Starting phenix.real_space_refine on Fri Sep 11 03:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.cif" model { file = "/net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gdg_4390/09_2026/6gdg_4390.cif" } resolution = 4.11 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= 0.001 sd= 0.012 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 49 5.16 5 C 4611 2.51 5 N 1246 2.21 5 O 1317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1913 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2377 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 9, 'GLN:plan1': 5, 'ARG:plan': 14, 'GLU:plan': 7, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 262 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1721 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 928 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.55, per 1000 atoms: 0.21 Number of scatterers: 7223 At special positions: 0 Unit cell: (92.02, 125.19, 78.11, 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 49 16.00 O 1317 8.00 N 1246 7.00 C 4611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 0.52 Conformation dependent library (CDL) restraints added in 555.4 milliseconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 42.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.853A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 59 removed outlier: 3.510A pdb=" N PHE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 69 removed outlier: 3.791A pdb=" N ILE A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 108 removed outlier: 3.612A pdb=" N ILE A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 117 through 137 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.635A pdb=" N VAL A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.673A pdb=" N LYS A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 259 removed outlier: 3.782A pdb=" N PHE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 266 through 288 removed outlier: 3.858A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.719A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.865A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'D' and resid 13 through 40 removed outlier: 3.803A pdb=" N LYS D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 removed outlier: 4.071A pdb=" N ILE D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 57' Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 252 through 269 removed outlier: 3.813A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 294 removed outlier: 3.520A pdb=" N LYS D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 302 removed outlier: 4.118A pdb=" N TYR D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.529A pdb=" N ALA D 306 " --> pdb=" O PRO D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 341 removed outlier: 3.546A pdb=" N ILE D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 335 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 381 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.581A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.616A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.657A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.920A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.649A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.021A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.066A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.706A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.657A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.719A pdb=" N HIS D 41 " --> pdb=" O HIS D 220 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE D 222 " --> pdb=" O HIS D 41 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 43 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE D 212 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 243 through 244 Processing sheet with id=AB1, first strand: chain 'D' and resid 247 through 249 Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.626A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.549A pdb=" N THR E 122 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1083 