Starting phenix.real_space_refine on Wed Feb 4 04:23:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kx6_62624/02_2026/9kx6_62624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kx6_62624/02_2026/9kx6_62624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kx6_62624/02_2026/9kx6_62624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kx6_62624/02_2026/9kx6_62624.map" model { file = "/net/cci-nas-00/data/ceres_data/9kx6_62624/02_2026/9kx6_62624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kx6_62624/02_2026/9kx6_62624.cif" } resolution = 3.11 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= -0.000 sd= 0.017 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 57 5.16 5 C 5485 2.51 5 N 1483 2.21 5 O 1591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8616 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2134 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 277} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'HIS:plan': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1537 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2469 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'GLU:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 83 Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 444 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1656 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 1.90, per 1000 atoms: 0.22 Number of scatterers: 8616 At special positions: 0 Unit cell: (97.767, 117.32, 147.226, 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 57 16.00 O 1591 8.00 N 1483 7.00 C 5485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 54 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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: 0.51 Conformation dependent library (CDL) restraints added in 219.7 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 40 through 62 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 69 through 88 removed outlier: 3.729A pdb=" N ILE A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TRP A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.789A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.875A pdb=" N ILE A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 140 Processing helix chain 'A' and resid 149 through 173 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 200 through 231 removed outlier: 4.855A pdb=" N LEU A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 238 through 269 removed outlier: 3.877A pdb=" N LEU A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 275 through 305 removed outlier: 3.798A pdb=" N VAL A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'B' and resid 9 through 32 removed outlier: 3.600A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 208 through 217 removed outlier: 5.042A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.735A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.570A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 7 through 26 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.509A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 15 through 26 removed outlier: 4.472A pdb=" N CYS D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR D 23 " --> pdb=" O LYS D 19 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 25 " --> pdb=" O CYS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 44 through 65 removed outlier: 3.988A pdb=" N THR D 52 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.609A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.839A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.513A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 3.741A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 340 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 62 removed outlier: 3.563A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.384A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.794A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.588A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.200A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.694A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP H 36 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.340A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.539A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1227 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: 1.09 Time building geometry restraints manager: 0.69 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: 2814 1.35 - 1.47: 2156 1.47 - 1.59: 3746 1.59 - 1.71: 0 1.71 - 1.83: 72 Bond restraints: 8788 Sorted by residual: bond pdb=" C VAL A 52 " pdb=" N PRO A 53 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 6.02e+00 bond pdb=" C ILE A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 