Starting phenix.real_space_refine on Sun Apr 5 01:05:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ode_70356/04_2026/9ode_70356.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ode_70356/04_2026/9ode_70356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ode_70356/04_2026/9ode_70356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ode_70356/04_2026/9ode_70356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ode_70356/04_2026/9ode_70356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ode_70356/04_2026/9ode_70356.map" } resolution = 2.5 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= 0.040 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 50 5.16 5 C 4239 2.51 5 N 1102 2.21 5 O 1199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6590 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2445 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 364 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2107 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1644 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'EID': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.46, per 1000 atoms: 0.22 Number of scatterers: 6590 At special positions: 0 Unit cell: (72, 102.72, 132.48, 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 50 16.00 O 1199 8.00 N 1102 7.00 C 4239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.09 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " 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: 0.63 Conformation dependent library (CDL) restraints added in 380.6 milliseconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 45.9% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.104A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.529A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 95 removed outlier: 3.612A pdb=" N VAL D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.511A pdb=" N ALA D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 131 removed outlier: 3.799A pdb=" N GLN D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 171 removed outlier: 3.885A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 179 removed outlier: 3.588A pdb=" N LEU D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 removed outlier: 3.552A pdb=" N LYS D 185 " --> pdb=" O PRO D 181 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.760A pdb=" N GLY D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.842A pdb=" N LYS D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 239 " --> pdb=" O CYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 260 removed outlier: 3.703A pdb=" N LYS D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 306 removed outlier: 3.614A pdb=" N LEU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 336 removed outlier: 3.910A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N CYS D 330 " --> pdb=" O TYR D 326 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.878A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.631A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.630A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.609A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.628A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.511A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.744A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.605A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.766A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.831A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.851A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.874A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.882A 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 278 removed outlier: 3.812A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.837A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1011 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: 1.17 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1066 1.31 - 1.44: 1821 1.44 - 1.57: 3764 1.57 - 1.70: 0 1.70 - 1.83: 70 Bond restraints: 6721 Sorted by residual: bond pdb=" C03 EID D 601 " pdb=" N05 EID D 601 " ideal model delta sigma weight residual 1.363 1.458 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C27 EID D 601 " pdb=" O29 EID D 601 " ideal model delta sigma weight residual 1.318 1.400 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N THR D 180 " pdb=" CA THR D 180 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.11e-02 8.12e+03 1.03e+01 bond pdb=" N CYS B 149 " pdb=" CA CYS B 149 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N LEU D 121 " pdb=" CA LEU D 121 " ideal model delta sigma weight residual 1.462 1.488 -0.026 8.50e-03 1.38e+04 9.26e+00 ... (remaining 6716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8558 1.87 - 3.75: 527 3.75 - 5.62: 61 5.62 - 7.50: 6 7.50 - 9.37: 3 Bond angle restraints: 9155 Sorted by residual: angle pdb=" N ARG B 197 " pdb=" CA ARG B 197 " pdb=" C ARG B 197 " ideal model delta sigma weight residual 113.72 108.83 4.89 1.30e+00 5.92e-01 1.41e+01 angle pdb=" C GLN A 52 " pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " ideal model delta sigma weight residual 110.88 105.09 5.79 1.57e+00 4.06e-01 1.36e+01 angle pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " pdb=" CG PHE B 151 " ideal model delta sigma weight residual 113.80 117.45 -3.65 1.00e+00 1.00e+00 1.34e+01 angle pdb=" CA CYS B 149 " pdb=" C CYS B 149 " pdb=" O CYS B 149 " ideal model delta sigma weight residual 120.70 116.86 3.84 1.08e+00 8.57e-01 1.27e+01 angle pdb=" N PRO B 236 " pdb=" CA PRO B 236 " pdb=" C PRO B 236 " ideal model delta sigma weight residual 112.47 119.78 -7.31 2.06e+00 2.36e-01 1.26e+01 ... (remaining 9150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3589 17.17 - 34.35: 298 34.35 - 51.52: 48 51.52 - 68.69: 29 68.69 - 85.87: 1 Dihedral angle restraints: 3965 sinusoidal: 1399 harmonic: 2566 Sorted by residual: 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 93.00 152.15 -59.15 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB GLU C 47 " pdb=" CG GLU C 47 " pdb=" CD GLU C 47 " pdb=" OE1 GLU C 47 " ideal model delta sinusoidal sigma weight residual 0.00 85.87 -85.87 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CD ARG B 49 " pdb=" NE ARG B 49 " pdb=" CZ ARG B 49 " pdb=" NH1 ARG B 49 " ideal model delta sinusoidal sigma weight residual 0.00 -26.21 26.21 1 1.00e+01 1.00e-02 9.87e+00 ... (remaining 3962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 767 0.052 - 0.105: 246 0.105 - 0.157: 66 0.157 - 0.209: 11 0.209 - 0.262: 7 Chirality restraints: 1097 Sorted by residual: chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE A 55 " pdb=" N ILE A 55 " pdb=" C ILE A 55 " pdb=" CB ILE A 55 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA CYS B 149 " pdb=" N CYS B 149 " pdb=" C CYS B 149 " pdb=" CB CYS B 149 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1094 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 49 " -0.474 9.50e-02 1.11e+02 2.13e-01 2.77e+01 pdb=" NE ARG B 49 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 49 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 49 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 49 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 236 " -0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C VAL D 236 " 0.088 2.00e-02 2.50e+03 pdb=" O VAL D 236 " -0.033 2.00e-02 2.50e+03 pdb=" N PHE D 237 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 237 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C PHE D 237 " -0.067 2.00e-02 2.50e+03 pdb=" O PHE D 237 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 238 " 0.023 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1073 2.76 - 3.30: 5961 3.30 - 3.83: 10219 3.83 - 4.37: 12579 4.37 - 4.90: 21655 Nonbonded interactions: 51487 Sorted by model distance: nonbonded pdb=" NH2 ARG B 22 " pdb=" OD2 ASP B 258 " model vdw 2.231 3.120 nonbonded pdb=" NE2 GLN C 18 " pdb=" OE2 GLU C 22 " model vdw 2.251 3.120 nonbonded pdb=" O TYR A 230 " pdb=" ND2 ASN A 241 " model vdw 2.267 3.120 nonbonded pdb=" O ILE D 290 " pdb=" OG1 THR D 294 " model vdw 2.320 3.040 nonbonded pdb=" OD1 ASN D 137 " pdb=" OG1 THR D 208 " model vdw 2.327 3.040 ... (remaining 51482 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: 5.260 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.950 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.006 0.095 6723 Z= 0.408 Angle : 0.963 9.371 9159 Z= 0.611 Chirality : 0.057 0.262 1097 Planarity : 0.014 0.213 1145 Dihedral : 14.077 85.868 2287 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 0.76 % Allowed : 12.10 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.00 (0.25), residues: 856 helix: -1.54 (0.23), residues: 377 sheet: 0.54 (0.41), residues: 154 loop : -1.84 (0.28), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.004 ARG B 283 TYR 0.024 0.002 TYR D 336 PHE 0.014 0.002 PHE A 196 TRP 0.029 0.003 TRP D 318 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 6721) covalent geometry : angle 0.95771 ( 9155) SS BOND : bond 0.04238 ( 2) SS BOND : angle 5.03148 ( 4) hydrogen bonds : bond 0.20729 ( 349) hydrogen bonds : angle 6.57528 ( 1011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.223 Fit side-chains REVERT: B 75 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8349 (mt0) REVERT: C 25 ILE cc_start: 0.6095 (pt) cc_final: 0.5716 (pt) REVERT: D 194 LEU cc_start: 0.7857 (tm) cc_final: 0.7272 (pp) outliers start: 5 outliers final: 1 residues processed: 127 average time/residue: 0.5362 time to fit residues: 71.6411 Evaluate side-chains 105 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.0050 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.167511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120665 restraints weight = 6718.032| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.86 r_work: 0.3219 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 6723 Z= 0.129 Angle : 0.561 7.170 9159 Z= 0.302 Chirality : 0.042 0.152 1097 Planarity : 0.004 0.045 1145 Dihedral : 4.945 44.352 962 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.12 % Allowed : 12.25 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.28), residues: 856 helix: 1.22 (0.27), residues: 378 sheet: 1.38 (0.41), residues: 156 loop : -1.72 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 283 TYR 0.023 0.001 TYR D 149 PHE 0.012 0.001 PHE B 199 TRP 0.013 0.001 TRP D 318 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6721) covalent geometry : angle 0.55733 ( 9155) SS BOND : bond 0.00768 ( 2) SS BOND : angle 3.01325 ( 4) hydrogen bonds : bond 0.05954 ( 349) hydrogen bonds : angle 4.16756 ( 1011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.259 Fit side-chains REVERT: D 185 LYS cc_start: 0.6410 (mttt) cc_final: 0.6115 (mttm) REVERT: D 194 LEU cc_start: 0.7457 (tm) cc_final: 0.6521 (mm) REVERT: A 24 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7199 (ttm110) outliers start: 14 outliers final: 5 residues processed: 111 average time/residue: 0.5338 time to fit residues: 62.2820 Evaluate side-chains 102 