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: 1.13 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2335 1.34 - 1.46: 906 1.46 - 1.58: 4070 1.58 - 1.70: 0 1.70 - 1.81: 65 Bond restraints: 7376 Sorted by residual: bond pdb=" C4 NEC A 400 " pdb=" C5 NEC A 400 " ideal model delta sigma weight residual 1.385 1.474 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C5 NEC A 400 " pdb=" C6 NEC A 400 " ideal model delta sigma weight residual 1.407 1.488 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" CA VAL A 188 " pdb=" CB VAL A 188 " ideal model delta sigma weight residual 1.539 1.560 -0.021 5.40e-03 3.43e+04 1.47e+01 bond pdb=" C8 NEC A 400 " pdb=" N7 NEC A 400 " ideal model delta sigma weight residual 1.302 1.359 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" CA ILE A 64 " pdb=" CB ILE A 64 " ideal model delta sigma weight residual 1.540 1.571 -0.031 1.25e-02 6.40e+03 6.01e+00 ... (remaining 7371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9227 1.97 - 3.94: 807 3.94 - 5.92: 41 5.92 - 7.89: 4 7.89 - 9.86: 3 Bond angle restraints: 10082 Sorted by residual: angle pdb=" N ASP D 229 " pdb=" CA ASP D 229 " pdb=" C ASP D 229 " ideal model delta sigma weight residual 112.38 118.19 -5.81 1.22e+00 6.72e-01 2.26e+01 angle pdb=" CA VAL A 188 " pdb=" C VAL A 188 " pdb=" N PRO A 189 " ideal model delta sigma weight residual 120.83 118.29 2.54 6.10e-01 2.69e+00 1.73e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 108.38 113.47 -5.09 1.35e+00 5.49e-01 1.42e+01 angle pdb=" C PHE D 302 " pdb=" N PRO D 303 " pdb=" CA PRO D 303 " ideal model delta sigma weight residual 119.47 123.82 -4.35 1.16e+00 7.43e-01 1.40e+01 angle pdb=" N THR E 104 " pdb=" CA THR E 104 " pdb=" C THR E 104 " ideal model delta sigma weight residual 108.38 113.31 -4.93 1.35e+00 5.49e-01 1.34e+01 ... (remaining 10077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3953 16.99 - 33.99: 251 33.99 - 50.98: 63 50.98 - 67.97: 12 67.97 - 84.96: 4 Dihedral angle restraints: 4283 sinusoidal: 1387 harmonic: 2896 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 146 " pdb=" CB CYS A 146 " ideal model delta sinusoidal sigma weight residual 93.00 177.96 -84.96 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -163.29 77.29 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CA THR B 159 " pdb=" C THR B 159 " pdb=" N SER B 160 " pdb=" CA SER B 160 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 703 0.044 - 0.087: 338 0.087 - 0.131: 105 0.131 - 0.174: 37 0.174 - 0.218: 15 Chirality restraints: 1198 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TRP D 234 " pdb=" N TRP D 234 " pdb=" C TRP D 234 " pdb=" CB TRP D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1195 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 188 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 189 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 284 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 285 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 138 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 139 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.025 5.00e-02 4.00e+02 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2865 2.94 - 3.43: 7370 3.43 - 3.92: 11934 3.92 - 4.41: 13287 4.41 - 4.90: 22747 Nonbonded interactions: 58203 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.449 3.040 nonbonded pdb=" OG1 THR E 104 " pdb=" OD1 ASP E 106 " model vdw 2.471 3.040 nonbonded pdb=" OG SER B 227 " pdb=" OH TYR E 32 " model vdw 2.486 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.509 3.120 nonbonded pdb=" O GLN D 380 " pdb=" OE1 GLU D 382 " model vdw 2.537 3.040 ... (remaining 58198 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 group one per residue 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: 0.210 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.008 0.089 7381 Z= 0.546 Angle : 1.102 9.859 10092 Z= 0.739 Chirality : 0.061 0.218 1198 Planarity : 0.004 0.052 1283 Dihedral : 12.807 79.978 2394 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.89 % Favored : 94.60 % Rotamer: Outliers : 2.07 % Allowed : 6.80 % Favored : 91.12 % 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: -3.15 (0.21), residues: 981 helix: -1.30 (0.21), residues: 357 sheet: -2.83 (0.35), residues: 135 loop : -2.46 (0.23), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 291 TYR 0.009 0.001 TYR B 124 PHE 0.014 0.002 PHE D 208 TRP 0.017 0.001 TRP D 234 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.55 ( 7376) covalent geometry : angle 1.10276 / 0.74 (10082) SS BOND : bond 0.00417 / 0.24 ( 5) SS BOND : angle 0.42834 / 0.26 ( 10) hydrogen bonds : bond 0.25478 / 17.78 ( 378) hydrogen bonds : angle 9.54611 / 7.01 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 306 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.8227 (t) cc_final: 0.7849 (p) REVERT: A 34 ASN cc_start: 0.7194 (t0) cc_final: 0.6900 (t0) REVERT: A 38 GLN cc_start: 0.8132 (pt0) cc_final: 0.7557 (pt0) REVERT: A 82 CYS cc_start: 0.8532 (m) cc_final: 0.8010 (t) REVERT: A 129 TRP cc_start: 0.6886 (m100) cc_final: 0.6671 (m-10) REVERT: A 135 ILE cc_start: 0.8309 (mt) cc_final: 0.8091 (tt) REVERT: A 145 ASN cc_start: 0.7660 (t0) cc_final: 0.6839 (p0) REVERT: A 193 MET cc_start: 0.7549 (mtp) cc_final: 0.7347 (mtm) REVERT: A 199 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7934 (ttp-110) REVERT: A 290 TYR cc_start: 0.8657 (t80) cc_final: 0.8406 (t80) REVERT: B 111 TYR cc_start: 0.8582 (m-80) cc_final: 0.8201 (m-80) REVERT: B 125 ASN cc_start: 0.7963 (t0) cc_final: 0.7606 (p0) REVERT: B 187 VAL cc_start: 0.8688 (t) cc_final: 0.8405 (t) REVERT: B 218 CYS cc_start: 0.8586 (t) cc_final: 0.8335 (t) REVERT: B 290 ASP cc_start: 0.7257 (m-30) cc_final: 0.7033 (m-30) REVERT: B 325 MET cc_start: 0.8630 (ttm) cc_final: 0.8105 (tpt) REVERT: C 21 MET cc_start: 0.6129 (ttm) cc_final: 0.5835 (mmm) REVERT: D 17 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8709 (tppt) REVERT: D 252 ASP cc_start: 0.8738 (m-30) cc_final: 0.8306 (t0) REVERT: D 268 ASN cc_start: 0.9355 (m-40) cc_final: 0.9154 (m-40) REVERT: D 270 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8146 (ttt90) REVERT: D 272 LEU cc_start: 0.9230 (mt) cc_final: 0.9007 (mp) REVERT: D 334 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7827 (mm-30) REVERT: D 346 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8735 (mtp85) REVERT: D 361 ASN cc_start: 0.8566 (m-40) cc_final: 0.8265 (m110) REVERT: D 383 LEU cc_start: 0.7660 (tp) cc_final: 0.7437 (mt) REVERT: E 20 LEU cc_start: 0.7879 (mt) cc_final: 0.7590 (mt) REVERT: E 60 TYR cc_start: 0.9074 (m-80) cc_final: 0.8525 (m-80) REVERT: E 68 PHE cc_start: 0.8183 (m-10) cc_final: 0.6736 (m-10) REVERT: E 69 THR cc_start: 0.8530 (m) cc_final: 0.8164 (p) REVERT: E 72 ARG cc_start: 0.8157 (ptm160) cc_final: 0.7621 (ttm110) REVERT: E 74 ASN cc_start: 0.6872 (m-40) cc_final: 0.6050 (t0) REVERT: E 80 TYR cc_start: 0.7378 (m-80) cc_final: 0.6911 (m-80) outliers start: 14 outliers final: 4 residues processed: 315 average time/residue: 0.0761 time to fit residues: 32.1280 Evaluate side-chains 189 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 38 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 257 GLN D 347 HIS E 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122842 restraints weight = 14693.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124783 restraints weight = 9772.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126240 restraints weight = 7195.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127006 restraints weight = 5750.