Starting phenix.real_space_refine on Thu Mar 13 14:03:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwk_37891/03_2025/8wwk_37891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwk_37891/03_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_37891/03_2025/8wwk_37891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwk_37891/03_2025/8wwk_37891.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwk_37891/03_2025/8wwk_37891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwk_37891/03_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-5624/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: 5.40, 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: 2.04 Conformation dependent library (CDL) restraints added in 1.1 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: 2.48 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.600 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 38.730 ------------------------------------------------------------------------------- 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 9158 Z= 0.100 Angle : 0.392 5.837 12427 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 *********************** 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 : 0.975 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: 1.3810 time to fit residues: 279.1256 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 : 0.903 ------------------------------------------------------------------------------- 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 9158 Z= 0.195 Angle : 0.527 5.643 12427 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 *********************** 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 : 1.011 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: 1.3821 time to fit residues: 235.6879 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 : 0.916 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.5982 ------------------------------------------------------------------------------- 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 B 259 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 = 0.3852 r_free = 0.3852 target = 0.167139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129702 restraints weight = 8882.320| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.74 r_work: 0.3146 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9158 Z= 0.174 Angle : 0.489 5.339 12427 Z= 0.265 Chirality : 0.041 0.136 1426 Planarity : 0.004 0.056 1570 Dihedral : 5.137 59.688 1267 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.79 % Allowed : 10.01 % Favored : 87.20 % 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: 1.53 (0.25), residues: 1144 helix: 2.58 (0.25), residues: 393 sheet: 0.43 (0.30), residues: 274 loop : 0.12 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.005 0.000 ARG R 322 *********************** 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 171 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: A 29 LYS cc_start: 0.8212 (tttt) cc_final: 0.7725 (ttpp) REVERT: A 33 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: B 130 GLU cc_start: 0.8505 (mp0) cc_final: 0.8114 (mp0) REVERT: B 217 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8405 (pmm) REVERT: E 43 LYS cc_start: 0.8634 (mmtm) cc_final: 0.7965 (mtmt) REVERT: E 77 ASN cc_start: 0.8357 (m-40) cc_final: 0.7953 (m-40) REVERT: R 142 TRP cc_start: 0.6966 (m-90) cc_final: 0.5875 (m100) REVERT: R 187 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7183 (mm) REVERT: R 252 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5966 (mpp-170) REVERT: R 356 LEU cc_start: 0.8108 (mm) cc_final: 0.7908 (mm) outliers start: 27 outliers final: 14 residues processed: 153 average time/residue: 1.5781 time to fit residues: 255.9100 Evaluate side-chains 161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 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 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: 0.0870 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 67 optimal weight: 0.0000 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 50 optimal weight: 0.0980 overall best weight: 0.5764 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.168269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130116 restraints weight = 8752.455| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.70 r_work: 0.3046 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9158 Z= 0.169 Angle : 0.481 5.273 12427 Z= 0.261 Chirality : 0.041 0.134 1426 Planarity : 0.004 0.056 1570 Dihedral : 5.129 59.362 1267 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.30 % Allowed : 10.32 % Favored : 86.38 % 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: 1.53 (0.25), residues: 1144 helix: 2.66 (0.25), residues: 393 sheet: 0.36 (0.30), residues: 275 loop : 0.09 (0.29), residues: 476 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 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR E 190 ARG 0.004 0.000 ARG A 32 *********************** 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 