Starting phenix.real_space_refine on Tue Apr 29 21:45:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwk_37891/04_2025/8wwk_37891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwk_37891/04_2025/8wwk_37891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwk_37891/04_2025/8wwk_37891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwk_37891/04_2025/8wwk_37891.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwk_37891/04_2025/8wwk_37891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwk_37891/04_2025/8wwk_37891.cif" } resolution = 2.61 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= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5712 2.51 5 N 1519 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8967 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.35, per 1000 atoms: 0.60 Number of scatterers: 8967 At special positions: 0 Unit cell: (88.81, 117.7, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1668 8.00 N 1519 7.00 C 5712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " 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 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 38.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.572A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.289A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.920A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.663A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.085A 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: 4.317A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 108 through 138 removed outlier: 3.573A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix removed outlier: 3.819A pdb=" N SER R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 164 Processing helix chain 'R' and resid 164 through 174 removed outlier: 5.108A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 3.892A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.725A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.824A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 302 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.027A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.317A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.804A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.797A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.170A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.873A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.095A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.164A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.545A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.505A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.141A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB7, first strand: chain 'L' and resid 8 through 9 485 hydrogen bonds defined for protein. 1329 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: 2.74 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2888 1.34 - 1.46: 2186 1.46 - 1.58: 3985 1.58 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9158 Sorted by residual: bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.447 0.010 9.20e-03 1.18e+04 1.30e+00 bond pdb=" C LEU A 39 " pdb=" N GLY A 40 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.70e-01 bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.239 1.234 0.005 8.50e-03 1.38e+04 3.64e-01 bond pdb=" C MET R 165 " pdb=" N PRO R 166 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.18e-01 bond pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 1.502 1.515 -0.013 2.30e-02 1.89e+03 3.12e-01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 12233 1.17 - 2.33: 148 2.33 - 3.50: 34 3.50 - 4.67: 7 4.67 - 5.84: 5 Bond angle restraints: 12427 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.88e+00 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 112.83 -3.49 2.08e+00 2.31e-01 2.82e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 122.14 -5.84 3.50e+00 8.16e-02 2.78e+00 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.16 114.03 -2.87 1.76e+00 3.23e-01 2.65e+00 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 124.82 127.34 -2.52 1.78e+00 3.16e-01 2.01e+00 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 5228 16.13 - 32.25: 166 32.25 - 48.38: 28 48.38 - 64.50: 6 64.50 - 80.63: 1 Dihedral angle restraints: 5429 sinusoidal: 2063 harmonic: 3366 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LYS R 139 " pdb=" C LYS R 139 " pdb=" N LEU R 140 " pdb=" CA LEU R 140 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.08e+00 