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127838 restraints weight = 4970.050| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7381 Z= 0.147 Angle : 0.630 9.781 10092 Z= 0.337 Chirality : 0.044 0.156 1198 Planarity : 0.005 0.065 1283 Dihedral : 4.928 33.970 1060 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.15 % Allowed : 3.55 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.39 (0.25), residues: 981 helix: 0.64 (0.25), residues: 371 sheet: -2.11 (0.32), residues: 197 loop : -1.71 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 228 TYR 0.029 0.002 TYR B 59 PHE 0.013 0.002 PHE D 330 TRP 0.019 0.002 TRP B 339 HIS 0.017 0.002 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 7376) covalent geometry : angle 0.62878 / 0.34 (10082) SS BOND : bond 0.00348 / 0.16 ( 5) SS BOND : angle 1.56269 / 0.94 ( 10) hydrogen bonds : bond 0.04857 / 3.42 ( 378) hydrogen bonds : angle 5.86747 / 4.31 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7773 (t0) cc_final: 0.7074 (p0) REVERT: A 182 PHE cc_start: 0.8407 (t80) cc_final: 0.7956 (t80) REVERT: B 166 CYS cc_start: 0.7878 (m) cc_final: 0.7631 (m) REVERT: B 188 MET cc_start: 0.7732 (mmm) cc_final: 0.6867 (mmm) REVERT: B 230 ASN cc_start: 0.7820 (m-40) cc_final: 0.7539 (m110) REVERT: C 36 ASP cc_start: 0.7337 (t0) cc_final: 0.7095 (t70) REVERT: D 17 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8510 (tppt) REVERT: D 233 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8052 (mmmt) REVERT: D 239 ASN cc_start: 0.8379 (p0) cc_final: 0.7881 (p0) REVERT: D 274 THR cc_start: 0.8177 (p) cc_final: 0.7841 (p) REVERT: D 298 ILE cc_start: 0.7899 (mp) cc_final: 0.7665 (mp) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.0756 time to fit residues: 24.1419 Evaluate side-chains 152 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN B 156 GLN E 31 ASN E 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118412 restraints weight = 14705.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120007 restraints weight = 10068.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121368 restraints weight = 7737.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122462 restraints weight = 6328.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122959 restraints weight = 5436.559| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7381 Z= 0.177 Angle : 0.634 11.956 10092 Z= 0.334 Chirality : 0.044 0.157 1198 Planarity : 0.005 0.053 1283 Dihedral : 4.880 35.903 1060 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.76 (0.26), residues: 981 helix: 1.20 (0.26), residues: 366 sheet: -1.80 (0.33), residues: 203 loop : -1.33 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 137 TYR 0.026 0.002 TYR B 59 PHE 0.021 0.002 PHE D 366 TRP 0.023 0.002 TRP B 332 HIS 0.008 0.002 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 7376) covalent geometry : angle 0.62872 / 0.33 (10082) SS BOND : bond 0.00282 / 0.17 ( 5) SS BOND : angle 2.65310 / 1.90 ( 10) hydrogen bonds : bond 0.04435 / 3.09 ( 378) hydrogen bonds : angle 5.50558 / 4.11 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7764 (t0) cc_final: 0.7007 (p0) REVERT: A 182 PHE cc_start: 0.8537 (t80) cc_final: 0.8266 (t80) REVERT: A 237 ILE cc_start: 0.7906 (tt) cc_final: 0.7644 (tp) REVERT: A 276 LEU cc_start: 0.9353 (tp) cc_final: 0.8786 (tp) REVERT: B 166 CYS cc_start: 0.7972 (m) cc_final: 0.7678 (m) REVERT: B 188 MET cc_start: 0.7779 (mmm) cc_final: 0.7270 (mmm) REVERT: C 36 ASP cc_start: 0.7281 (t0) cc_final: 0.7065 (t70) REVERT: D 17 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8519 (tppt) REVERT: D 222 PHE cc_start: 0.5895 (t80) cc_final: 0.4366 (t80) REVERT: D 233 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8465 (mmtt) REVERT: D 239 ASN cc_start: 0.8488 (p0) cc_final: 0.8150 (p0) REVERT: D 369 CYS cc_start: 0.8265 (m) cc_final: 0.7898 (m) REVERT: E 79 LEU cc_start: 0.8540 (tp) cc_final: 0.8316 (tp) REVERT: E 125 THR cc_start: 0.7686 (p) cc_final: 0.7480 (t) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0779 time to fit residues: 20.2816 Evaluate side-chains 147 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 64 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119333 restraints weight = 15013.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121148 restraints weight = 10042.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122387 restraints weight = 7491.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123435 restraints weight = 6089.