178 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8341 (mt-10) REVERT: A 17 LYS cc_start: 0.8376 (mttt) cc_final: 0.7986 (mtpt) REVERT: A 28 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: A 29 LYS cc_start: 0.8111 (tttt) cc_final: 0.7609 (ttpp) REVERT: A 33 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: B 217 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8455 (pmm) REVERT: E 43 LYS cc_start: 0.8628 (mmtm) cc_final: 0.7830 (mtmt) REVERT: E 77 ASN cc_start: 0.8361 (m-40) cc_final: 0.7979 (m-40) REVERT: E 160 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.6762 (mmm160) REVERT: R 142 TRP cc_start: 0.6996 (m-90) cc_final: 0.5766 (m100) REVERT: R 187 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7074 (mm) REVERT: R 252 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6871 (mpt90) outliers start: 32 outliers final: 18 residues processed: 160 average time/residue: 1.3917 time to fit residues: 235.8440 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.166543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128964 restraints weight = 8726.021| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.74 r_work: 0.3013 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9158 Z= 0.236 Angle : 0.519 6.066 12427 Z= 0.280 Chirality : 0.043 0.171 1426 Planarity : 0.004 0.057 1570 Dihedral : 5.292 58.672 1267 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.41 % Allowed : 10.84 % Favored : 85.76 % 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: 1.41 (0.25), residues: 1144 helix: 2.59 (0.25), residues: 394 sheet: 0.22 (0.29), residues: 285 loop : 0.04 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.002 PHE B 151 TYR 0.013 0.002 TYR R 341 ARG 0.004 0.000 ARG A 32 *********************** 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 180 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8409 (mt-10) REVERT: A 17 LYS cc_start: 0.8381 (mttt) cc_final: 0.7976 (mtpt) REVERT: A 28 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: A 29 LYS cc_start: 0.8107 (tttt) cc_final: 0.7618 (ttpp) REVERT: A 33 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: B 42 ARG cc_start: 0.7018 (tpt170) cc_final: 0.6276 (tpt170) REVERT: C 58 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: E 43 LYS cc_start: 0.8628 (mmtm) cc_final: 0.7854 (mtmt) REVERT: E 77 ASN cc_start: 0.8414 (m-40) cc_final: 0.7962 (m-40) REVERT: E 160 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.6774 (mmm160) REVERT: E 234 GLU cc_start: 0.8899 (pt0) cc_final: 0.8656 (pt0) REVERT: R 142 TRP cc_start: 0.6937 (m-90) cc_final: 0.5672 (m100) REVERT: R 250 TYR cc_start: 0.8179 (m-80) cc_final: 0.7928 (m-10) REVERT: R 252 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.5959 (mpp-170) outliers start: 33 outliers final: 22 residues processed: 163 average time/residue: 1.4895 time to fit residues: 256.9888 Evaluate side-chains 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 31 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 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 = 0.3824 r_free = 0.3824 target = 0.164602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126043 restraints weight = 8723.431| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.70 r_work: 0.3001 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9158 Z= 0.267 Angle : 0.544 6.675 12427 Z= 0.293 Chirality : 0.043 0.179 1426 Planarity : 0.004 0.059 1570 Dihedral : 5.449 58.497 1267 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.82 % Allowed : 10.63 % Favored : 85.55 % 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: 1.31 (0.25), residues: 1144 helix: 2.51 (0.25), residues: 394 sheet: 0.22 (0.29), residues: 297 loop : -0.08 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE B 151 TYR 0.014 0.002 TYR R 341 ARG 0.006 0.001 ARG A 208 *********************** 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 182 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.919 Fit side-chains REVERT: A 28 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: A 29 LYS cc_start: 0.8116 (tttt) cc_final: 0.7613 (ttpp) REVERT: A 33 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: A 270 LYS cc_start: 0.8485 (mttt) cc_final: 0.8035 (mttp) REVERT: B 42 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6318 (tpt170) REVERT: C 58 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: E 43 LYS cc_start: 0.8635 (mmtm) cc_final: 0.7837 (mtmt) REVERT: E 77 ASN cc_start: 0.8439 (m-40) cc_final: 0.7967 (m-40) REVERT: E 160 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.6783 (mmm160) REVERT: E 234 GLU cc_start: 0.8906 (pt0) cc_final: 0.8670 (pt0) REVERT: R 142 TRP cc_start: 0.6929 (m-90) cc_final: 0.5639 (m100) REVERT: R 165 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8002 (ttt) REVERT: R 250 TYR cc_start: 0.8230 (m-80) cc_final: 0.7953 (m-10) REVERT: R 252 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6007 (mpp-170) outliers start: 37 outliers final: 19 residues processed: 163 average time/residue: 