431 (12084) *********************** 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 : 0.976 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: 1.1252 time to fit residues: 193.9351 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 : 0.925 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126466 restraints weight = 10218.735| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.00 r_work: 0.3236 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8908 Z= 0.166 Angle : 0.570 6.148 12093 Z= 0.303 Chirality : 0.043 0.218 1377 Planarity : 0.004 0.045 1524 Dihedral : 6.045 104.865 1237 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.62 % Allowed : 27.36 % Favored : 68.02 % 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: 0.13 (0.25), residues: 1115 helix: 1.52 (0.27), residues: 364 sheet: 0.06 (0.30), residues: 291 loop : -1.04 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 1) link_NAG-ASN : angle 4.21806 ( 3) hydrogen bonds : bond 0.05001 ( 413) hydrogen bonds : angle 4.70802 ( 1146) SS BOND : bond 0.00627 ( 3) SS BOND : angle 1.61754 ( 6) covalent geometry : bond 0.00390 ( 8904) covalent geometry : angle 0.56491 (12084) *********************** 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 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7378 (ptpt) REVERT: R 227 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7298 (ptpt) REVERT: A 276 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: A 313 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5588 (pmm-80) REVERT: S 43 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8855 (mmmt) REVERT: S 83 MET cc_start: 0.9242 (mtm) cc_final: 0.8987 (mtp) REVERT: S 235 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6872 (t80) REVERT: B 52 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8344 (mtt90) REVERT: B 195 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7641 (p0) REVERT: B 197 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7808 (mmt-90) REVERT: B 219 ARG cc_start: 0.8450 (mmt90) cc_final: 0.8235 (mmt180) REVERT: B 293 ASN cc_start: 0.8378 (m-40) cc_final: 0.8059 (m-40) outliers start: 42 outliers final: 20 residues processed: 156 average time/residue: 1.0469 time to fit residues: 175.1708 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.163336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125105 restraints weight = 10149.622| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.96 r_work: 0.3202 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8908 Z= 0.246 Angle : 0.636 9.194 12093 Z= 0.335 Chirality : 0.046 0.236 1377 Planarity : 0.004 0.047 1524 Dihedral : 6.051 95.706 1237 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.60 % Allowed : 27.25 % 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: 0.02 (0.25), residues: 1115 helix: 1.51 (0.27), residues: 364 sheet: 0.03 (0.30), residues: 280 loop : -1.18 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE S 29 TYR 0.028 0.002 TYR S 235 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 1) link_NAG-ASN : angle 3.60133 ( 3) hydrogen bonds : bond 0.05321 ( 413) hydrogen bonds : angle 4.70609 ( 1146) SS BOND : bond 0.00599 ( 3) SS BOND : angle 1.45662 ( 6) covalent geometry : bond 0.00592 ( 8904) covalent geometry : angle 0.63288 (12084) *********************** 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 170 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7670 (mtmm) cc_final: 0.7388 (ptpt) REVERT: R 227 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7321 (ptpt) REVERT: A 257 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7930 (ptmt) REVERT: A 276 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 313 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5625 (pmm-80) REVERT: S 83 MET cc_start: 0.9284 (mtm) cc_final: 0.9016 (mtp) REVERT: S 235 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.7067 (t80) REVERT: B 52 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8348 (mtt90) REVERT: B 195 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7575 (p0) REVERT: B 197 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7792 (mmt-90) REVERT: B 336 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9004 (mp) outliers start: 51 outliers final: 26 residues processed: 154 average time/residue: 1.0549 time to fit residues: 174.2722 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 VAL 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 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 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: 5.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 77 ASN B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125682 restraints weight = 10047.391| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.97 r_work: 0.3223 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8908 Z= 0.196 Angle : 0.599 7.889 12093 Z= 0.316 Chirality : 0.044 0.230 1377 Planarity : 0.004 0.043 1524 Dihedral : 5.895 94.069 1237 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.93 % Allowed : 27.03 % 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: 0.09 (0.25), residues: 1115 helix: 1.67 (0.27), residues: 363 sheet: 0.01 (0.30), residues: 280 loop : -1.19 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.003 0.001 HIS A 322 PHE 0.015 0.001 PHE A 334 TYR 0.028 0.002 TYR S 235 ARG 0.002 0.000 ARG R 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 1) link_NAG-ASN : angle 3.88732 ( 3) hydrogen bonds : bond 0.04836 ( 413) hydrogen bonds : angle 4.54886 ( 1146) SS BOND : bond 0.00760 ( 3) SS BOND : angle 1.84273 ( 6) covalent