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123815 restraints weight = 5202.546| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7381 Z= 0.144 Angle : 0.583 6.453 10092 Z= 0.312 Chirality : 0.043 0.207 1198 Planarity : 0.004 0.053 1283 Dihedral : 4.738 25.310 1060 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -0.38 (0.26), residues: 981 helix: 1.51 (0.27), residues: 367 sheet: -1.63 (0.31), residues: 220 loop : -1.05 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.022 0.001 TYR B 59 PHE 0.017 0.002 PHE D 330 TRP 0.033 0.002 TRP B 339 HIS 0.004 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7376) covalent geometry : angle 0.58206 / 0.31 (10082) SS BOND : bond 0.00192 / 0.11 ( 5) SS BOND : angle 1.12018 / 0.68 ( 10) hydrogen bonds : bond 0.03977 / 2.77 ( 378) hydrogen bonds : angle 5.21854 / 3.93 ( 1083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7723 (t0) cc_final: 0.6939 (p0) REVERT: A 182 PHE cc_start: 0.8553 (t80) cc_final: 0.8307 (t80) REVERT: A 237 ILE cc_start: 0.7754 (tt) cc_final: 0.7529 (tp) REVERT: A 276 LEU cc_start: 0.9317 (tp) cc_final: 0.8798 (tp) REVERT: B 230 ASN cc_start: 0.7829 (m-40) cc_final: 0.7597 (m110) REVERT: B 296 VAL cc_start: 0.8971 (t) cc_final: 0.8745 (t) REVERT: C 36 ASP cc_start: 0.7377 (t0) cc_final: 0.7174 (t70) REVERT: D 17 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8523 (tppt) REVERT: D 222 PHE cc_start: 0.5729 (t80) cc_final: 0.4206 (t80) REVERT: D 233 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8230 (mmmt) REVERT: D 265 SER cc_start: 0.8696 (m) cc_final: 0.8460 (t) REVERT: D 269 ASN cc_start: 0.8590 (t0) cc_final: 0.8254 (t0) REVERT: E 60 TYR cc_start: 0.8637 (m-80) cc_final: 0.8407 (m-10) REVERT: E 125 THR cc_start: 0.7777 (p) cc_final: 0.7572 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0738 time to fit residues: 18.8769 Evaluate side-chains 140 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 0.0020 chunk 81 optimal weight: 4.9990 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123118 restraints weight = 14473.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125053 restraints weight = 9560.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126449 restraints weight = 7027.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127229 restraints weight = 5623.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128203 restraints weight = 4857.560| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7381 Z= 0.118 Angle : 0.568 7.244 10092 Z= 0.299 Chirality : 0.043 0.190 1198 Planarity : 0.004 0.052 1283 Dihedral : 4.586 31.764 1060 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.11 (0.27), residues: 981 helix: 1.64 (0.27), residues: 369 sheet: -1.43 (0.33), residues: 210 loop : -0.86 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 199 TYR 0.016 0.001 TYR B 59 PHE 0.020 0.002 PHE A 257 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7376) covalent geometry : angle 0.56476 / 0.30 (10082) SS BOND : bond 0.00556 / 0.44 ( 5) SS BOND : angle 1.90118 / 1.41 ( 10) hydrogen bonds : bond 0.03732 / 2.60 ( 378) hydrogen bonds : angle 5.04519 / 3.80 ( 1083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7780 (t0) cc_final: 0.7023 (p0) REVERT: A 174 MET cc_start: 0.8238 (tpp) cc_final: 0.7675 (mmt) REVERT: A 237 ILE cc_start: 0.7674 (tt) cc_final: 0.7404 (tp) REVERT: A 245 CYS cc_start: 0.8047 (m) cc_final: 0.7843 (m) REVERT: A 276 LEU cc_start: 0.9289 (tp) cc_final: 0.8817 (tp) REVERT: B 188 MET cc_start: 0.8003 (mmm) cc_final: 0.7413 (mmm) REVERT: B 230 ASN cc_start: 0.7705 (m-40) cc_final: 0.7134 (m110) REVERT: B 308 LEU cc_start: 0.8311 (mt) cc_final: 0.7951 (mt) REVERT: C 36 ASP cc_start: 0.7323 (t0) cc_final: 0.7122 (t70) REVERT: D 17 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8497 (tppt) REVERT: D 222 PHE cc_start: 0.5489 (t80) cc_final: 0.4119 (t80) REVERT: D 233 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8363 (mmtt) REVERT: E 32 TYR cc_start: 0.7613 (m-80) cc_final: 0.7384 (m-80) REVERT: E 65 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7770 (mtpp) REVERT: E 125 THR cc_start: 0.7717 (p) cc_final: 0.7516 (t) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.0799 time to fit residues: 21.0729 Evaluate side-chains 141 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121029 restraints weight = 14623.