dihedral pdb=" N LYS A 312 " pdb=" CA LYS A 312 " pdb=" CB LYS A 312 " pdb=" CG LYS A 312 " ideal model delta sinusoidal sigma weight residual 180.00 -127.96 -52.04 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 5426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 875 0.026 - 0.051: 316 0.051 - 0.077: 136 0.077 - 0.102: 63 0.102 - 0.128: 36 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-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 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1423 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO E 107 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO B 194 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 782 2.74 - 3.28: 8784 3.28 - 3.82: 15448 3.82 - 4.36: 19349 4.36 - 4.90: 32640 Nonbonded interactions: 77003 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.242 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.283 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.291 3.040 ... (remaining 76998 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.080 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.002 0.017 9162 Z= 0.075 Angle : 0.392 5.837 12435 Z= 0.207 Chirality : 0.039 0.128 1426 Planarity : 0.003 0.050 1570 Dihedral : 8.406 80.627 3245 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.72 % Allowed : 2.58 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1144 helix: 1.16 (0.25), residues: 394 sheet: 0.97 (0.30), residues: 288 loop : 0.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS B 62 PHE 0.009 0.001 PHE B 199 TYR 0.010 0.001 TYR E 190 ARG 0.001 0.000 ARG R 224 Details of bonding type rmsd hydrogen bonds : bond 0.23641 ( 472) hydrogen bonds : angle 7.28709 ( 1329) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.56807 ( 8) covalent geometry : bond 0.00152 ( 9158) covalent geometry : angle 0.39179 (12427) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.935 Fit side-chains REVERT: A 8 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 10 LYS cc_start: 0.8813 (mttt) cc_final: 0.8530 (mtmp) REVERT: A 29 LYS cc_start: 0.8064 (tttt) cc_final: 0.7657 (ttpp) REVERT: B 25 CYS cc_start: 0.7906 (p) cc_final: 0.6766 (m) REVERT: B 130 GLU cc_start: 0.8313 (mp0) cc_final: 0.8105 (mp0) REVERT: C 21 MET cc_start: 0.7082 (mmm) cc_final: 0.6469 (tmt) REVERT: C 47 GLU cc_start: 0.7999 (pt0) cc_final: 0.7741 (mp0) REVERT: E 43 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8073 (mtmt) REVERT: E 77 ASN cc_start: 0.8277 (m-40) cc_final: 0.7925 (m-40) REVERT: E 223 ASP cc_start: 0.8634 (m-30) cc_final: 0.8395 (m-30) REVERT: R 142 TRP cc_start: 0.6869 (m-90) cc_final: 0.5954 (m100) REVERT: R 252 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6406 (mpp-170) outliers start: 7 outliers final: 5 residues processed: 190 average time/residue: 1.2811 time to fit residues: 258.9245 Evaluate side-chains 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 220 GLN B 259 GLN R 194 ASN R 281 GLN R 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129767 restraints weight = 8705.978| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.69 r_work: 0.3118 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9162 Z= 0.140 Angle : 0.527 5.643 12435 Z= 0.286 Chirality : 0.042 0.136 1426 Planarity : 0.004 0.054 1570 Dihedral : 5.107 55.938 1267 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.79 % Allowed : 7.84 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1144 helix: 2.26 (0.25), residues: 394 sheet: 0.59 (0.29), residues: 279 loop : 0.20 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.013 0.002 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.006 0.001 ARG R 303 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 472) hydrogen bonds : angle 4.93907 ( 1329) SS BOND : bond 0.00435 ( 4) SS BOND : angle 0.73037 ( 8) covalent geometry : bond 0.00295 ( 9158) covalent geometry : angle 0.52684 (12427) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.049 Fit side-chains REVERT: A 8 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8387 (mt-10) REVERT: A 28 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: A 29 LYS cc_start: 0.8230 (tttt) cc_final: 0.7757 (ttpp) REVERT: A 33 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: A 308 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 130 GLU cc_start: 0.8471 (mp0) cc_final: 0.8105 (mp0) REVERT: B 170 ASP cc_start: 0.8971 (t70) cc_final: 0.8752 (t70) REVERT: B 217 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8411 (pmm) REVERT: E 43 LYS cc_start: 