Starting phenix.real_space_refine on Wed Aug 5 03:10:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uwm_64560/08_2026/9uwm_64560.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uwm_64560/08_2026/9uwm_64560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uwm_64560/08_2026/9uwm_64560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uwm_64560/08_2026/9uwm_64560.map" model { file = "/net/cci-nas-00/data/ceres_data/9uwm_64560/08_2026/9uwm_64560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uwm_64560/08_2026/9uwm_64560.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.008 sd= 0.043 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 59 5.16 5 C 5190 2.51 5 N 1404 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8128 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2492 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 91 Chain: "D" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 270 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "G" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 349 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3067 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 16, 'TRANS': 352} Time building chain proxies: 1.41, per 1000 atoms: 0.17 Number of scatterers: 8128 At special positions: 0 Unit cell: (90.52, 95.63, 148.19, 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 59 16.00 O 1475 8.00 N 1404 7.00 C 5190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 2 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " 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: 0.43 Conformation dependent library (CDL) restraints added in 281.6 milliseconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 47.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.855A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.853A pdb=" N HIS A 57 " --> pdb=" O MET A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.361A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.879A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.580A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.638A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 358 removed outlier: 4.526A pdb=" N ARG A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 20 Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.679A pdb=" N ASN D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 36' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 137 removed outlier: 4.079A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.978A pdb=" N LYS R 143 " --> pdb=" O PRO R 139 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 210 through 215 removed outlier: 3.519A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.966A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 267 removed outlier: 4.378A pdb=" N TYR R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 284 removed outlier: 3.836A pdb=" N LEU R 271 " --> pdb=" O TRP R 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 removed outlier: 3.665A pdb=" N ALA R 341 " --> pdb=" O MET R 337 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL R 342 " --> pdb=" O TYR R 338 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 353 through 359 removed outlier: 3.911A pdb=" N VAL R 357 " --> pdb=" O GLY R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 381 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.307A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.917A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.155A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.949A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.847A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.509A 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: 4.605A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.545A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 3.548A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.537A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB2, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AB3, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.701A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1194 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: 0.99 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2640 1.35 - 1.46: 2076 1.46 - 1.58: 3524 1.58 - 1.70: 0 1.70 - 1.81: 85 Bond restraints: 8325 Sorted by residual: bond pdb=" CA CYS D 7 " pdb=" C CYS D 7 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.80e-02 3.09e+03 9.66e-01 bond pdb=" CB PRO R 216 " pdb=" CG PRO R 216 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 9.02e-01 bond pdb=" CA LEU D 27 " pdb=" CB LEU D 27 " ideal model delta sigma weight residual 1.534 1.544 -0.010 1.41e-02 5.03e+03 