geometry : bond 0.00470 ( 8904) covalent geometry : angle 0.59478 (12084) *********************** 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 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7278 (ptpt) REVERT: R 112 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8549 (mt0) REVERT: R 227 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7329 (ptpt) REVERT: R 288 MET cc_start: 0.8593 (ptm) cc_final: 0.8309 (ptt) REVERT: A 21 ARG cc_start: 0.8312 (ptm-80) cc_final: 0.8004 (ptp90) REVERT: A 257 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7957 (ptmt) REVERT: A 276 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 312 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8375 (mptt) REVERT: A 313 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5630 (pmm-80) REVERT: S 83 MET cc_start: 0.9240 (mtm) cc_final: 0.9023 (mtp) REVERT: S 235 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7019 (t80) REVERT: B 52 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8426 (mtt90) REVERT: B 195 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7666 (p0) REVERT: B 197 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7780 (mmt-90) REVERT: B 318 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8216 (mp) REVERT: B 336 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8998 (mp) outliers start: 54 outliers final: 30 residues processed: 162 average time/residue: 1.0909 time to fit residues: 189.0806 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 : 0.880 ------------------------------------------------------------------------------- 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 A residue 253 ILE 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 312 LYS 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 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 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=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: 0.4980 chunk 6 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.0270 chunk 97 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.166972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127830 restraints weight = 10000.227| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.96 r_work: 0.3262 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8908 Z= 0.126 Angle : 0.546 8.744 12093 Z= 0.285 Chirality : 0.042 0.193 1377 Planarity : 0.004 0.047 1524 Dihedral : 5.518 90.411 1237 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.95 % Allowed : 28.57 % Favored : 66.48 % 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: 1.99 (0.27), residues: 363 sheet: -0.06 (0.29), residues: 297 loop : -1.06 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.016 0.001 PHE A 334 TYR 0.024 0.001 TYR S 235 ARG 0.002 0.000 ARG A 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 1) link_NAG-ASN : angle 3.87629 ( 3) hydrogen bonds : bond 0.04110 ( 413) hydrogen bonds : angle 4.35428 ( 1146) SS BOND : bond 0.00540 ( 3) SS BOND : angle 1.34808 ( 6) covalent geometry : bond 0.00286 ( 8904) covalent geometry : angle 0.54169 (12084) *********************** 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 175 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7517 (mtmm) cc_final: 0.7167 (ptpt) REVERT: R 101 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7444 (mtt-85) REVERT: R 106 MET cc_start: 0.8734 (tpp) cc_final: 0.8294 (mmp) REVERT: R 112 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: A 21 ARG cc_start: 0.8253 (ptm-80) cc_final: 0.7923 (ptp90) REVERT: A 207 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6877 (tt0) REVERT: A 257 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7882 (ptmt) REVERT: A 276 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: A 313 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5512 (pmm-80) REVERT: S 83 MET cc_start: 0.9155 (mtm) cc_final: 0.8858 (mtp) REVERT: S 235 TYR cc_start: 0.7337 (OUTLIER) cc_final: 0.6894 (t80) REVERT: B 52 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8401 (mtt90) REVERT: B 197 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7793 (mmt-90) REVERT: B 336 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8980 (mp) outliers start: 45 outliers final: 23 residues processed: 162 average time/residue: 1.1588 time to fit residues: 200.6322 Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 195 LEU 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 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 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU 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: 2.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 40.0000 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.165134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126151 restraints weight = 10224.781| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.05 r_work: 0.3202 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8908 Z= 0.184 Angle : 0.593 8.541 12093 Z= 0.311 Chirality : 0.044 0.215 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.683 90.416 1237 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.93 % Allowed : 26.81 % 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: -0.12 (0.29), residues: 297 loop : -1.06 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.004 0.001 HIS A 322 PHE 0.016 0.001 PHE A 334 TYR 0.025 0.002 TYR S 235 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 1) link_NAG-ASN : angle 3.69935 ( 3) hydrogen bonds : bond 0.04582 ( 413) hydrogen bonds : angle 4.43075 ( 1146) SS BOND : bond 0.00555 ( 3) SS