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 311 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114760 restraints weight = 6690.041| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.70 r_work: 0.3172 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6723 Z= 0.162 Angle : 0.600 10.020 9159 Z= 0.321 Chirality : 0.043 0.161 1097 Planarity : 0.004 0.052 1145 Dihedral : 4.876 35.752 960 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.78 % Allowed : 13.31 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 856 helix: 1.96 (0.27), residues: 374 sheet: 1.52 (0.40), residues: 155 loop : -1.54 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.017 0.002 TYR D 149 PHE 0.017 0.002 PHE B 151 TRP 0.012 0.002 TRP D 318 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6721) covalent geometry : angle 0.59309 ( 9155) SS BOND : bond 0.03130 ( 2) SS BOND : angle 4.48532 ( 4) hydrogen bonds : bond 0.06727 ( 349) hydrogen bonds : angle 4.09099 ( 1011) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.281 Fit side-chains REVERT: B 190 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8116 (tt) REVERT: B 304 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8235 (ttm170) REVERT: B 318 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (mt) REVERT: D 194 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6556 (mm) REVERT: D 221 PHE cc_start: 0.6324 (m-80) cc_final: 0.5921 (m-80) REVERT: A 24 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7049 (ttm110) outliers start: 25 outliers final: 7 residues processed: 115 average time/residue: 0.5042 time to fit residues: 61.1570 Evaluate side-chains 104 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 78 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 28 optimal weight: 0.0270 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.165638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122676 restraints weight = 6715.023| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.71 r_work: 0.3227 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 6723 Z= 0.115 Angle : 0.504 7.138 9159 Z= 0.270 Chirality : 0.041 0.143 1097 Planarity : 0.003 0.050 1145 Dihedral : 4.526 33.775 960 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.72 % Allowed : 14.52 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 856 helix: 2.29 (0.27), residues: 380 sheet: 1.67 (0.41), residues: 154 loop : -1.51 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.019 0.001 TYR D 149 PHE 0.012 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6721) covalent geometry : angle 0.49890 ( 9155) SS BOND : bond 0.02053 ( 2) SS BOND : angle 3.42434 ( 4) hydrogen bonds : bond 0.05061 ( 349) hydrogen bonds : angle 3.78363 ( 1011) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.252 Fit side-chains REVERT: B 190 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8020 (tt) REVERT: B 318 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8512 (mt) REVERT: D 194 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6235 (mm) REVERT: D 243 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6908 (mpt) REVERT: A 24 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6954 (ttp-110) REVERT: A 245 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6565 (mm-30) outliers start: 18 outliers final: 7 residues processed: 112 average time/residue: 0.4613 time to fit residues: 54.8403 Evaluate side-chains 108 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.115326 restraints weight = 6658.104| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.80 r_work: 0.3120 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 6723 Z= 0.206 Angle : 0.664 12.645 9159 Z= 0.354 Chirality : 0.045 0.173 1097 Planarity : 0.004 0.054 1145 Dihedral : 5.212 40.972 960 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.18 % Allowed : 14.22 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 856 helix: 2.13 (0.27), residues: 375 sheet: 1.69 (0.41), residues: 152 loop : -1.38 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 52 TYR 0.019 0.002 TYR D 149 PHE 0.025 0.002 PHE B 151 TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6721) covalent geometry : angle 0.65204 ( 9155) SS BOND : bond 0.04048 ( 2) SS BOND : angle 5.96566 ( 4) hydrogen bonds : bond 0.07552 ( 349) hydrogen bonds : angle 4.14927 ( 1011) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.157 Fit side-chains REVERT: B 61 MET cc_start: 0.8774 (ppp) cc_final: 0.8549 (ppp) REVERT: B 190 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 273 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8903 (mp) REVERT: B 304 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8229 (ttm170) REVERT: B 318 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8718 (mt) REVERT: D 76 SER cc_start: 0.7264 (m) cc_final: 0.6696 (m) REVERT: D 194 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6414 (mm) REVERT: A 24 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6961 (ttm110) REVERT: A 207 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: A 245 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6715 (mm-30) outliers start: 21 outliers final: 11 residues processed: 105 average time/residue: 0.5712 time to fit residues: 62.9227 Evaluate side-chains 114 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120012 restraints weight = 6755.281| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.82 r_work: 0.3197 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6723 Z= 0.126 Angle : 0.534 8.204 9159 Z= 0.284 Chirality : 0.041 0.146 