5.34e-01 bond pdb=" C ARG R 362 " pdb=" N PRO R 363 " ideal model delta sigma weight residual 1.331 1.339 -0.008 1.20e-02 6.94e+03 4.64e-01 bond pdb=" CA ILE D 26 " pdb=" CB ILE D 26 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.48e-01 ... (remaining 8320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 11241 2.21 - 4.41: 62 4.41 - 6.62: 8 6.62 - 8.83: 0 8.83 - 11.04: 1 Bond angle restraints: 11312 Sorted by residual: angle pdb=" CA LEU D 27 " pdb=" CB LEU D 27 " pdb=" CG LEU D 27 " ideal model delta sigma weight residual 116.30 127.34 -11.04 3.50e+00 8.16e-02 9.94e+00 angle pdb=" C PRO D 25 " pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta sigma weight residual 121.97 126.03 -4.06 1.80e+00 3.09e-01 5.08e+00 angle pdb=" N GLU B 215 " pdb=" CA GLU B 215 " pdb=" C GLU B 215 " ideal model delta sigma weight residual 114.04 111.30 2.74 1.24e+00 6.50e-01 4.90e+00 angle pdb=" N ARG R 362 " pdb=" CA ARG R 362 " pdb=" C ARG R 362 " ideal model delta sigma weight residual 109.81 114.65 -4.84 2.21e+00 2.05e-01 4.80e+00 angle pdb=" C THR D 4 " pdb=" N ALA D 5 " pdb=" CA ALA D 5 " ideal model delta sigma weight residual 121.54 125.53 -3.99 1.91e+00 2.74e-01 4.36e+00 ... (remaining 11307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.95: 4584 11.95 - 23.89: 233 23.89 - 35.83: 68 35.83 - 47.78: 15 47.78 - 59.72: 6 Dihedral angle restraints: 4906 sinusoidal: 1866 harmonic: 3040 Sorted by residual: dihedral pdb=" CB CYS D 2 " pdb=" SG CYS D 2 " pdb=" SG CYS D 7 " pdb=" CB CYS D 7 " ideal model delta sinusoidal sigma weight residual 93.00 129.36 -36.36 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 123.08 -30.08 1 1.00e+01 1.00e-02 1.29e+01 dihedral pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" CB TYR B 59 " pdb=" CG TYR B 59 " ideal model delta sinusoidal sigma weight residual -180.00 -120.28 -59.72 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 807 0.027 - 0.054: 284 0.054 - 0.082: 102 0.082 - 0.109: 51 0.109 - 0.136: 18 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CB ILE D 26 " pdb=" CA ILE D 26 " pdb=" CG1 ILE D 26 " pdb=" CG2 ILE D 26 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CG LEU D 27 " pdb=" CB LEU D 27 " pdb=" CD1 LEU D 27 " pdb=" CD2 LEU D 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1259 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 294 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO A 295 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO A 299 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 321 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ARG R 321 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG R 321 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL R 322 " -0.009 2.00e-02 2.50e+03 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1342 2.76 - 3.30: 7888 3.30 - 3.83: 13755 3.83 - 4.37: 15558 4.37 - 4.90: 27100 Nonbonded interactions: 65643 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR R 149 " pdb=" O LEU R 202 " model vdw 2.246 3.040 nonbonded pdb=" O ASP A 335 " pdb=" ND2 ASN A 338 " model vdw 2.276 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.294 3.040 nonbonded pdb=" O PHE A 330 " pdb=" NH1 ARG A 341 " model vdw 2.319 3.120 ... (remaining 65638 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: 4.010 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 6.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 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 0.047 8329 Z= 0.091 Angle : 0.445 11.036 11320 Z= 0.240 Chirality : 0.037 0.136 1262 Planarity : 0.004 0.060 1442 Dihedral : 8.386 59.724 2928 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.47 % Rotamer: Outliers : 1.06 % Allowed : 5.30 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.27), residues: 1026 helix: 2.57 (0.26), residues: 426 sheet: 0.97 (0.38), residues: 182 loop : -0.28 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 341 TYR 0.008 0.001 TYR R 149 PHE 0.008 0.001 PHE A 189 TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.09 ( 8325) covalent geometry : angle 0.44495 / 0.24 (11312) SS BOND : bond 0.00121 / 0.06 ( 4) SS BOND : angle 0.62338 / 0.31 ( 8) hydrogen bonds : bond 0.14857 / 9.41 ( 418) hydrogen bonds : angle 6.06687 / 4.41 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 226 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 ARG cc_start: 0.5976 (tpp-160) cc_final: 0.5694 (ttm-80) REVERT: B 217 MET cc_start: 0.4914 (pp-130) cc_final: 0.4599 (ppp) REVERT: B 234 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.5397 (t80) REVERT: D 1 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.4144 (tptt) REVERT: R 147 VAL cc_start: 0.7733 (t) cc_final: 0.7465 (p) REVERT: R 343 LYS cc_start: 0.7086 (tttm) cc_final: 0.6872 (ttpp) outliers start: 9 outliers final: 3 residues processed: 233 average time/residue: 0.0906 time to fit residues: 27.0192 Evaluate side-chains 145 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain D residue 2 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 216 ASN A 329 HIS A 351 GLN A 357 GLN B 155 ASN B 259 GLN D 18 HIS R 179 GLN R 186 ASN R 201 HIS ** R 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.172698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.136701 restraints weight = 12103.604| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.15 r_work: 0.3661 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8329 Z= 0.226 Angle : 0.634 6.923 11320 Z= 0.340 Chirality : 0.046 0.253 1262 Planarity : 0.005 0.055 1442 Dihedral : 5.336 57.763 1141 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.12 % Favored : 96.78 % Rotamer: Outliers : 3.65 % Allowed : 10.25 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.26), residues: 1026 helix: 2.42 (0.25), residues: 427 sheet: 1.07 (0.40), residues: 157 loop : -0.50 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 31 TYR 0.025 0.002 TYR R 234 PHE 0.024 0.003 PHE A 223 TRP 0.016 0.002 TRP B 99 HIS 0.009 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 ( 8325) covalent geometry : angle 0.63372 / 0.34 (11312) SS BOND : bond 0.00257 / 0.13 ( 4) SS BOND : angle 1.02489 / 0.57 ( 8) hydrogen bonds : bond 0.04323 / 2.85 ( 418) hydrogen bonds : angle 4.59804 / 3.28 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.7502 (ppp) cc_final: 0.7071 (ppp) REVERT: B 105 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.5676 (m-80) REVERT: B 198 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6075 (pp) REVERT: B 217 MET cc_start: 0.6068 (pp-130) cc_final: 0.5265 (ppp) REVERT: B 234 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.6086 (t80) REVERT: B 250 CYS cc_start: 0.6349 (OUTLIER) cc_final: 0.5748 (t) REVERT: D 1 LYS cc_start: 0.4907 (OUTLIER) cc_final: 0.3910 (tptt) REVERT: R 260 ARG cc_start: 0.8094 (ptt-90) cc_final: 0.6431 (mmm160) REVERT: R 340 LYS cc_start: 0.7970 (mmtp) cc_final: 0.7616 (mttp) REVERT: R 397 GLU cc_start: 0.7300 (pm20) cc_final: 0.6927 (pm20) outliers start: 31 outliers final: 14 residues processed: 168 average time/residue: 0.0780 time to fit residues: 17.6281 Evaluate side-chains 145 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 378 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS D 18 HIS R 257 GLN ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 377 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.173101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.137156 restraints weight = 11857.035| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.01 r_work: 0.3672 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8329 Z= 0.163 Angle : 0.556 6.844 11320 Z= 0.298 Chirality : 0.042 0.185 1262 Planarity : 0.004 0.049 1442 Dihedral : 4.694 52.518 1138 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 3.42 % Allowed : 11.90 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1026 helix: 2.48 (0.25), residues: 427 sheet: 0.60 (0.40), residues: 168 loop : -0.38 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 174 TYR 0.018 0.001 TYR R 149 PHE 0.022 0.002 PHE B 199 TRP 0.014 0.001 TRP R 267 HIS 0.010 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 8325) covalent geometry : angle 0.55387 / 0.30 (11312) SS BOND : bond 0.00373 / 0.19 ( 4) SS BOND : angle 1.80241 / 0.95 ( 8) hydrogen bonds : bond 0.03786 / 2.50 ( 418) hydrogen bonds : angle 4.39663 / 3.12 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.7435 (ppp) cc_final: 0.7122 (ppp) REVERT: B 217 MET cc_start: 0.6335 (pp-130) cc_final: 0.5708 (pp-130) REVERT: B 234 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6128 (t80) REVERT: D 1 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.4053 (tptt) REVERT: R 280 THR cc_start: 0.6174 (m) cc_final: 0.5950 (t) REVERT: R 340 LYS cc_start: 0.7944 (mmtp) cc_final: 0.7558 (mttp) REVERT: R 397 GLU cc_start: 0.7215 (pm20) cc_final: 0.6987 (pm20) REVERT: R 408 GLN cc_start: 0.6923 (mt0) cc_final: 0.6507 (mt0) outliers start: 29 outliers final: 17 residues processed: 156 average time/residue: 0.0784 time to fit residues: 16.4132 Evaluate side-chains 143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.173586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.137911 restraints weight = 12066.880| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.13 r_work: 0.3681 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8329 Z= 0.135 Angle : 0.528 7.040 11320 Z= 0.281 Chirality : 0.041 0.173 1262 Planarity : 0.004 0.047 