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123220 restraints weight = 9502.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124839 restraints weight = 6927.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125798 restraints weight = 5496.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126393 restraints weight = 4684.496| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7381 Z= 0.126 Angle : 0.574 7.553 10092 Z= 0.299 Chirality : 0.042 0.216 1198 Planarity : 0.004 0.052 1283 Dihedral : 4.559 33.547 1060 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 (0.27), residues: 981 helix: 1.77 (0.27), residues: 370 sheet: -1.21 (0.33), residues: 210 loop : -0.86 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 199 TYR 0.019 0.001 TYR B 59 PHE 0.021 0.002 PHE D 366 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7376) covalent geometry : angle 0.57114 / 0.30 (10082) SS BOND : bond 0.00172 / 0.08 ( 5) SS BOND : angle 1.98275 / 1.39 ( 10) hydrogen bonds : bond 0.03690 / 2.55 ( 378) hydrogen bonds : angle 4.90082 / 3.71 ( 1083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7684 (t0) cc_final: 0.7036 (p0) REVERT: A 174 MET cc_start: 0.8050 (tpp) cc_final: 0.7617 (mmt) REVERT: A 276 LEU cc_start: 0.9270 (tp) cc_final: 0.8811 (tp) REVERT: B 51 LEU cc_start: 0.6902 (mp) cc_final: 0.6495 (mp) REVERT: B 188 MET cc_start: 0.7783 (mmm) cc_final: 0.7312 (mmm) REVERT: B 230 ASN cc_start: 0.7877 (m-40) cc_final: 0.7465 (m110) REVERT: B 308 LEU cc_start: 0.8232 (mt) cc_final: 0.7858 (mt) REVERT: C 21 MET cc_start: 0.7087 (mmm) cc_final: 0.6836 (mmm) REVERT: D 17 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8491 (tppt) REVERT: D 56 ILE cc_start: 0.7426 (mm) cc_final: 0.7209 (mm) REVERT: D 222 PHE cc_start: 0.5495 (t80) cc_final: 0.4085 (t80) REVERT: E 32 TYR cc_start: 0.7736 (m-80) cc_final: 0.7482 (m-80) REVERT: E 125 THR cc_start: 0.7897 (p) cc_final: 0.7656 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0763 time to fit residues: 19.3010 Evaluate side-chains 145 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 66 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 ASN B 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122834 restraints weight = 14590.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124860 restraints weight = 9533.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126122 restraints weight = 6979.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127372 restraints weight = 5640.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127910 restraints weight = 4742.909| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7381 Z= 0.119 Angle : 0.561 6.818 10092 Z= 0.296 Chirality : 0.043 0.181 1198 Planarity : 0.004 0.051 1283 Dihedral : 4.447 32.426 1060 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.14 (0.27), residues: 981 helix: 1.81 (0.27), residues: 374 sheet: -1.07 (0.34), residues: 213 loop : -0.84 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 199 TYR 0.015 0.001 TYR B 59 PHE 0.020 0.002 PHE B 292 TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 7376) covalent geometry : angle 0.55840 / 0.30 (10082) SS BOND : bond 0.00330 / 0.24 ( 5) SS BOND : angle 1.70790 / 1.18 ( 10) hydrogen bonds : bond 0.03596 / 2.49 ( 378) hydrogen bonds : angle 4.78346 / 3.63 ( 1083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.7182 (t0) cc_final: 0.6852 (t0) REVERT: A 120 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7740 (mtp180) REVERT: A 145 ASN cc_start: 0.7710 (t0) cc_final: 0.7025 (p0) REVERT: A 245 CYS cc_start: 0.8023 (m) cc_final: 0.7813 (m) REVERT: A 276 LEU cc_start: 0.9306 (tp) cc_final: 0.8848 (tp) REVERT: B 188 MET cc_start: 0.7895 (mmm) cc_final: 0.7023 (mmm) REVERT: B 230 ASN cc_start: 0.7810 (m-40) cc_final: 0.7320 (m110) REVERT: B 332 TRP cc_start: 0.8358 (m-10) cc_final: 0.8036 (m-10) REVERT: C 21 MET cc_start: 0.7104 (mmm) cc_final: 0.6851 (mmm) REVERT: D 17 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8426 (tppt) REVERT: D 221 MET cc_start: 0.7612 (tpp) cc_final: 0.7250 (tpp) REVERT: D 222 PHE cc_start: 0.5279 (t80) cc_final: 0.3951 (t80) REVERT: D 233 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8403 (mmtt) REVERT: E 125 THR cc_start: 0.7861 (p) cc_final: 0.7330 (t) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0799 time to fit residues: 20.7886 Evaluate side-chains 144 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120940 restraints weight = 14688.