Starting phenix.real_space_refine on Thu Feb 5 07:20:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mdu_48180/02_2026/9mdu_48180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mdu_48180/02_2026/9mdu_48180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mdu_48180/02_2026/9mdu_48180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mdu_48180/02_2026/9mdu_48180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mdu_48180/02_2026/9mdu_48180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mdu_48180/02_2026/9mdu_48180.map" } resolution = 2.9 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= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8253 atoms to isotropic. 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 48 5.16 5 C 6116 2.51 5 N 1451 2.21 5 O 1508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9123 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "A" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2277 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2282 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Time building chain proxies: 2.49, per 1000 atoms: 0.27 Number of scatterers: 9123 At special positions: 0 Unit cell: (83.46, 95.23, 93.09, 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 48 16.00 O 1508 8.00 N 1451 7.00 C 6116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 186 " distance=2.01 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 186 " 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: 0.78 Conformation dependent library (CDL) restraints added in 491.5 milliseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 78.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 36 through 65 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 72 through 100 removed outlier: 3.574A pdb=" N TYR B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 104 through 139 removed outlier: 4.492A pdb=" N LEU B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 154 through 167 removed outlier: 4.069A pdb=" N VAL B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Proline residue: B 163 - end of helix Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 192 through 227 removed outlier: 3.705A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 236 through 267 removed outlier: 3.519A pdb=" N THR B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 254 - end of helix Processing helix chain 'B' and resid 273 through 292 removed outlier: 3.562A pdb=" N HIS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 removed outlier: 4.061A pdb=" N ASN B 298 " --> pdb=" O HIS B 294 " (cutoff:3.500A) Proline residue: B 299 - end of helix removed outlier: 3.744A pdb=" N TYR B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 63 Processing helix chain 'A' and resid 72 through 100 removed outlier: 3.827A pdb=" N TYR A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 3.510A pdb=" N VAL A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 139 removed outlier: 3.813A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.884A pdb=" N VAL A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 192 through 229 removed outlier: 3.906A pdb=" N VAL A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Proline residue: A 211 - end of helix removed outlier: 3.957A pdb=" N HIS A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 267 Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 274 through 291 removed outlier: 3.643A pdb=" N ASN A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'C' and resid 40 through 63 Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.752A pdb=" N THR C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Proline residue: C 92 - end of helix Processing helix chain 'C' and resid 105 through 139 removed outlier: 3.841A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.925A pdb=" N VAL C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 192 through 209 removed outlier: 4.046A pdb=" N VAL C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 224 Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.734A pdb=" N THR C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.570A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 63 Proline residue: D 42 - end of helix Processing helix chain 'D' and resid 71 through 100 removed outlier: 3.817A pdb=" N LYS D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Proline residue: D 92 - end of helix Processing helix chain 'D' and resid 105 through 139 removed outlier: 3.816A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 167 removed outlier: 5.217A pdb=" N VAL D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Proline residue: D 163 - end of helix Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 192 through 226 removed outlier: 6.061A pdb=" N LEU D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Proline residue: D 211 - end of helix removed outlier: 3.521A pdb=" N ILE D 222 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 238 through 267 removed outlier: 3.503A pdb=" N LEU D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Proline residue: D 254 - end of helix Processing helix chain 'D' and resid 273 through 292 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.509A pdb=" N LEU D 301 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 175 through 178 removed outlier: 3.516A pdb=" N ASP B 187 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 178 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 178 Processing sheet with id=AA3, first strand: chain 'C' and resid 175 through 180 Processing sheet with id=AA4, first strand: chain 'D' and resid 175 through 180 624 hydrogen bonds defined for protein. 