1442 Dihedral : 4.582 51.280 1138 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 3.18 % Allowed : 12.60 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1026 helix: 2.55 (0.25), residues: 429 sheet: 0.46 (0.40), residues: 168 loop : -0.41 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 31 TYR 0.017 0.001 TYR R 149 PHE 0.015 0.002 PHE A 223 TRP 0.013 0.001 TRP B 99 HIS 0.006 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8325) covalent geometry : angle 0.52576 / 0.28 (11312) SS BOND : bond 0.00464 / 0.24 ( 4) SS BOND : angle 1.78079 / 0.97 ( 8) hydrogen bonds : bond 0.03494 / 2.34 ( 418) hydrogen bonds : angle 4.25369 / 3.01 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.6532 (pp-130) cc_final: 0.5639 (ppp) REVERT: B 234 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.6111 (t80) REVERT: B 250 CYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6012 (t) REVERT: D 1 LYS cc_start: 0.4950 (OUTLIER) cc_final: 0.3957 (tptt) REVERT: R 280 THR cc_start: 0.6106 (m) cc_final: 0.5904 (t) REVERT: R 340 LYS cc_start: 0.7822 (mmtp) cc_final: 0.7462 (mttp) REVERT: R 408 GLN cc_start: 0.6891 (mt0) cc_final: 0.6460 (mt0) outliers start: 27 outliers final: 16 residues processed: 149 average time/residue: 0.0801 time to fit residues: 16.1621 Evaluate side-chains 144 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.171550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.134084 restraints weight = 12023.590| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.16 r_work: 0.3639 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8329 Z= 0.160 Angle : 0.549 8.711 11320 Z= 0.290 Chirality : 0.042 0.186 1262 Planarity : 0.004 0.046 1442 Dihedral : 4.740 52.671 1138 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 3.30 % Allowed : 13.19 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 1026 helix: 2.47 (0.25), residues: 427 sheet: 0.26 (0.39), residues: 168 loop : -0.43 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 31 TYR 0.018 0.001 TYR R 234 PHE 0.023 0.002 PHE B 199 TRP 0.014 0.001 TRP B 99 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 8325) covalent geometry : angle 0.54741 / 0.29 (11312) SS BOND : bond 0.00311 / 0.16 ( 4) SS BOND : angle 1.72965 / 0.94 ( 8) hydrogen bonds : bond 0.03599 / 2.44 ( 418) hydrogen bonds : angle 4.24879 / 3.01 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.6530 (pp-130) cc_final: 0.5926 (pp-130) REVERT: B 234 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.6323 (t80) REVERT: B 250 CYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6179 (t) REVERT: D 1 LYS cc_start: 0.5044 (OUTLIER) cc_final: 0.4032 (tptt) REVERT: R 340 LYS cc_start: 0.7823 (mmtp) cc_final: 0.7408 (mttp) REVERT: R 397 GLU cc_start: 0.7156 (pm20) cc_final: 0.6924 (pm20) REVERT: R 408 GLN cc_start: 0.6917 (mt0) cc_final: 0.6514 (mt0) outliers start: 28 outliers final: 19 residues processed: 147 average time/residue: 0.0701 time to fit residues: 14.1878 Evaluate side-chains 142 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.171471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.135704 restraints weight = 11981.678| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.07 r_work: 0.3641 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8329 Z= 0.140 Angle : 0.528 8.561 11320 Z= 0.280 Chirality : 0.041 0.176 1262 Planarity : 0.004 0.044 1442 Dihedral : 4.633 51.601 1138 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 3.42 % Allowed : 14.13 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1026 helix: 2.46 (0.25), residues: 427 sheet: -0.04 (0.39), residues: 179 loop : -0.34 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 31 TYR 0.016 0.001 TYR R 149 PHE 0.024 0.002 PHE B 199 TRP 0.012 0.001 TRP B 99 HIS 0.011 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8325) covalent geometry : angle 0.52611 / 0.28 (11312) SS BOND : bond 0.00351 / 0.18 ( 4) SS BOND : angle 1.73475 / 0.95 ( 8) hydrogen bonds : bond 0.03427 / 2.32 ( 418) hydrogen bonds : angle 4.18852 / 2.97 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8147 (pp) REVERT: B 199 PHE cc_start: 0.6792 (p90) cc_final: 0.6536 (p90) REVERT: B 217 MET cc_start: 0.6529 (pp-130) cc_final: 0.5993 (pp-130) REVERT: B 234 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6379 (t80) REVERT: B 250 CYS cc_start: 0.6484 (OUTLIER) cc_final: 0.6234 (t) REVERT: D 1 LYS cc_start: 0.5063 (OUTLIER) cc_final: 0.4129 (mmtt) REVERT: R 77 ASP cc_start: 0.7330 (t0) cc_final: 0.7016 (t0) REVERT: R 99 PHE cc_start: 0.7843 (m-80) cc_final: 0.7570 (m-80) REVERT: R 133 MET cc_start: 0.6833 (pmm) cc_final: 0.6114 (pmm) REVERT: R 336 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7134 (t-90) REVERT: R 