0.8638 (mmtm) cc_final: 0.7968 (mtmt) REVERT: E 77 ASN cc_start: 0.8309 (m-40) cc_final: 0.7845 (m-40) REVERT: E 160 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.7291 (ttm170) REVERT: R 142 TRP cc_start: 0.6958 (m-90) cc_final: 0.5861 (m100) REVERT: R 165 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8046 (ttt) REVERT: R 187 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7231 (mm) REVERT: R 235 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7839 (mp) REVERT: R 252 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6017 (mpp-170) REVERT: R 356 LEU cc_start: 0.8219 (mm) cc_final: 0.8015 (mm) outliers start: 27 outliers final: 10 residues processed: 161 average time/residue: 1.3718 time to fit residues: 233.9943 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 50 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 322 HIS B 156 GLN B 259 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.166106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128523 restraints weight = 8855.281| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.74 r_work: 0.3127 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 0.032 9162 Z= 0.143 Angle : 0.512 5.814 12435 Z= 0.277 Chirality : 0.042 0.148 1426 Planarity : 0.004 0.056 1570 Dihedral : 5.246 58.872 1267 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.10 % Allowed : 9.60 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1144 helix: 2.51 (0.25), residues: 393 sheet: 0.40 (0.29), residues: 275 loop : 0.07 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.014 0.002 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.005 0.000 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 472) hydrogen bonds : angle 4.71898 ( 1329) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.79691 ( 8) covalent geometry : bond 0.00312 ( 9158) covalent geometry : angle 0.51167 (12427) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: A 29 LYS cc_start: 0.8210 (tttt) cc_final: 0.7719 (ttpp) REVERT: A 33 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: B 217 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8489 (pmm) REVERT: E 23 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7862 (p) REVERT: E 43 LYS cc_start: 0.8622 (mmtm) cc_final: 0.7941 (mtmt) REVERT: E 77 ASN cc_start: 0.8382 (m-40) cc_final: 0.7953 (m-40) REVERT: E 160 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.7289 (ttm170) REVERT: E 234 GLU cc_start: 0.8838 (pt0) cc_final: 0.8630 (pt0) REVERT: R 142 TRP cc_start: 0.6939 (m-90) cc_final: 0.5880 (m100) REVERT: R 250 TYR cc_start: 0.8266 (m-80) cc_final: 0.8040 (m-10) REVERT: R 252 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6806 (mpt90) outliers start: 30 outliers final: 16 residues processed: 157 average time/residue: 1.3451 time to fit residues: 223.9570 Evaluate side-chains 161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 322 HIS B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128499 restraints weight = 8708.879| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.71 r_work: 0.2989 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9162 Z= 0.174 Angle : 0.542 6.664 12435 Z= 0.292 Chirality : 0.043 0.188 1426 Planarity : 0.004 0.059 1570 Dihedral : 5.439 58.963 1267 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.02 % Allowed : 9.29 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1144 helix: 2.48 (0.25), residues: 393 sheet: 0.23 (0.29), residues: 299 loop : 0.01 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE B 151 TYR 0.013 0.002 TYR R 341 ARG 0.004 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 472) hydrogen bonds : angle 4.75375 ( 1329) SS BOND : bond 0.00382 ( 4) SS BOND : angle 0.84372 ( 8) covalent geometry : bond 0.00394 ( 9158) covalent geometry : angle 0.54171 (12427) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 28 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: A 29 LYS cc_start: 0.8148 (tttt) cc_final: 0.7662 (ttpp) REVERT: A 33 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: B 42 ARG cc_start: 0.7013 (tpt170) cc_final: 0.6260 (tpt170) REVERT: B 217 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8432 (pmm) REVERT: C 58 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: E 43 LYS cc_start: 0.8657 (mmtm) cc_final: 0.7859 (mtmt) REVERT: E 77 ASN cc_start: 0.8432 (m-40) cc_final: 0.7936 (m-40) REVERT: E 160 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.6819 (mmm160) REVERT: E 234 GLU cc_start: 0.8913 (pt0) cc_final: 0.8686 (pt0) REVERT: R 142 TRP cc_start: 