1.4714 time to fit residues: 253.3588 Evaluate side-chains 166 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 C residue 58 GLU 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 152 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.0470 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 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 = 0.3866 r_free = 0.3866 target = 0.168320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131259 restraints weight = 8900.963| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.66 r_work: 0.3164 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9158 Z= 0.137 Angle : 0.466 5.203 12427 Z= 0.252 Chirality : 0.041 0.172 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.053 54.853 1266 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.68 % Allowed : 12.38 % Favored : 84.93 % 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: 1.50 (0.25), residues: 1144 helix: 2.76 (0.25), residues: 394 sheet: 0.24 (0.29), residues: 274 loop : 0.01 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.000 ARG A 208 *********************** 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 176 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.941 Fit side-chains REVERT: A 17 LYS cc_start: 0.8349 (mttt) cc_final: 0.7990 (mtpt) REVERT: A 28 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: A 29 LYS cc_start: 0.8164 (tttt) cc_final: 0.7686 (ttpp) REVERT: A 243 MET cc_start: 0.8584 (tpp) cc_final: 0.8351 (ttm) REVERT: A 270 LYS cc_start: 0.8530 (mttt) cc_final: 0.8089 (mttp) REVERT: B 57 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8146 (ptpt) REVERT: E 43 LYS cc_start: 0.8644 (mmtm) cc_final: 0.7913 (mtpt) REVERT: E 77 ASN cc_start: 0.8382 (m-40) cc_final: 0.7975 (m-40) REVERT: E 234 GLU cc_start: 0.8861 (pt0) cc_final: 0.8607 (pt0) REVERT: R 142 TRP cc_start: 0.6965 (m-90) cc_final: 0.5745 (m100) REVERT: R 250 TYR cc_start: 0.8245 (m-80) cc_final: 0.7978 (m-10) outliers start: 26 outliers final: 14 residues processed: 160 average time/residue: 1.3602 time to fit residues: 230.8232 Evaluate side-chains 159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 172 GLU 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 183 THR Chi-restraints excluded: chain R residue 249 LEU 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: 7.9990 chunk 66 optimal weight: 0.0770 chunk 28 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN 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 = 0.3874 r_free = 0.3874 target = 0.169028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132142 restraints weight = 8956.173| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.77 r_work: 0.3086 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9158 Z= 0.132 Angle : 0.462 5.809 12427 Z= 0.249 Chirality : 0.041 0.133 1426 Planarity : 0.004 0.058 1570 Dihedral : 4.529 42.329 1262 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.17 % Allowed : 12.59 % Favored : 85.24 % 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: 1.56 (0.25), residues: 1144 helix: 2.86 (0.25), residues: 396 sheet: 0.23 (0.29), residues: 274 loop : 0.01 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 170 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR E 190 ARG 0.010 0.000 ARG A 208 *********************** 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 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.007 Fit side-chains REVERT: A 8 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 17 LYS cc_start: 0.8355 (mttt) cc_final: 0.7966 (mtpt) REVERT: A 28 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: A 29 LYS cc_start: 0.8101 (tttt) cc_final: 0.7572 (ttpp) REVERT: A 270 LYS cc_start: 0.8511 (mttt) cc_final: 0.7937 (mttp) REVERT: E 43 LYS cc_start: 0.8578 (mmtm) cc_final: 0.7763 (mtpt) REVERT: E 77 ASN cc_start: 0.8366 (m-40) cc_final: 0.8004 (m-40) REVERT: R 142 TRP cc_start: 0.6857 (m-90) cc_final: 0.5630 (m100) REVERT: R 250 TYR cc_start: 0.8161 (m-80) cc_final: 0.7906 (m-10) REVERT: R 252 ARG cc_start: 0.6938 (mpt90) cc_final: 0.5891 (mpp-170) REVERT: R 345 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6976 (mm-40) outliers start: 21 outliers final: 18 residues processed: 153 average time/residue: 1.4935 time to fit residues: 241.7407 Evaluate side-chains 161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN 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 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 183 THR Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 4 MET 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: 3.9990 chunk 84 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN 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 = 0.3836 r_free = 0.3836 target = 0.165584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128105 restraints weight = 8825.985| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.67 r_work: 0.3116 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9158 Z= 0.267 Angle : 0.557 7.425 12427 Z= 0.296 Chirality : 