340 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7445 (mttp) REVERT: R 397 GLU cc_start: 0.7081 (pm20) cc_final: 0.6880 (pm20) REVERT: R 408 GLN cc_start: 0.6965 (mt0) cc_final: 0.6573 (mt0) outliers start: 29 outliers final: 17 residues processed: 146 average time/residue: 0.0702 time to fit residues: 13.9710 Evaluate side-chains 145 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 336 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 32 optimal weight: 0.0980 chunk 23 optimal weight: 30.0000 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.173200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.136793 restraints weight = 12216.287| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.16 r_work: 0.3682 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8329 Z= 0.118 Angle : 0.530 9.392 11320 Z= 0.281 Chirality : 0.040 0.158 1262 Planarity : 0.004 0.044 1442 Dihedral : 4.545 49.518 1138 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 3.06 % Allowed : 15.08 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1026 helix: 2.52 (0.25), residues: 428 sheet: 0.20 (0.41), residues: 161 loop : -0.48 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.017 0.001 TYR R 149 PHE 0.022 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.010 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8325) covalent geometry : angle 0.52718 / 0.28 (11312) SS BOND : bond 0.00629 / 0.32 ( 4) SS BOND : angle 2.18152 / 1.13 ( 8) hydrogen bonds : bond 0.03253 / 2.24 ( 418) hydrogen bonds : angle 4.09013 / 2.89 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 45 MET cc_start: 0.6841 (mtm) cc_final: 0.6354 (mtp) REVERT: B 117 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8040 (pp) REVERT: B 199 PHE cc_start: 0.6756 (p90) cc_final: 0.6522 (p90) REVERT: B 217 MET cc_start: 0.6599 (pp-130) cc_final: 0.6005 (pp-130) REVERT: B 234 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.6247 (t80) REVERT: B 250 CYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6277 (t) REVERT: B 273 ILE cc_start: 0.7526 (mt) cc_final: 0.7280 (mt) REVERT: D 1 LYS cc_start: 0.5164 (OUTLIER) cc_final: 0.4284 (mmtp) REVERT: R 77 ASP cc_start: 0.7126 (t0) cc_final: 0.6819 (t0) REVERT: R 79 TRP cc_start: 0.5332 (m-90) cc_final: 0.4400 (m-90) REVERT: R 99 PHE cc_start: 0.7720 (m-80) cc_final: 0.7465 (m-80) REVERT: R 336 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6962 (t-90) REVERT: R 340 LYS cc_start: 0.7847 (mmtp) cc_final: 0.7363 (mttp) REVERT: R 408 GLN cc_start: 0.6895 (mt0) cc_final: 0.6512 (mt0) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.0790 time to fit residues: 15.6941 Evaluate side-chains 143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 336 HIS Chi-restraints excluded: chain R residue 346 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 0.0040 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.173314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137740 restraints weight = 12080.302| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.21 r_work: 0.3660 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8329 Z= 0.119 Angle : 0.526 10.790 11320 Z= 0.278 Chirality : 0.040 0.153 1262 Planarity : 0.004 0.044 1442 Dihedral : 4.413 49.887 1137 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 3.06 % Allowed : 15.67 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.27), residues: 1026 helix: 2.57 (0.25), residues: 422 sheet: 0.27 (0.41), residues: 159 loop : -0.51 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.016 0.001 TYR R 149 PHE 0.019 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.011 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8325) covalent geometry : angle 0.52345 / 0.28 (11312) SS BOND : bond 0.00413 / 0.21 ( 4) SS BOND : angle 1.88716 / 0.99 ( 8) hydrogen bonds : bond 0.03210 / 2.19 ( 418) hydrogen bonds : angle 4.04258 / 2.84 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 45 MET cc_start: 0.6564 (mtm) cc_final: 0.6115 (mtp) REVERT: B 217 MET cc_start: 0.6470 (pp-130) cc_final: 0.5709 (ppp) REVERT: B 234 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.6182 (t80) REVERT: B 273 ILE cc_start: 0.7342 (mt) cc_final: 0.7016 (mt) REVERT: D 1 LYS cc_start: 0.5391 (OUTLIER) cc_final: 0.4686 (mmtp) REVERT: R 77 ASP cc_start: 0.7038 (t0) cc_final: 0.6642 (t0) REVERT: R 79 TRP cc_start: 0.5326 (m-90) cc_final: 0.4354 (m-90) REVERT: R 99 PHE cc_start: 0.7597 (m-80) cc_final: 0.7365 (m-80) REVERT: R 336 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6755 (t-90) outliers start: 26 outliers final: 16 residues processed: 144 average time/residue: 0.0748 time to fit residues: 14.8003 Evaluate side-chains 142 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 