1.336 1.353 -0.018 1.08e-02 8.57e+03 2.63e+00 bond pdb=" CA VAL A 52 " pdb=" CB VAL A 52 " ideal model delta sigma weight residual 1.534 1.545 -0.010 6.80e-03 2.16e+04 2.23e+00 bond pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.59e+00 bond pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.19e+00 ... (remaining 8783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 11585 1.29 - 2.57: 321 2.57 - 3.86: 60 3.86 - 5.14: 22 5.14 - 6.43: 6 Bond angle restraints: 11994 Sorted by residual: angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.91e+00 angle pdb=" C THR B 324 " pdb=" N CYS B 325 " pdb=" CA CYS B 325 " ideal model delta sigma weight residual 122.61 126.60 -3.99 1.56e+00 4.11e-01 6.55e+00 angle pdb=" CA GLN A 34 " pdb=" CB GLN A 34 " pdb=" CG GLN A 34 " ideal model delta sigma weight residual 114.10 118.94 -4.84 2.00e+00 2.50e-01 5.87e+00 angle pdb=" N PHE C 292 " pdb=" CA PHE C 292 " pdb=" CB PHE C 292 " ideal model delta sigma weight residual 113.65 110.20 3.45 1.47e+00 4.63e-01 5.52e+00 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" CB VAL A 52 " ideal model delta sigma weight residual 110.50 111.97 -1.47 6.30e-01 2.52e+00 5.48e+00 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 4757 16.40 - 32.80: 321 32.80 - 49.20: 59 49.20 - 65.60: 12 65.60 - 82.01: 5 Dihedral angle restraints: 5154 sinusoidal: 1711 harmonic: 3443 Sorted by residual: dihedral pdb=" CB CYS D 34 " pdb=" SG CYS D 34 " pdb=" SG CYS D 55 " pdb=" CB CYS D 55 " ideal model delta sinusoidal sigma weight residual -86.00 -150.51 64.51 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CA ASP C 291 " pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA PHE C 151 " pdb=" C PHE C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 764 0.025 - 0.050: 384 0.050 - 0.076: 173 0.076 - 0.101: 73 0.101 - 0.126: 40 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA CYS B 325 " pdb=" N CYS B 325 " pdb=" C CYS B 325 " pdb=" CB CYS B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE H 189 " pdb=" N ILE H 189 " pdb=" C ILE H 189 " pdb=" CB ILE H 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1431 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 214 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 215 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 209 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C MET A 209 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A 209 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 210 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.023 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 661 2.74 - 3.28: 9106 3.28 - 3.82: 14504 3.82 - 4.36: 16945 4.36 - 4.90: 29576 Nonbonded interactions: 70792 Sorted by model distance: nonbonded pdb=" OG1 THR C 65 " pdb=" O PRO C 107 " model vdw 2.198 3.040 nonbonded pdb=" NH1 ARG B 15 " pdb=" O VAL C 90 " model vdw 2.205 3.120 nonbonded pdb=" O MET C 325 " pdb=" ND2 ASN C 340 " model vdw 2.243 3.120 nonbonded pdb=" ND2 ASN C 230 " pdb=" OD1 ASP C 246 " model vdw 2.256 3.120 nonbonded pdb=" OE1 GLU B 217 " pdb=" NZ LYS C 57 " model vdw 2.260 3.120 ... (remaining 70787 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: 1.420 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 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 : 0.003 0.034 8794 Z= 0.128 Angle : 0.562 6.429 12006 Z= 0.309 Chirality : 0.041 0.126 1434 Planarity : 0.004 0.047 1526 Dihedral : 11.942 82.005 2912 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 0.05 (0.26), residues: 1175 helix: 1.00 (0.27), residues: 401 sheet: -0.39 (0.33), residues: 244 loop : -0.40 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 191 TYR 0.021 0.001 TYR B 297 PHE 0.015 0.001 PHE B 275 TRP 0.010 0.001 TRP A 74 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8788) covalent geometry : angle 0.56161 (11994) SS BOND : bond 0.00198 ( 6) SS BOND : angle 1.02428 ( 12) hydrogen bonds : bond 0.20075 ( 437) hydrogen bonds : angle 7.02919 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 74 TRP cc_start: 0.7493 (m100) cc_final: 0.7136 (m100) REVERT: A 78 LEU cc_start: 0.7511 (tp) cc_final: 0.7291 (tt) REVERT: A 99 HIS cc_start: 0.7203 (m170) cc_final: 0.6991 (m170) REVERT: B 32 LYS cc_start: 0.7397 (mttt) cc_final: 0.7167 (mttt) REVERT: B 198 ARG cc_start: 0.6359 (mtm180) cc_final: 0.6138 (mtp180) REVERT: C 127 LYS cc_start: 0.8384 (mmtp) cc_final: 0.8094 (mmmt) REVERT: C 158 VAL cc_start: 0.5603 (p) cc_final: 0.5401 (m) REVERT: C 263 THR cc_start: 0.7181 (m) cc_final: 0.6922 (p) REVERT: H 18 ARG cc_start: 0.7215 (ptm160) cc_final: 0.6629 (mtm180) REVERT: H 105 SER cc_start: 0.6446 (t) cc_final: 0.6183 (p) REVERT: H 184 SER cc_start: 0.6756 (p) cc_final: 0.5982 (p) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0786 