1851 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: 1.47 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 466 1.23 - 1.38: 3012 1.38 - 1.53: 4592 1.53 - 1.67: 1249 1.67 - 1.82: 60 Bond restraints: 9379 Sorted by residual: bond pdb=" C GLN A 233 " pdb=" N LYS A 234 " ideal model delta sigma weight residual 1.335 1.089 0.247 1.32e-02 5.74e+03 3.49e+02 bond pdb=" C LYS B 230 " pdb=" N GLY B 231 " ideal model delta sigma weight residual 1.335 1.175 0.160 1.20e-02 6.94e+03 1.78e+02 bond pdb=" CA PHE C 40 " pdb=" C PHE C 40 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.34e-02 5.57e+03 3.21e+01 bond pdb=" CA SER B 178 " pdb=" CB SER B 178 " ideal model delta sigma weight residual 1.527 1.455 0.073 1.30e-02 5.92e+03 3.13e+01 bond pdb=" CA SER D 224 " pdb=" CB SER D 224 " ideal model delta sigma weight residual 1.534 1.456 0.078 1.58e-02 4.01e+03 2.42e+01 ... (remaining 9374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.36: 12662 7.36 - 14.71: 75 14.71 - 22.07: 22 22.07 - 29.42: 12 29.42 - 36.78: 3 Bond angle restraints: 12774 Sorted by residual: angle pdb=" C PRO B 27 " pdb=" CA PRO B 27 " pdb=" CB PRO B 27 " ideal model delta sigma weight residual 111.56 74.78 36.78 1.65e+00 3.67e-01 4.97e+02 angle pdb=" N CYS B 28 " pdb=" CA CYS B 28 " pdb=" CB CYS B 28 " ideal model delta sigma weight residual 110.49 144.01 -33.52 1.69e+00 3.50e-01 3.93e+02 angle pdb=" C HIS B 228 " pdb=" CA HIS B 228 " pdb=" CB HIS B 228 " ideal model delta sigma weight residual 111.14 84.39 26.75 1.39e+00 5.18e-01 3.70e+02 angle pdb=" C ASN B 37 " pdb=" CA ASN B 37 " pdb=" CB ASN B 37 " ideal model delta sigma weight residual 110.90 139.69 -28.79 1.58e+00 4.01e-01 3.32e+02 angle pdb=" O GLN A 233 " pdb=" C GLN A 233 " pdb=" N LYS A 234 " ideal model delta sigma weight residual 122.59 98.95 23.64 1.33e+00 5.65e-01 3.16e+02 ... (remaining 12769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4799 18.01 - 36.02: 476 36.02 - 54.03: 130 54.03 - 72.04: 39 72.04 - 90.05: 10 Dihedral angle restraints: 5454 sinusoidal: 2120 harmonic: 3334 Sorted by residual: dihedral pdb=" C PRO B 27 " pdb=" N PRO B 27 " pdb=" CA PRO B 27 " pdb=" CB PRO B 27 " ideal model delta harmonic sigma weight residual -120.70 -78.31 -42.39 0 2.50e+00 1.60e-01 2.88e+02 dihedral pdb=" C SER D 229 " pdb=" N SER D 229 " pdb=" CA SER D 229 " pdb=" CB SER D 229 " ideal model delta harmonic sigma weight residual -122.60 -164.25 41.65 0 2.50e+00 1.60e-01 2.78e+02 dihedral pdb=" N SER D 229 " pdb=" C SER D 229 " pdb=" CA SER D 229 " pdb=" CB SER D 229 " ideal model delta harmonic sigma weight residual 122.80 161.84 -39.04 0 2.50e+00 1.60e-01 2.44e+02 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.354: 1471 0.354 - 0.707: 18 0.707 - 1.061: 5 1.061 - 1.415: 0 1.415 - 1.768: 1 Chirality restraints: 1495 Sorted by residual: chirality pdb=" CA SER D 229 " pdb=" N SER D 229 " pdb=" C SER D 229 " pdb=" CB SER D 229 " both_signs ideal model delta sigma weight residual False 2.51 0.74 1.77 2.00e-01 2.50e+01 7.82e+01 chirality pdb=" CA ILE D 223 " pdb=" N ILE D 223 " pdb=" C ILE D 223 " pdb=" CB ILE D 223 " both_signs ideal model delta sigma weight residual False 2.43 1.42 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" CA ASN B 37 " pdb=" N ASN B 37 " pdb=" C ASN B 37 " pdb=" CB ASN B 37 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.54e+01 ... (remaining 1492 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 30 " -1.055 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG D 30 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D 30 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 30 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 30 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 235 " 0.991 9.50e-02 1.11e+02 4.44e-01 1.20e+02 pdb=" NE ARG D 235 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG D 235 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 235 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 235 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 235 " 0.918 9.50e-02 1.11e+02 4.11e-01 1.03e+02 pdb=" NE ARG B 235 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 235 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 235 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 235 " 0.023 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.63: 6 1.63 - 2.45: 79 2.45 - 3.27: 9971 3.27 - 4.08: 24538 4.08 - 4.90: 45951 Warning: very small nonbonded interaction distances. Nonbonded interactions: 80545 Sorted by model distance: nonbonded pdb=" ND1 HIS D 232 " pdb=" NH2 ARG D 235 " model vdw 0.816 3.200 nonbonded pdb=" CE1 HIS D 232 " pdb=" NH2 ARG D 235 " model vdw 1.085 3.340 nonbonded pdb=" ND1 HIS D 232 " pdb=" CZ ARG D 235 " model vdw 1.304 3.350 nonbonded pdb=" OD1 ASP A 181 " pdb=" NE ARG A 183 " model vdw 1.343 3.120 nonbonded pdb=" O SER B 229 " pdb=" O LYS B 230 " model vdw 1.406 3.040 ... (remaining 80540 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 305) selection = (chain 'B' and resid 26 through 305) selection = (chain 'C' and resid 26 through 305) selection = (chain 'D' and resid 26 through 305) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 0.247 9383 Z= 0.543 Angle : 1.790 36.781 12782 Z= 1.130 Chirality : 0.112 1.768 1495 Planarity : 0.027 0.473 1540 Dihedral : 16.488 90.046 3284 Min Nonbonded Distance : 0.816 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.89 % Favored : 91.76 % Rotamer: Outliers : 6.68 % Allowed : 3.49 % Favored : 89.83 % Cbeta Deviations : 3.