336 HIS Chi-restraints excluded: chain R residue 346 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.168818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131227 restraints weight = 12125.941| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.50 r_work: 0.3555 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8329 Z= 0.232 Angle : 0.661 19.286 11320 Z= 0.340 Chirality : 0.044 0.196 1262 Planarity : 0.004 0.044 1442 Dihedral : 4.962 55.728 1137 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 3.30 % Allowed : 15.90 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1026 helix: 2.06 (0.25), residues: 423 sheet: -0.01 (0.41), residues: 158 loop : -0.53 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 49 TYR 0.027 0.002 TYR R 234 PHE 0.026 0.002 PHE B 199 TRP 0.019 0.002 TRP B 99 HIS 0.011 0.002 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 ( 8325) covalent geometry : angle 0.65885 / 0.34 (11312) SS BOND : bond 0.00346 / 0.18 ( 4) SS BOND : angle 1.89281 / 1.01 ( 8) hydrogen bonds : bond 0.04054 / 2.73 ( 418) hydrogen bonds : angle 4.45311 / 3.14 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 234 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6236 (t80) REVERT: R 332 GLU cc_start: 0.7111 (tp30) cc_final: 0.6737 (mm-30) REVERT: R 336 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6799 (t-90) outliers start: 28 outliers final: 24 residues processed: 143 average time/residue: 0.0861 time to fit residues: 16.8667 Evaluate side-chains 146 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 336 HIS Chi-restraints excluded: chain R residue 346 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 42 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN R 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.170897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133303 restraints weight = 11990.930| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.31 r_work: 0.3611 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8329 Z= 0.138 Angle : 0.584 16.029 11320 Z= 0.304 Chirality : 0.041 0.162 1262 Planarity : 0.004 0.044 1442 Dihedral : 4.724 52.553 1137 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 2.83 % Allowed : 17.08 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.27), residues: 1026 helix: 2.26 (0.25), residues: 423 sheet: -0.12 (0.39), residues: 177 loop : -0.41 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 250 TYR 0.017 0.001 TYR R 149 PHE 0.027 0.002 PHE B 199 TRP 0.016 0.001 TRP B 99 HIS 0.011 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8325) covalent geometry : angle 0.58265 / 0.30 (11312) SS BOND : bond 0.00383 / 0.19 ( 4) SS BOND : angle 1.72678 / 0.91 ( 8) hydrogen bonds : bond 0.03446 / 2.38 ( 418) hydrogen bonds : angle 4.24188 / 2.98 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7218 (tm-30) REVERT: B 217 MET cc_start: 0.6710 (pp-130) cc_final: 0.5868 (ppp) REVERT: B 252 LEU cc_start: 0.8041 (tp) cc_final: 0.7676 (mt) REVERT: D 1 LYS cc_start: 0.5537 (OUTLIER) cc_final: 0.4802 (mmtt) REVERT: R 336 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.7071 (t-90) outliers start: 24 outliers final: 21 residues processed: 138 average time/residue: 0.0788 time to fit residues: 14.7735 Evaluate side-chains 143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 178 CYS Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 336 HIS Chi-restraints excluded: chain R residue 346 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 71 optimal weight: 0.0970 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.172833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.136044 restraints weight = 12093.554| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.10 r_work: 0.3687 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8329 Z= 0.119 Angle : 0.555 12.003 11320 Z= 0.290 Chirality : 0.040 0.149 1262 Planarity : 0.004 0.043 1442 Dihedral : 4.265 41.567 1135 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 2.59 % Allowed : 17.20 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.27), residues: 1026 helix: 2.41 (0.25), residues: 422 sheet: -0.04 (0.39), residues: 180 loop : -0.39 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.017 0.001 TYR R 149 PHE 0.028 0.001 PHE B 199 TRP 0.017 0.001 TRP B 82 HIS 0.011 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8325) covalent geometry : angle 0.55424 / 0.29 (11312) SS BOND : bond 0.00389 / 0.19 ( 4) SS BOND : angle 1.51221 / 0.79 ( 8) hydrogen bonds : bond 0.03220 / 2.24 ( 418) hydrogen bonds : angle 4.06619 / 2.85 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2593.10 seconds wall clock time: 44 minutes 47.85 seconds (2687.85 seconds total)