0.044 0.216 1426 Planarity : 0.004 0.057 1570 Dihedral : 4.815 43.006 1258 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 1.40 (0.25), residues: 1144 helix: 2.69 (0.25), residues: 396 sheet: 0.15 (0.29), residues: 284 loop : -0.06 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.004 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 *********************** 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 172 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.985 Fit side-chains REVERT: A 17 LYS cc_start: 0.8370 (mttt) cc_final: 0.7987 (mtpt) REVERT: A 28 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: A 29 LYS cc_start: 0.8195 (tttt) cc_final: 0.7742 (ttpp) REVERT: A 33 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: A 270 LYS cc_start: 0.8526 (mttt) cc_final: 0.8084 (mttp) REVERT: B 42 ARG cc_start: 0.7066 (tpt170) cc_final: 0.6664 (tpt170) REVERT: E 43 LYS cc_start: 0.8634 (mmtm) cc_final: 0.7868 (mtpt) REVERT: E 77 ASN cc_start: 0.8436 (m-40) cc_final: 0.7978 (m-40) REVERT: E 160 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.6849 (mmm160) REVERT: E 234 GLU cc_start: 0.8847 (pt0) cc_final: 0.8605 (pt0) REVERT: R 142 TRP cc_start: 0.6967 (m-90) cc_final: 0.5756 (m100) REVERT: R 250 TYR cc_start: 0.8243 (m-80) cc_final: 0.7973 (m-10) REVERT: R 345 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7052 (mm-40) outliers start: 27 outliers final: 19 residues processed: 161 average time/residue: 1.6337 time to fit residues: 278.5138 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 135 VAL 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 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 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN 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: 1.9990 chunk 82 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 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 = 0.3848 r_free = 0.3848 target = 0.166650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129457 restraints weight = 8858.767| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.72 r_work: 0.3125 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9158 Z= 0.200 Angle : 0.530 9.618 12427 Z= 0.281 Chirality : 0.042 0.156 1426 Planarity : 0.004 0.058 1570 Dihedral : 4.786 43.095 1258 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.27 % Allowed : 12.90 % 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: 1.42 (0.25), residues: 1144 helix: 2.74 (0.25), residues: 396 sheet: 0.11 (0.29), residues: 284 loop : -0.04 (0.30), residues: 464 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 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR R 341 ARG 0.009 0.001 ARG A 208 ********************** 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 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.939 Fit side-chains REVERT: A 8 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 17 LYS cc_start: 0.8381 (mttt) cc_final: 0.8000 (mtpt) REVERT: A 28 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: A 29 LYS cc_start: 0.8204 (tttt) cc_final: 0.7735 (ttpp) REVERT: A 270 LYS cc_start: 0.8536 (mttt) cc_final: 0.8103 (mttp) REVERT: B 42 ARG cc_start: 0.7078 (tpt170) cc_final: 0.6677 (tpt170) REVERT: E 43 LYS cc_start: 0.8637 (mmtm) cc_final: 0.7864 (mtpt) REVERT: E 77 ASN cc_start: 0.8407 (m-40) cc_final: 0.7970 (m-40) REVERT: E 160 ARG cc_start: 0.7515 (mtp-110) cc_final: 0.6841 (mmm160) REVERT: E 234 GLU cc_start: 0.8862 (pt0) cc_final: 0.8621 (pt0) REVERT: R 142 TRP cc_start: 0.6961 (m-90) cc_final: 0.5717 (m100) REVERT: R 250 TYR cc_start: 0.8220 (m-80) cc_final: 0.7943 (m-10) REVERT: R 345 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7026 (mm110) outliers start: 22 outliers final: 17 residues processed: 155 average time/residue: 1.5923 time to fit residues: 262.6486 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 183 THR Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN 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: 0.8980 chunk 97 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 156 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 = 0.3863 r_free = 0.3863 target = 0.167874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130686 restraints weight = 8840.102| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.64 r_work: 0.3153 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9158 Z= 0.191 Angle : 0.522 7.604 12427 Z= 0.277 Chirality : 0.042 0.197 1426 Planarity : 0.004 0.058 1570 Dihedral : 4.762 42.980 1258 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.37 % Allowed : 12.90 % 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: 1.43 (0.25), residues: 1144 helix: 2.76 (0.25), residues: 396 sheet: 0.12 (0.29), residues: 277 loop : -0.06 (0.29), residues: 471 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 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR R 341 ARG 0.009 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8349.42 seconds wall clock time: 145 minutes 11.14 seconds (8711.14 seconds total)