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122881 restraints weight = 9778.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124423 restraints weight = 7278.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125315 restraints weight = 5825.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125834 restraints weight = 5009.378| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7381 Z= 0.146 Angle : 0.586 9.679 10092 Z= 0.309 Chirality : 0.044 0.247 1198 Planarity : 0.004 0.053 1283 Dihedral : 4.540 32.196 1060 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.14 (0.27), residues: 981 helix: 1.84 (0.27), residues: 376 sheet: -1.11 (0.34), residues: 213 loop : -0.88 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 314 TYR 0.018 0.001 TYR B 59 PHE 0.021 0.002 PHE D 330 TRP 0.022 0.002 TRP E 36 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7376) covalent geometry : angle 0.58419 / 0.31 (10082) SS BOND : bond 0.00238 / 0.15 ( 5) SS BOND : angle 1.71078 / 1.17 ( 10) hydrogen bonds : bond 0.03686 / 2.54 ( 378) hydrogen bonds : angle 4.83996 / 3.69 ( 1083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7694 (t0) cc_final: 0.6987 (p0) REVERT: A 274 ILE cc_start: 0.7898 (mt) cc_final: 0.7543 (pt) REVERT: A 276 LEU cc_start: 0.9320 (tp) cc_final: 0.8954 (tp) REVERT: B 188 MET cc_start: 0.7834 (mmm) cc_final: 0.6946 (mmm) REVERT: B 230 ASN cc_start: 0.7818 (m-40) cc_final: 0.7525 (m110) REVERT: C 21 MET cc_start: 0.7174 (mmm) cc_final: 0.6803 (mmm) REVERT: D 221 MET cc_start: 0.7801 (tpp) cc_final: 0.7567 (tpp) REVERT: D 222 PHE cc_start: 0.5325 (t80) cc_final: 0.3987 (t80) REVERT: D 233 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8392 (mmtt) REVERT: E 95 TYR cc_start: 0.8608 (m-80) cc_final: 0.8314 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0699 time to fit residues: 17.2567 Evaluate side-chains 138 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 253 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120960 restraints weight = 14528.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122590 restraints weight = 9821.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124005 restraints weight = 7463.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124728 restraints weight = 6036.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125713 restraints weight = 5245.763| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7381 Z= 0.146 Angle : 0.596 8.601 10092 Z= 0.312 Chirality : 0.044 0.225 1198 Planarity : 0.004 0.051 1283 Dihedral : 4.570 31.148 1060 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.15 % Allowed : 0.74 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.23 (0.27), residues: 981 helix: 1.81 (0.27), residues: 376 sheet: -0.92 (0.35), residues: 214 loop : -0.79 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 199 TYR 0.017 0.001 TYR B 59 PHE 0.020 0.002 PHE A 257 TRP 0.022 0.002 TRP E 36 HIS 0.007 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 7376) covalent geometry : angle 0.59429 / 0.31 (10082) SS BOND : bond 0.00275 / 0.19 ( 5) SS BOND : angle 1.67589 / 1.15 ( 10) hydrogen bonds : bond 0.03690 / 2.55 ( 378) hydrogen bonds : angle 4.79806 / 3.65 ( 1083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7762 (t0) cc_final: 0.6998 (p0) REVERT: A 241 LEU cc_start: 0.8124 (mp) cc_final: 0.7546 (mp) REVERT: A 245 CYS cc_start: 0.8123 (m) cc_final: 0.7644 (m) REVERT: A 274 ILE cc_start: 0.7783 (mt) cc_final: 0.7550 (pt) REVERT: B 188 MET cc_start: 0.7824 (mmm) cc_final: 0.6948 (mmm) REVERT: B 230 ASN cc_start: 0.7877 (m-40) cc_final: 0.7601 (m110) REVERT: C 21 MET cc_start: 0.7216 (mmm) cc_final: 0.6836 (mmm) REVERT: D 17 LYS cc_start: 