1097 Planarity : 0.003 0.051 1145 Dihedral : 4.720 37.863 960 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.03 % Allowed : 14.83 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.29), residues: 856 helix: 2.49 (0.27), residues: 374 sheet: 1.67 (0.41), residues: 155 loop : -1.34 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 52 TYR 0.019 0.001 TYR D 149 PHE 0.014 0.001 PHE B 151 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6721) covalent geometry : angle 0.52759 ( 9155) SS BOND : bond 0.02566 ( 2) SS BOND : angle 4.12228 ( 4) hydrogen bonds : bond 0.05382 ( 349) hydrogen bonds : angle 3.82693 ( 1011) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.262 Fit side-chains REVERT: B 190 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 304 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8213 (ttm170) REVERT: B 318 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8547 (mt) REVERT: D 76 SER cc_start: 0.7254 (m) cc_final: 0.6674 (m) REVERT: D 194 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6277 (mm) REVERT: D 202 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.6377 (t) REVERT: A 24 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.7065 (ttp-110) REVERT: A 207 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: A 245 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6554 (mm-30) outliers start: 20 outliers final: 7 residues processed: 108 average time/residue: 0.5018 time to fit residues: 57.2894 Evaluate side-chains 113 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** D 188 ASN ** 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 = 0.3887 r_free = 0.3887 target = 0.164195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120493 restraints weight = 6651.352| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.86 r_work: 0.3192 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6723 Z= 0.125 Angle : 0.531 8.708 9159 Z= 0.280 Chirality : 0.041 0.148 1097 Planarity : 0.003 0.051 1145 Dihedral : 4.625 38.712 960 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.18 % Allowed : 15.43 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.29), residues: 856 helix: 2.72 (0.27), residues: 369 sheet: 1.74 (0.41), residues: 155 loop : -1.25 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.019 0.001 TYR D 149 PHE 0.015 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6721) covalent geometry : angle 0.52519 ( 9155) SS BOND : bond 0.02213 ( 2) SS BOND : angle 3.77305 ( 4) hydrogen bonds : bond 0.05278 ( 349) hydrogen bonds : angle 3.76304 ( 1011) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.248 Fit side-chains REVERT: B 190 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8079 (tt) REVERT: B 304 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8204 (ttm170) REVERT: B 318 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8534 (mt) REVERT: D 76 SER cc_start: 0.7252 (m) cc_final: 0.6673 (m) REVERT: D 194 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6126 (mm) REVERT: D 202 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6343 (t) REVERT: A 24 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7105 (ttp-110) REVERT: A 207 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 245 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6579 (mm-30) REVERT: A 313 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7591 (mtp-110) outliers start: 21 outliers final: 7 residues processed: 110 average time/residue: 0.4944 time to fit residues: 57.4523 Evaluate side-chains 112 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 26 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** D 188 ASN ** 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 = 0.3899 r_free = 0.3899 target = 0.165319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122395 restraints weight = 6724.307| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.67 r_work: 0.3222 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 6723 Z= 0.116 Angle : 0.509 8.973 9159 Z= 0.269 Chirality : 0.041 0.143 1097 Planarity : 0.003 0.051 1145 Dihedral : 4.500 37.292 960 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.42 % Allowed : 16.04 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.29), residues: 856 helix: 2.81 (0.27), residues: 369 sheet: 1.75 (0.41), residues: 155 loop : -1.16 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.018 0.001 TYR D 149 PHE 0.014 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6721) covalent geometry : angle 0.50460 ( 9155) SS BOND : bond 0.01924 ( 2) SS BOND : angle 3.20298 ( 4) hydrogen bonds : bond 0.04906 ( 349) hydrogen bonds : angle 3.69461 ( 1011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.299 Fit side-chains REVERT: B 190 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 304 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8184 (ttm170) REVERT: B 318 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8509 (mt) REVERT: D 76 SER cc_start: 0.7239 (m) cc_final: 0.6662 (m) REVERT: D 194 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6115 (mm) REVERT: D 202 VAL cc_start: 0.6638 (OUTLIER) cc_final: 0.6319 (t) REVERT: A 24 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7085 (ttp-110) REVERT: A 207 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: A 242 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8172 (mtm-85) REVERT: A 245 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: A 313 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.7591 (mtp-110) outliers start: 16 outliers final: 