0.6982 (m-90) cc_final: 0.5713 (m100) REVERT: R 165 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7992 (ttt) REVERT: R 250 TYR cc_start: 0.8233 (m-80) cc_final: 0.8028 (m-10) REVERT: R 252 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6828 (mpt90) outliers start: 39 outliers final: 19 residues processed: 164 average time/residue: 1.3589 time to fit residues: 235.7983 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.166073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128716 restraints weight = 8673.221| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.72 r_work: 0.3093 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9162 Z= 0.195 Angle : 0.563 7.277 12435 Z= 0.303 Chirality : 0.044 0.190 1426 Planarity : 0.004 0.061 1570 Dihedral : 5.569 58.829 1267 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.82 % Allowed : 10.32 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1144 helix: 2.39 (0.25), residues: 394 sheet: 0.18 (0.28), residues: 299 loop : -0.10 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.017 0.002 PHE B 151 TYR 0.014 0.002 TYR R 341 ARG 0.006 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 472) hydrogen bonds : angle 4.79357 ( 1329) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.93331 ( 8) covalent geometry : bond 0.00444 ( 9158) covalent geometry : angle 0.56314 (12427) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.902 Fit side-chains REVERT: A 28 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: A 29 LYS cc_start: 0.8212 (tttt) cc_final: 0.7744 (ttpp) REVERT: A 33 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: A 270 LYS cc_start: 0.8495 (mttt) cc_final: 0.7963 (mttp) REVERT: B 42 ARG cc_start: 0.6952 (tpt170) cc_final: 0.6246 (tpt170) REVERT: C 58 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: E 43 LYS cc_start: 0.8657 (mmtm) cc_final: 0.7926 (mtmt) REVERT: E 65 LYS cc_start: 0.8019 (tttt) cc_final: 0.7666 (ttmm) REVERT: E 160 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.6891 (mmm160) REVERT: E 234 GLU cc_start: 0.8856 (pt0) cc_final: 0.8619 (pt0) REVERT: R 142 TRP cc_start: 0.6946 (m-90) cc_final: 0.5666 (m100) REVERT: R 165 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7888 (ttt) REVERT: R 250 TYR cc_start: 0.8319 (m-80) cc_final: 0.8082 (m-10) REVERT: R 252 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6908 (mpt90) outliers start: 37 outliers final: 20 residues processed: 163 average time/residue: 1.4359 time to fit residues: 247.8275 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 0.0570 chunk 99 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128445 restraints weight = 8751.370| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.70 r_work: 0.3009 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9162 Z= 0.135 Angle : 0.507 5.893 12435 Z= 0.274 Chirality : 0.042 0.134 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.381 58.104 1266 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.61 % Allowed : 10.94 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1144 helix: 2.58 (0.25), residues: 394 sheet: 0.11 (0.29), residues: 283 loop : -0.04 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 341 ARG 0.005 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 472) hydrogen bonds : angle 4.59806 ( 1329) SS BOND : bond 0.00250 ( 4) SS BOND : angle 1.52982 ( 8) covalent geometry : bond 0.00296 ( 9158) covalent geometry : angle 0.50523 (12427) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.908 Fit side-chains REVERT: A 28 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: A 29 LYS cc_start: 0.8115 (tttt) cc_final: 0.7613 (ttpp) REVERT: A 33 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: A 243 MET cc_start: 0.8516 (tpp) cc_final: 0.8281 (ttm) REVERT: A 270 LYS cc_start: 0.8488 (mttt) cc_final: 0.7932 (mttp) REVERT: B 42 ARG cc_start: 0.7040 (tpt170) cc_final: 0.6300 (tpt170) REVERT: C 58 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: E 43 LYS cc_start: 0.8632 (mmtm) cc_final: 0.7841 (mtmt) REVERT: E 65 LYS cc_start: 0.7994 (tttt) cc_final: 0.7596 (ttmm) REVERT: E 77 ASN cc_start: 0.8585 (m-40) cc_final: 0.8018 (m-40) REVERT: E 160 ARG cc_start: 0.7594 (mtp-110) cc_final: 0.7289 (ttm170) REVERT: E 234 GLU cc_start: 0.8934 (pt0) cc_final: 0.8696 (pt0) REVERT: R 142 TRP cc_start: 0.6891 (m-90) cc_final: 0.5598 (m100) REVERT: R 165 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7844 (ttt) REVERT: R 250 TYR cc_start: 0.8214 (m-80) cc_final: 0.7966 (m-10) REVERT: R 252 