0.8562 (mmpt) cc_final: 0.8291 (tppt) REVERT: D 221 MET cc_start: 0.7605 (tpp) cc_final: 0.7306 (tpp) REVERT: D 222 PHE cc_start: 0.5281 (t80) cc_final: 0.4002 (t80) REVERT: D 233 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8392 (mmtt) REVERT: E 95 TYR cc_start: 0.8570 (m-80) cc_final: 0.8293 (m-80) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.0685 time to fit residues: 16.5650 Evaluate side-chains 134 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.0050 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 95 optimal weight: 0.0030 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN D 19 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120664 restraints weight = 14709.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122551 restraints weight = 9814.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123995 restraints weight = 7291.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124764 restraints weight = 5853.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125426 restraints weight = 5069.253| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7381 Z= 0.137 Angle : 0.587 9.019 10092 Z= 0.308 Chirality : 0.043 0.238 1198 Planarity : 0.004 0.051 1283 Dihedral : 4.580 31.033 1060 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 (0.27), residues: 981 helix: 1.88 (0.27), residues: 375 sheet: -0.83 (0.35), residues: 212 loop : -0.83 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 199 TYR 0.012 0.001 TYR B 59 PHE 0.024 0.002 PHE D 330 TRP 0.033 0.002 TRP B 332 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7376) covalent geometry : angle 0.58530 / 0.31 (10082) SS BOND : bond 0.00302 / 0.18 ( 5) SS BOND : angle 1.68560 / 1.15 ( 10) hydrogen bonds : bond 0.03649 / 2.52 ( 378) hydrogen bonds : angle 4.75572 / 3.62 ( 1083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7791 (t0) cc_final: 0.7021 (p0) REVERT: A 241 LEU cc_start: 0.8147 (mp) cc_final: 0.7479 (mp) REVERT: A 245 CYS cc_start: 0.8018 (m) cc_final: 0.7473 (m) REVERT: B 188 MET cc_start: 0.7804 (mmm) cc_final: 0.6949 (mmm) REVERT: B 230 ASN cc_start: 0.7787 (m-40) cc_final: 0.7357 (m110) REVERT: B 293 ASN cc_start: 0.7705 (m-40) cc_final: 0.7047 (p0) REVERT: B 332 TRP cc_start: 0.8424 (m-10) cc_final: 0.8114 (m-10) REVERT: C 21 MET cc_start: 0.7206 (mmm) cc_final: 0.6910 (mmm) REVERT: D 221 MET cc_start: 0.7527 (tpp) cc_final: 0.7148 (tpp) REVERT: D 222 PHE cc_start: 0.5264 (t80) cc_final: 0.4006 (t80) REVERT: D 233 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8404 (mmtt) REVERT: E 95 TYR cc_start: 0.8696 (m-80) cc_final: 0.8385 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0713 time to fit residues: 17.2392 Evaluate side-chains 133 residues out of total 845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 42 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.122247 restraints weight = 14655.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124120 restraints weight = 9818.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125489 restraints weight = 7288.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126300 restraints weight = 5868.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127126 restraints weight = 5044.001| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7381 Z= 0.126 Angle : 0.578 8.170 10092 Z= 0.301 Chirality : 0.043 0.216 1198 Planarity : 0.004 0.051 1283 Dihedral : 4.492 31.234 1060 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.35 (0.28), residues: 981 helix: 1.92 (0.27), residues: 374 sheet: -0.80 (0.36), residues: 212 loop : -0.78 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 199 TYR 0.021 0.001 TYR A 290 PHE 0.015 0.001 PHE A 257 TRP 0.030 0.002 TRP B 332 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7376) covalent geometry : angle 0.57656 / 0.30 (10082) SS BOND : bond 0.00295 / 0.21 ( 5) SS BOND : angle 1.59136 / 1.09 ( 10) hydrogen bonds : bond 0.03535 / 2.44 ( 378) hydrogen bonds : angle 4.72106 / 3.58 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.55 seconds wall clock time: 23 minutes 31.19 seconds (1411.19 seconds total)