7 residues processed: 109 average time/residue: 0.4876 time to fit residues: 56.2082 Evaluate side-chains 109 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 0.0770 chunk 45 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** D 188 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.164745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121020 restraints weight = 6728.824| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.81 r_work: 0.3205 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 6723 Z= 0.123 Angle : 0.525 9.172 9159 Z= 0.277 Chirality : 0.041 0.145 1097 Planarity : 0.003 0.051 1145 Dihedral : 4.632 37.414 960 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.72 % Allowed : 16.49 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.29), residues: 856 helix: 2.85 (0.27), residues: 370 sheet: 1.64 (0.41), residues: 162 loop : -1.06 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.017 0.001 TYR D 149 PHE 0.015 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6721) covalent geometry : angle 0.51992 ( 9155) SS BOND : bond 0.02112 ( 2) SS BOND : angle 3.40475 ( 4) hydrogen bonds : bond 0.05079 ( 349) hydrogen bonds : angle 3.71200 ( 1011) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.291 Fit side-chains REVERT: B 190 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 304 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8184 (ttm170) REVERT: B 318 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8511 (mt) REVERT: D 76 SER cc_start: 0.7208 (m) cc_final: 0.6594 (m) REVERT: D 118 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7028 (p) REVERT: D 194 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6090 (mm) REVERT: D 202 VAL cc_start: 0.6610 (OUTLIER) cc_final: 0.6272 (t) REVERT: D 263 ARG cc_start: 0.7518 (mtp180) cc_final: 0.7200 (tpp80) REVERT: A 24 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7084 (ttp-110) REVERT: A 207 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: A 245 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6550 (mm-30) REVERT: A 313 ARG cc_start: 0.7821 (mtp-110) cc_final: 0.7609 (mtp-110) outliers start: 18 outliers final: 7 residues processed: 102 average time/residue: 0.5515 time to fit residues: 59.0214 Evaluate side-chains 109 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** D 188 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.163862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120175 restraints weight = 6663.340| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.83 r_work: 0.3186 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6723 Z= 0.130 Angle : 0.536 9.244 9159 Z= 0.283 Chirality : 0.041 0.148 1097 Planarity : 0.003 0.052 1145 Dihedral : 4.652 39.634 960 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.57 % Allowed : 16.79 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.29), residues: 856 helix: 2.82 (0.27), residues: 370 sheet: 1.78 (0.41), residues: 155 loop : -1.08 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.017 0.001 TYR D 149 PHE 0.016 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6721) covalent geometry : angle 0.53051 ( 9155) SS BOND : bond 0.02349 ( 2) SS BOND : angle 3.67278 ( 4) hydrogen bonds : bond 0.05388 ( 349) hydrogen bonds : angle 3.76539 ( 1011) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.247 Fit side-chains REVERT: B 190 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 304 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8195 (ttm170) REVERT: B 318 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8548 (mt) REVERT: D 76 SER cc_start: 0.7228 (m) cc_final: 0.6624 (m) REVERT: D 118 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7098 (p) REVERT: D 194 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6150 (mm) REVERT: D 202 VAL cc_start: 0.6606 (OUTLIER) cc_final: 0.6267 (t) REVERT: D 263 ARG cc_start: 0.7522 (mtp180) cc_final: 0.7208 (tpp80) REVERT: A 24 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7111 (ttp-110) REVERT: A 207 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: A 245 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: A 313 ARG cc_start: 0.7839 (mtp-110) cc_final: 0.7627 (mtp-110) outliers start: 17 outliers final: 6 residues processed: 106 average time/residue: 0.5469 time to fit residues: 60.9001 Evaluate side-chains 112 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** D 188 ASN ** 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 = 0.3856 r_free = 0.3856 target = 0.161157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113957 restraints weight = 6613.975| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.13 r_work: 0.3111 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 6723 Z= 0.172 Angle : 0.611 11.501 9159 Z= 0.322 Chirality : 0.044 0.157 1097 Planarity : 0.004 0.052 1145 Dihedral : 4.953 38.146 960 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.57 % Allowed : 16.64 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.29), residues: 856 helix: 2.64 (0.27), residues: 369 sheet: 1.68 (0.41), residues: 156 loop : -1.14 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.018 0.002 TYR D 149 PHE 0.022 0.002 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6721) covalent geometry : angle 0.60295 ( 9155) SS BOND : bond 0.03354 ( 2) SS BOND : angle 4.68072 ( 4) hydrogen bonds : bond 0.06656 ( 349) hydrogen bonds : angle 3.97993 ( 1011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.31 seconds wall clock time: 55 minutes 46.63 seconds (3346.63 seconds total)