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6795 (mpt90) outliers start: 35 outliers final: 21 residues processed: 161 average time/residue: 1.4514 time to fit residues: 246.7834 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128614 restraints weight = 8879.506| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.76 r_work: 0.3123 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9162 Z= 0.133 Angle : 0.505 6.646 12435 Z= 0.272 Chirality : 0.042 0.183 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.323 57.159 1266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.10 % Allowed : 11.46 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1144 helix: 2.65 (0.25), residues: 394 sheet: 0.11 (0.29), residues: 278 loop : -0.03 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.004 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 472) hydrogen bonds : angle 4.55732 ( 1329) SS BOND : bond 0.00253 ( 4) SS BOND : angle 1.26328 ( 8) covalent geometry : bond 0.00291 ( 9158) covalent geometry : angle 0.50391 (12427) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.014 Fit side-chains REVERT: A 28 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: A 29 LYS cc_start: 0.8165 (tttt) cc_final: 0.7696 (ttpp) REVERT: A 32 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7639 (mtt90) REVERT: A 33 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: A 270 LYS cc_start: 0.8521 (mttt) cc_final: 0.8074 (mttp) REVERT: B 42 ARG cc_start: 0.7044 (tpt170) cc_final: 0.6351 (tpt170) REVERT: C 58 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: E 43 LYS cc_start: 0.8629 (mmtm) cc_final: 0.7847 (mtpt) REVERT: E 77 ASN cc_start: 0.8583 (m-40) cc_final: 0.8036 (m-40) REVERT: E 160 ARG cc_start: 0.7507 (mtp-110) cc_final: 0.7238 (ttm170) REVERT: E 234 GLU cc_start: 0.8868 (pt0) cc_final: 0.8660 (pt0) REVERT: R 142 TRP cc_start: 0.6972 (m-90) cc_final: 0.5707 (m100) REVERT: R 165 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7928 (ttt) REVERT: R 250 TYR cc_start: 0.8251 (m-80) cc_final: 0.8032 (m-10) REVERT: R 252 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.5867 (mpp-170) outliers start: 30 outliers final: 18 residues processed: 158 average time/residue: 1.4184 time to fit residues: 237.2987 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131840 restraints weight = 8857.545| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.73 r_work: 0.3053 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9162 Z= 0.107 Angle : 0.478 5.909 12435 Z= 0.258 Chirality : 0.041 0.136 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.156 55.672 1266 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.89 % Allowed : 11.76 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1144 helix: 2.76 (0.26), residues: 396 sheet: 0.13 (0.29), residues: 276 loop : -0.01 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE B 151 TYR 0.012 0.001 TYR E 190 ARG 0.010 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 472) hydrogen bonds : angle 4.42670 ( 1329) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.02347 ( 8) covalent geometry : bond 0.00224 ( 9158) covalent geometry : angle 0.47784 (12427) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.912 Fit side-chains REVERT: A 17 LYS cc_start: 0.8362 (mttt) cc_final: 0.7975 (mtpt) REVERT: A 28 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: A 29 LYS cc_start: 0.8119 (tttt) cc_final: 0.7594 (ttpp) REVERT: A 270 LYS cc_start: 0.8504 (mttt) cc_final: 0.8040 (mttp) REVERT: B 170 ASP cc_start: 0.8793 (t70) cc_final: 0.8559 (t70) REVERT: E 43 LYS cc_start: 0.8643 (mmtm) cc_final: 0.7839 (mtpt) REVERT: E 77 ASN cc_start: 0.8566 (m-40) cc_final: 0.8064 (m-40) REVERT: E 234 GLU cc_start: 0.8897 (pt0) cc_final: 0.8676 (pt0) REVERT: R 142 TRP cc_start: 0.6958 (m-90) cc_final: 0.5722 (m100) REVERT: R 165 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7860 (ttt) REVERT: R 252 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6017 (mpp-170) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 1.4868 time to fit residues: 244.9614 Evaluate side-chains 159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.165976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127357 restraints weight = 8825.145| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.75 r_work: 0.3008 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9162 Z= 0.155 Angle : 0.540 7.267 12435 Z= 0.289 Chirality : 0.043 0.190 1426 Planarity : 0.004 0.059 1570 Dihedral : 5.359 55.467 1266 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.10 % Allowed : 12.07 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1144 helix: 2.66 (0.25), residues: 396 sheet: 0.11 (0.29), residues: 284 loop : -0.04 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.002 PHE B 151 TYR 0.013 0.002 TYR R 341 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 472) hydrogen bonds : angle 4.67817 ( 1329) SS BOND : bond 0.00294 ( 4) SS BOND : angle 2.07524 ( 8) covalent geometry : bond 0.00350 ( 9158) covalent geometry : angle 0.53792 (12427) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.033 Fit side-chains REVERT: A 17 LYS cc_start: 0.8383 (mttt) cc_final: 0.7981 (mtpt) REVERT: A 28 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: A 29 LYS cc_start: 0.8087 (tttt) cc_final: 0.7540 (ttpp) REVERT: A 270 LYS cc_start: 0.8494 (mttt) cc_final: 0.8024 (mttp) REVERT: B 42 ARG cc_start: 0.7063 (tpt170) cc_final: 0.6315 (tpt170) REVERT: E 43 LYS cc_start: 0.8596 (mmtm) cc_final: 0.7729 (mtpt) REVERT: E 77 ASN cc_start: 0.8584 (m-40) cc_final: 0.8081 (m-40) REVERT: E 160 ARG cc_start: 0.7572 (mtp-110) cc_final: 0.6758 (mmm160) REVERT: E 234 GLU cc_start: 0.8932 (pt0) cc_final: 0.8703 (pt0) REVERT: R 142 TRP cc_start: 0.6889 (m-90) cc_final: 0.5624 (m100) REVERT: R 165 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7831 (ttt) REVERT: R 252 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6625 (mtt90) outliers start: 30 outliers final: 20 residues processed: 161 average time/residue: 1.4868 time to fit residues: 252.6806 Evaluate side-chains 166 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.166637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129027 restraints weight = 8850.260| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.69 r_work: 0.3007 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9162 Z= 0.140 Angle : 0.533 9.325 12435 Z= 0.283 Chirality : 0.043 0.167 1426 Planarity : 0.004 0.059 1570 Dihedral : 5.406 57.624 1266 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.48 % Allowed : 12.80 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1144 helix: 2.68 (0.25), residues: 396 sheet: 0.08 (0.29), residues: 283 loop : -0.04 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 248 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 472) hydrogen bonds : angle 4.61321 ( 1329) SS BOND : bond 0.00250 ( 4) SS BOND : angle 1.82527 ( 8) covalent geometry : bond 0.00310 ( 9158) covalent geometry : angle 0.53099 (12427) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.991 Fit side-chains REVERT: A 8 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 17 LYS cc_start: 0.8404 (mttt) cc_final: 0.8004 (mtpt) REVERT: A 28 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: A 29 LYS cc_start: 0.8122 (tttt) cc_final: 0.7587 (ttpp) REVERT: A 270 LYS cc_start: 0.8502 (mttt) cc_final: 0.8033 (mttp) REVERT: B 42 ARG cc_start: 0.7074 (tpt170) cc_final: 0.6330 (tpt170) REVERT: E 43 LYS cc_start: 0.8642 (mmtm) cc_final: 0.7827 (mtpt) REVERT: E 77 ASN cc_start: 0.8578 (m-40) cc_final: 0.8088 (m-40) REVERT: E 160 ARG cc_start: 0.7555 (mtp-110) cc_final: 0.7250 (ttm170) REVERT: E 234 GLU cc_start: 0.8943 (pt0) cc_final: 0.8691 (pt0) REVERT: R 142 TRP cc_start: 0.6943 (m-90) cc_final: 0.5689 (m100) REVERT: R 165 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7863 (ttt) REVERT: R 252 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6034 (mpp-170) outliers start: 24 outliers final: 19 residues processed: 153 average time/residue: 1.7098 time to fit residues: 276.1689 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128874 restraints weight = 8834.460| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.71 r_work: 0.3004 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9162 Z= 0.148 Angle : 0.540 7.332 12435 Z= 0.288 Chirality : 0.043 0.180 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.471 59.268 1266 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.79 % Allowed : 12.38 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1144 helix: 2.66 (0.25), residues: 396 sheet: 0.05 (0.29), residues: 284 loop : -0.05 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR R 341 ARG 0.009 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 472) hydrogen bonds : angle 4.64781 ( 1329) SS BOND : bond 0.00247 ( 4) SS BOND : angle 1.79343 ( 8) covalent geometry : bond 0.00331 ( 9158) covalent geometry : angle 0.53803 (12427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8535.53 seconds wall clock time: 147 minutes 50.61 seconds (8870.61 seconds total)