time to fit residues: 22.6964 Evaluate side-chains 186 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN B 214 HIS ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 268 ASN H 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.160511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144379 restraints weight = 14257.257| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.30 r_work: 0.3889 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8794 Z= 0.239 Angle : 0.667 7.002 12006 Z= 0.353 Chirality : 0.046 0.175 1434 Planarity : 0.005 0.065 1526 Dihedral : 4.573 15.912 1261 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.79 % Allowed : 11.35 % Favored : 86.86 % 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: -0.29 (0.25), residues: 1175 helix: 0.71 (0.26), residues: 408 sheet: -0.67 (0.32), residues: 250 loop : -0.56 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 134 TYR 0.023 0.002 TYR H 103 PHE 0.018 0.002 PHE B 200 TRP 0.032 0.003 TRP C 63 HIS 0.006 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 8788) covalent geometry : angle 0.66643 (11994) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.04712 ( 12) hydrogen bonds : bond 0.04968 ( 437) hydrogen bonds : angle 5.58594 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7969 (tp) cc_final: 0.7730 (tt) REVERT: B 32 LYS cc_start: 0.7821 (mttt) cc_final: 0.7535 (mttt) REVERT: B 198 ARG cc_start: 0.6772 (mtm180) cc_final: 0.6570 (mtp180) REVERT: B 245 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6999 (t-90) REVERT: B 303 TYR cc_start: 0.7736 (t80) cc_final: 0.7513 (t80) REVERT: B 307 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8542 (mm110) REVERT: C 48 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7459 (mmm160) REVERT: C 127 LYS cc_start: 0.8880 (mmtp) cc_final: 0.8519 (mmmt) REVERT: C 158 VAL cc_start: 0.7027 (p) cc_final: 0.6476 (m) REVERT: C 170 ASP cc_start: 0.8264 (t70) cc_final: 0.8005 (t0) REVERT: H 105 SER cc_start: 0.7278 (t) cc_final: 0.6845 (p) outliers start: 15 outliers final: 9 residues processed: 187 average time/residue: 0.1011 time to fit residues: 25.7880 Evaluate side-chains 184 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.165852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.149882 restraints weight = 13965.094| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.25 r_work: 0.3897 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8794 Z= 0.189 Angle : 0.618 6.806 12006 Z= 0.324 Chirality : 0.044 0.175 1434 Planarity : 0.005 0.055 1526 Dihedral : 4.497 15.854 1261 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.39 % Allowed : 15.53 % Favored : 82.08 % 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: -0.41 (0.25), residues: 1175 helix: 0.66 (0.26), residues: 411 sheet: -0.75 (0.31), residues: 247 loop : -0.67 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 207 TYR 0.022 0.002 TYR H 190 PHE 0.022 0.002 PHE B 200 TRP 0.037 0.002 TRP C 63 HIS 0.008 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8788) covalent geometry : angle 0.61737 (11994) SS BOND : bond 0.00245 ( 6) SS BOND : angle 1.00943 ( 12) hydrogen bonds : bond 0.04315 ( 437) hydrogen bonds : angle 5.35064 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7992 (tp) cc_final: 0.7765 (tt) REVERT: B 32 LYS cc_start: 0.7806 (mttt) cc_final: 0.7493 (mttt) REVERT: B 245 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6960 (t-90) REVERT: B 307 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8546 (mm110) REVERT: B 309 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7957 (mt-10) REVERT: C 127 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8519 (mmmt) REVERT: C 170 ASP cc_start: 0.8246 (t70) cc_final: 0.8000 (t0) REVERT: C 234 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: G 50 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6231 (mt) REVERT: G 61 PHE cc_start: 0.7551 (m-80) cc_final: 0.7080 (m-80) REVERT: H 105 SER cc_start: 0.7208 (t) cc_final: 0.6891 (p) outliers start: 20 outliers final: 12 residues processed: 183 average time/residue: 0.1052 time to fit residues: 26.3525 Evaluate side-chains 183 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.165000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.148957 restraints weight = 14184.401| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.26 r_work: 0.3897 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8794 Z= 0.184 Angle : 0.606 6.998 12006 Z= 0.315 Chirality : 0.044 0.155 1434 Planarity : 0.004 0.051 1526 Dihedral : 4.464 18.278 1261 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.94 % Allowed : 16.37 % Favored : 79.69 % 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: -0.43 (0.25), residues: 1175 helix: 0.71 (0.26), residues: 