BOND : angle 1.33942 ( 6) covalent geometry : bond 0.00439 ( 8904) covalent geometry : angle 0.58971 (12084) *********************** 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 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7179 (ptpt) REVERT: R 101 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7470 (mtt-85) REVERT: R 112 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8629 (mt0) REVERT: R 227 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7342 (ptpt) REVERT: A 207 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: A 257 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7911 (ptmt) REVERT: A 276 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 313 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5631 (pmm-80) REVERT: S 83 MET cc_start: 0.9205 (mtm) cc_final: 0.8906 (mtp) REVERT: S 235 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 52 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8458 (mtt90) REVERT: B 197 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7796 (mmt-90) REVERT: B 336 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8995 (mp) outliers start: 54 outliers final: 31 residues processed: 158 average time/residue: 1.2027 time to fit residues: 203.1763 Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 185 THR 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 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 262 THR 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 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 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 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN A 188 HIS S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125066 restraints weight = 10216.401| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.03 r_work: 0.3200 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8908 Z= 0.225 Angle : 0.624 8.691 12093 Z= 0.328 Chirality : 0.045 0.234 1377 Planarity : 0.004 0.046 1524 Dihedral : 5.875 90.935 1237 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: 0.11 (0.25), residues: 1115 helix: 1.72 (0.27), residues: 364 sheet: -0.07 (0.29), residues: 283 loop : -1.15 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 63 HIS 0.005 0.001 HIS A 188 PHE 0.016 0.002 PHE A 334 TYR 0.027 0.002 TYR S 235 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 1) link_NAG-ASN : angle 3.37758 ( 3) hydrogen bonds : bond 0.04887 ( 413) hydrogen bonds : angle 4.50937 ( 1146) SS BOND : bond 0.00538 ( 3) SS BOND : angle 1.40835 ( 6) covalent geometry : bond 0.00542 ( 8904) covalent geometry : angle 0.62088 (12084) *********************** 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 174 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7567 (mtmm) cc_final: 0.7164 (ptpt) REVERT: R 112 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8589 (mt0) REVERT: R 227 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7318 (ptpt) REVERT: A 207 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: A 257 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7905 (ptmt) REVERT: A 276 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 312 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8345 (mptt) REVERT: A 313 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.5632 (pmm-80) REVERT: S 83 MET cc_start: 0.9246 (mtm) cc_final: 0.8944 (mtp) REVERT: S 87 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7162 (mtm180) REVERT: S 235 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.7046 (t80) REVERT: B 52 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8410 (mtt90) REVERT: B 195 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7719 (p0) REVERT: B 197 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7777 (mmt180) REVERT: B 336 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8988 (mp) outliers start: 53 outliers final: 32 residues processed: 161 average time/residue: 1.1614 time to fit residues: 199.8189 Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 262 THR 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 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 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 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: 0.9980 chunk 100 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 55 HIS A 188 HIS B 32 GLN B 88 ASN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126666 restraints weight = 10128.360| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.02 r_work: 0.3240 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.003 0.044 8908 Z= 0.147 Angle : 0.574 8.357 12093 Z= 0.300 Chirality : 0.043 0.206 1377 Planarity : 0.004 0.044 1524 Dihedral : 5.604 88.643 1237 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.05 % Allowed : 27.25 % 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: 0.26 (0.25), residues: 1115 helix: 1.92 (0.27), residues: 363 sheet: -0.10 (0.29), residues: 296 loop : -1.06 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.001 PHE A 334 TYR 0.025 0.001 TYR S 235 ARG 0.002 0.000 ARG A 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 1) link_NAG-ASN : angle 3.68993 ( 3) hydrogen bonds : bond 0.04242 ( 413) hydrogen bonds : angle 4.36336 ( 1146) SS BOND : bond 0.00963 ( 3) SS BOND : angle 2.39986 ( 6) covalent geometry : bond 0.00345 ( 8904) covalent geometry : angle 0.56913 (12084) *********************** 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 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 123 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7524 (mtmm) cc_final: 0.7133 (ptpt) REVERT: R 101 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7440 (mtt-85) REVERT: R 112 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8607 (mt0) REVERT: R 227 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7340 (ptpt) REVERT: A 21 ARG cc_start: 0.8292 (ptm-80) cc_final: 0.7918 (ptp90) REVERT: A 207 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: A 257 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7908 (ptmt) REVERT: A 276 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 312 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8376 (mptt) REVERT: A 313 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5594 (pmm-80) REVERT: S 83 MET cc_start: 0.9144 (mtm) cc_final: 0.8889 (mtp) REVERT: S 235 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6979 (t80) REVERT: B 52 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8428 (mtt90) REVERT: B 195 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7768 (p0) REVERT: B 197 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7806 (mmt180) REVERT: B 336 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8968 (mp) outliers start: 46 outliers final: 30 residues processed: 155 average time/residue: 1.2147 time to fit residues: 201.0266 Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 A residue 201 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 262 THR 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 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 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 0.1980 chunk 15 optimal weight: 0.0170 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.0040 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.3030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN A 188 HIS S 183 GLN B 32 GLN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131650 restraints weight = 10146.844| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.98 r_work: 0.3336 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8908 Z= 0.103 Angle : 0.543 11.395 12093 Z= 0.280 Chirality : 0.041 0.159 1377 Planarity : 0.004 0.047 1524 Dihedral : 5.174 84.743 1237 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.19 % Allowed : 29.45 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1115 helix: 2.22 (0.27), residues: 363 sheet: 0.19 (0.30), residues: 274 loop : -0.98 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 322 PHE 0.020 0.001 PHE A 334 TYR 0.020 0.001 TYR S 235 ARG 0.002 0.000 ARG S 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 1) link_NAG-ASN : angle 3.49146 ( 3) hydrogen bonds : bond 0.03503 ( 413) hydrogen bonds : angle 4.16583 ( 1146) SS BOND : bond 0.00759 ( 3) SS BOND : angle 2.05727 ( 6) covalent geometry : bond 0.00219 ( 8904) covalent geometry : angle 0.53889 (12084) ********************** 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 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 28 LYS cc_start: 0.7430 (mtmm) cc_final: 0.7048 (ptpt) REVERT: R 101 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7496 (mtt-85) REVERT: R 112 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: A 21 ARG cc_start: 0.8259 (ptm-80) cc_final: 0.7898 (ptp90) REVERT: A 186 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7412 (tt0) REVERT: A 207 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6759 (tt0) REVERT: A 257 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7975 (ptmt) REVERT: A 276 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 313 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5563 (pmm-80) REVERT: S 87 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6951 (mtm180) REVERT: S 235 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6834 (t80) REVERT: B 52 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8395 (mtt90) REVERT: B 293 ASN cc_start: 0.8258 (m-40) cc_final: 0.7969 (m-40) outliers start: 29 outliers final: 13 residues processed: 157 average time/residue: 1.1009 time to fit residues: 184.7893 Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 194 LEU 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 78 THR Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 91 THR 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 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 67 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN A 188 HIS 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 = 0.3965 r_free = 0.3965 target = 0.170204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132267 restraints weight = 10095.186| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.99 r_work: 0.3315 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8908 Z= 0.110 Angle : 0.553 12.268 12093 Z= 0.284 Chirality : 0.041 0.167 1377 Planarity : 0.004 0.049 1524 Dihedral : 5.165 85.492 1237 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.53 % Allowed : 30.22 % 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: 0.61 (0.25), residues: 1115 helix: 2.27 (0.27), residues: 363 sheet: 0.26 (0.31), residues: 268 loop : -0.99 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 322 PHE 0.021 0.001 PHE A 334 TYR 0.020 0.001 TYR S 235 ARG 0.002 0.000 ARG A 15 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 1) link_NAG-ASN : angle 3.81888 ( 3) hydrogen bonds : bond 0.03640 ( 413) hydrogen bonds : angle 4.14311 ( 1146) SS BOND : bond 0.00748 ( 3) SS BOND : angle 1.85478 ( 6) covalent geometry : bond 0.00247 ( 8904) covalent geometry : angle 0.54808 (12084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7015.29 seconds wall clock time: 121 minutes 29.81 seconds (7289.81 seconds total)