409 sheet: -0.80 (0.31), residues: 247 loop : -0.72 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 207 TYR 0.024 0.002 TYR H 190 PHE 0.015 0.002 PHE B 275 TRP 0.050 0.002 TRP C 63 HIS 0.008 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8788) covalent geometry : angle 0.60496 (11994) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.01925 ( 12) hydrogen bonds : bond 0.04104 ( 437) hydrogen bonds : angle 5.27324 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7928 (tp) cc_final: 0.7690 (tt) REVERT: A 99 HIS cc_start: 0.7504 (m170) cc_final: 0.7289 (m170) REVERT: B 32 LYS cc_start: 0.7824 (mttt) cc_final: 0.7493 (mttt) REVERT: B 200 PHE cc_start: 0.7724 (m-10) cc_final: 0.7505 (m-10) REVERT: B 245 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6913 (t-90) REVERT: C 127 LYS cc_start: 0.8904 (mmtp) cc_final: 0.8523 (mmmt) REVERT: C 170 ASP cc_start: 0.8243 (t70) cc_final: 0.8011 (t0) REVERT: C 211 TRP cc_start: 0.6955 (OUTLIER) cc_final: 0.5393 (m-10) REVERT: C 234 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: G 50 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6395 (mt) REVERT: H 105 SER cc_start: 0.7204 (t) cc_final: 0.6858 (p) outliers start: 33 outliers final: 19 residues processed: 192 average time/residue: 0.1089 time to fit residues: 28.3408 Evaluate side-chains 188 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 239 ASN H 39 GLN H 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.161239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.145323 restraints weight = 14047.839| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.28 r_work: 0.3900 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8794 Z= 0.173 Angle : 0.618 10.753 12006 Z= 0.316 Chirality : 0.044 0.186 1434 Planarity : 0.004 0.046 1526 Dihedral : 4.409 20.137 1261 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.18 % Allowed : 16.85 % Favored : 78.97 % 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: -0.44 (0.24), residues: 1175 helix: 0.79 (0.26), residues: 406 sheet: -0.77 (0.31), residues: 237 loop : -0.83 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.023 0.002 TYR H 190 PHE 0.017 0.002 PHE B 275 TRP 0.060 0.002 TRP C 63 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8788) covalent geometry : angle 0.61790 (11994) SS BOND : bond 0.00250 ( 6) SS BOND : angle 1.00157 ( 12) hydrogen bonds : bond 0.03953 ( 437) hydrogen bonds : angle 5.20379 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7906 (tp) cc_final: 0.7661 (tt) REVERT: A 99 HIS cc_start: 0.7481 (m170) cc_final: 0.7258 (m170) REVERT: B 32 LYS cc_start: 0.7791 (mttt) cc_final: 0.7489 (mttt) REVERT: B 245 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6923 (t-90) REVERT: B 263 THR cc_start: 0.8446 (m) cc_final: 0.8096 (p) REVERT: B 336 PHE cc_start: 0.7853 (t80) cc_final: 0.7636 (t80) REVERT: C 127 LYS cc_start: 0.8951 (mmtp) cc_final: 0.8568 (mmmt) REVERT: C 170 ASP cc_start: 0.8268 (t70) cc_final: 0.8028 (t0) REVERT: C 211 TRP cc_start: 0.6986 (OUTLIER) cc_final: 0.5404 (m-10) REVERT: C 234 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: C 271 CYS cc_start: 0.7018 (p) cc_final: 0.6777 (p) REVERT: G 50 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6340 (mt) REVERT: H 105 SER cc_start: 0.7261 (t) cc_final: 0.6908 (p) outliers start: 35 outliers final: 24 residues processed: 191 average time/residue: 0.1043 time to fit residues: 26.9818 Evaluate side-chains 201 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 0.0870 chunk 116 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.163009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147216 restraints weight = 14072.947| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.27 r_work: 0.3920 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8794 Z= 0.131 Angle : 0.604 12.830 12006 Z= 0.305 Chirality : 0.043 0.168 1434 Planarity : 0.004 0.044 1526 Dihedral : 4.267 17.969 1261 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.94 % Allowed : 16.85 % Favored : 79.21 % 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: -0.29 (0.25), residues: 1175 helix: 0.96 (0.26), residues: 406 sheet: -0.76 (0.31), residues: 237 loop : -0.75 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.024 0.002 TYR H 190 PHE 0.016 0.002 PHE B 275 TRP 0.041 0.002 TRP C 63 HIS 0.011 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8788) covalent geometry : angle 0.60336 (11994) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.95585 ( 12) hydrogen bonds : bond 0.03636 ( 437) hydrogen bonds : angle 5.10495 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6435 (t0) cc_final: 0.6156 (t0) REVERT: A 78 LEU cc_start: 0.7929 (tp) cc_final: 0.7701 (tt) REVERT: B 32 LYS cc_start: 0.7741 (mttt) cc_final: 0.7444 (mttt) REVERT: B 245 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6864 (t-90) REVERT: B 263 THR cc_start: 0.8399 (m) cc_final: 0.8066 (p) REVERT: C 127 LYS cc_start: 0.8944 (mmtp) cc_final: 0.8547 (mmmt) REVERT: C 170 ASP cc_start: 0.8180 (t70) cc_final: 0.7977 (t0) REVERT: C 234 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: G 50 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6242 (mt) REVERT: H 105 SER cc_start: 0.7131 (t) cc_final: 0.6848 (p) outliers start: 33 outliers final: 22 residues processed: 191 average time/residue: 0.1059 time to fit residues: 27.3111 Evaluate side-chains 195 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 24 optimal weight: 0.0270 chunk 109 optimal weight: 0.5980 chunk 78 optimal weight: 0.0970 chunk 55 optimal weight: 0.3980 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN C 75 GLN C 110 ASN H 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.163735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147873 restraints weight = 14217.423| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.29 r_work: 0.3919 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8794 Z= 0.122 Angle : 0.602 14.574 12006 Z= 0.300 Chirality : 0.042 0.180 1434 Planarity : 0.004 0.045 1526 Dihedral : 4.157 18.038 1261 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.18 % Allowed : 17.56 % Favored : 78.26 % 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: -0.20 (0.25), residues: 1175 helix: 1.11 (0.26), residues: 405 sheet: -0.68 (0.32), residues: 235 loop : -0.77 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.024 0.002 TYR H 190 PHE 0.024 0.002 PHE B 200 TRP 0.033 0.002 TRP C 63 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8788) covalent geometry : angle 0.60128 (11994) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.94381 ( 12) hydrogen bonds : bond 0.03440 ( 437) hydrogen bonds : angle 5.02568 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6402 (t0) cc_final: 0.6128 (t0) REVERT: A 78 LEU cc_start: 0.7896 (tp) cc_final: 0.7657 (tt) REVERT: B 32 LYS cc_start: 0.7756 (mttt) cc_final: 0.7506 (mttt) REVERT: C 127 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8501 (mmmt) REVERT: C 234 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: H 91 THR cc_start: 0.5785 (OUTLIER) cc_final: 0.5386 (m) REVERT: H 105 SER cc_start: 0.7142 (t) cc_final: 0.6851 (p) outliers start: 35 outliers final: 27 residues processed: 192 average time/residue: 0.1018 time to fit residues: 26.6973 Evaluate side-chains 202 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.162070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.146125 restraints weight = 14006.929| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.27 r_work: 0.3894 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8794 Z= 0.169 Angle : 0.638 15.428 12006 Z= 0.317 Chirality : 0.043 0.180 1434 Planarity : 0.004 0.044 1526 Dihedral : 4.249 16.823 1261 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.66 % Allowed : 17.68 % Favored : 77.66 % 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: -0.30 (0.25), residues: 1175 helix: 1.05 (0.26), residues: 405 sheet: -0.71 (0.31), residues: 235 loop : -0.86 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.024 0.002 TYR H 190 PHE 0.029 0.002 PHE B 336 TRP 0.031 0.002 TRP C 63 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8788) covalent geometry : angle 0.63731 (11994) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.97698 ( 12) hydrogen bonds : bond 0.03727 ( 437) hydrogen bonds : angle 5.06028 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6527 (t0) cc_final: 0.6203 (t0) REVERT: A 78 LEU cc_start: 0.7903 (tp) cc_final: 0.7655 (tt) REVERT: B 32 LYS cc_start: 0.7772 (mttt) cc_final: 0.7465 (mttt) REVERT: B 200 PHE cc_start: 0.7607 (m-10) cc_final: 0.7363 (m-10) REVERT: C 127 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8493 (mmmt) REVERT: C 211 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.5409 (m-10) REVERT: C 234 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7334 (m-80) REVERT: G 50 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6486 (mt) REVERT: H 105 SER cc_start: 0.7228 (t) cc_final: 0.6864 (p) outliers start: 39 outliers final: 28 residues processed: 187 average time/residue: 0.1001 time to fit residues: 25.6894 Evaluate side-chains 200 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.161772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145706 restraints weight = 13935.274| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.27 r_work: 0.3889 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8794 Z= 0.170 Angle : 0.645 15.831 12006 Z= 0.321 Chirality : 0.043 0.190 1434 Planarity : 0.004 0.045 1526 Dihedral : 4.285 17.082 1261 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.30 % Allowed : 18.52 % Favored : 77.18 % 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: -0.39 (0.25), residues: 1175 helix: 0.97 (0.26), residues: 405 sheet: -0.73 (0.32), residues: 235 loop : -0.93 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.024 0.002 TYR H 190 PHE 0.025 0.002 PHE B 200 TRP 0.034 0.002 TRP C 63 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8788) covalent geometry : angle 0.64494 (11994) SS BOND : bond 0.00244 ( 6) SS BOND : angle 0.95962 ( 12) hydrogen bonds : bond 0.03757 ( 437) hydrogen bonds : angle 5.05463 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6539 (t0) cc_final: 0.6206 (t0) REVERT: A 78 LEU cc_start: 0.7909 (tp) cc_final: 0.7660 (tt) REVERT: B 32 LYS cc_start: 0.7794 (mttt) cc_final: 0.7539 (mttt) REVERT: B 263 THR cc_start: 0.8434 (m) cc_final: 0.8095 (p) REVERT: B 270 ASN cc_start: 0.7861 (t0) cc_final: 0.7539 (t0) REVERT: C 114 CYS cc_start: 0.7009 (t) cc_final: 0.6785 (t) REVERT: C 127 LYS cc_start: 0.8878 (mmtp) cc_final: 0.8461 (mmmt) REVERT: C 211 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.5410 (m-10) REVERT: C 234 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: G 50 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6559 (mt) REVERT: H 105 SER cc_start: 0.7184 (t) cc_final: 0.6824 (p) outliers start: 36 outliers final: 32 residues processed: 187 average time/residue: 0.1025 time to fit residues: 26.2489 Evaluate side-chains 203 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 2 optimal weight: 0.8980 chunk 70 optimal weight: 0.0470 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.0970 chunk 61 optimal weight: 0.0040 chunk 100 optimal weight: 0.0270 chunk 114 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 overall best weight: 0.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.165420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.149677 restraints weight = 13951.295| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.27 r_work: 0.3944 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8794 Z= 0.110 Angle : 0.621 16.609 12006 Z= 0.305 Chirality : 0.042 0.191 1434 Planarity : 0.004 0.048 1526 Dihedral : 4.098 19.304 1261 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.99 % Allowed : 20.19 % Favored : 76.82 % 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: -0.15 (0.25), residues: 1175 helix: 1.22 (0.26), residues: 404 sheet: -0.69 (0.31), residues: 247 loop : -0.78 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.027 0.002 TYR H 190 PHE 0.031 0.002 PHE B 200 TRP 0.026 0.002 TRP C 63 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8788) covalent geometry : angle 0.62041 (11994) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.94081 ( 12) hydrogen bonds : bond 0.03255 ( 437) hydrogen bonds : angle 4.89639 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.6355 (t0) cc_final: 0.6108 (t0) REVERT: A 78 LEU cc_start: 0.7926 (tp) cc_final: 0.7664 (tt) REVERT: B 32 LYS cc_start: 0.7745 (mttt) cc_final: 0.7506 (mttt) REVERT: C 127 LYS cc_start: 0.8902 (mmtp) cc_final: 0.8482 (mmmt) REVERT: C 234 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: G 50 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6470 (mt) REVERT: G 61 PHE cc_start: 0.7508 (m-80) cc_final: 0.6901 (m-80) REVERT: H 105 SER cc_start: 0.6937 (t) cc_final: 0.6691 (p) outliers start: 25 outliers final: 20 residues processed: 186 average time/residue: 0.0970 time to fit residues: 25.1530 Evaluate side-chains 183 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.0370 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.163153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.147301 restraints weight = 14015.202| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.27 r_work: 0.3909 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8794 Z= 0.153 Angle : 0.633 16.036 12006 Z= 0.315 Chirality : 0.043 0.186 1434 Planarity : 0.004 0.045 1526 Dihedral : 4.121 17.898 1261 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.23 % Allowed : 20.43 % Favored : 76.34 % 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: -0.25 (0.25), residues: 1175 helix: 1.11 (0.26), residues: 410 sheet: -0.68 (0.32), residues: 235 loop : -0.88 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 134 TYR 0.024 0.002 TYR H 190 PHE 0.028 0.002 PHE B 336 TRP 0.026 0.002 TRP C 63 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8788) covalent geometry : angle 0.63286 (11994) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.95049 ( 12) hydrogen bonds : bond 0.03491 ( 437) hydrogen bonds : angle 4.93013 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.63 seconds wall clock time: 51 minutes 9.53 seconds (3069.53 seconds total)