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.58 (0.25), residues: 1116 helix: -0.24 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.56 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 183 TYR 0.027 0.002 TYR D 121 PHE 0.020 0.002 PHE C 276 TRP 0.016 0.002 TRP C 283 HIS 0.006 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00836 ( 9379) covalent geometry : angle 1.78924 (12774) SS BOND : bond 0.00852 ( 4) SS BOND : angle 2.24333 ( 8) hydrogen bonds : bond 0.13867 ( 624) hydrogen bonds : angle 6.94217 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 85 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 179 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6632 (mm-30) REVERT: B 235 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4662 (mtp180) REVERT: A 70 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.6228 (ptp-170) REVERT: A 230 LYS cc_start: 0.5130 (OUTLIER) cc_final: 0.4507 (mmmt) REVERT: A 232 HIS cc_start: 0.1875 (OUTLIER) cc_final: 0.1540 (t-170) REVERT: A 234 LYS cc_start: 0.2217 (OUTLIER) cc_final: 0.1868 (tmtt) REVERT: A 235 ARG cc_start: 0.5146 (OUTLIER) cc_final: 0.3040 (ttm110) REVERT: C 25 LYS cc_start: 0.1660 (OUTLIER) cc_final: -0.0313 (tttp) REVERT: C 236 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6044 (mptt) REVERT: C 281 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8172 (m170) REVERT: C 282 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8378 (mtpp) REVERT: D 183 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6589 (mtp85) REVERT: D 233 GLN cc_start: 0.2181 (OUTLIER) cc_final: 0.1930 (pm20) outliers start: 67 outliers final: 17 residues processed: 144 average time/residue: 0.5244 time to fit residues: 81.1524 Evaluate side-chains 99 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 PRO Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 281 HIS Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 233 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN A 33 ASN A 232 HIS C 35 ASN C 233 GLN C 281 HIS C 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.144004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.109006 restraints weight = 9660.842| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.69 r_work: 0.3037 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9383 Z= 0.175 Angle : 0.651 6.646 12782 Z= 0.342 Chirality : 0.043 0.128 1495 Planarity : 0.005 0.044 1540 Dihedral : 9.230 82.816 1299 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.54 % Favored : 93.37 % Rotamer: Outliers : 4.29 % Allowed : 9.77 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.20 (0.25), residues: 1116 helix: -0.01 (0.18), residues: 885 sheet: -4.19 (0.96), residues: 12 loop : -3.58 (0.35), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 183 TYR 0.023 0.002 TYR D 121 PHE 0.018 0.001 PHE C 304 TRP 0.010 0.001 TRP C 283 HIS 0.012 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9379) covalent geometry : angle 0.65067 (12774) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.77338 ( 8) hydrogen bonds : bond 0.04681 ( 624) hydrogen bonds : angle 5.43513 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: B 35 ASN cc_start: 0.8480 (m-40) cc_final: 0.8279 (m-40) REVERT: B 149 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7986 (mtpp) REVERT: B 235 ARG cc_start: 0.6008 (OUTLIER) cc_final: 0.4616 (mtt-85) REVERT: A 30 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.6276 (ptt180) REVERT: A 132 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 230 LYS cc_start: 0.5061 (OUTLIER) cc_final: 0.3949 (mmmt) REVERT: A 235 ARG cc_start: 0.4533 (OUTLIER) cc_final: 0.2330 (ptp-110) REVERT: C 228 HIS cc_start: 0.5318 (OUTLIER) cc_final: 0.4702 (t70) REVERT: D 25 LYS cc_start: 0.4067 (OUTLIER) cc_final: 0.3772 (ptmm) outliers start: 43 outliers final: 13 residues processed: 116 average time/residue: 0.4051 time to fit residues: 51.5105 Evaluate side-chains 90 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 240 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 143 ASN B 200 GLN C 281 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106588 restraints weight = 9746.338| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.68 r_work: 0.2954 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9383 Z= 0.178 Angle : 0.613 7.827 12782 Z= 0.317 Chirality : 0.043 0.157 1495 Planarity : 0.005 0.050 1540 Dihedral : 6.951 72.603 1238 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.79 % Allowed : 12.66 % Favored : 83.55 % 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: -0.88 (0.25), residues: 1116 helix: 0.23 (0.18), residues: 884 sheet: -4.17 (0.94), residues: 12 loop : -3.52 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.018 0.002 TYR D 121 PHE 0.016 0.001 PHE A 248 TRP 0.010 0.001 TRP A 283 HIS 0.005 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9379) covalent geometry : angle 0.61261 (12774) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.55344 ( 8) hydrogen bonds : bond 0.04583 ( 624) hydrogen bonds : angle 5.25239 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.354 Fit side-chains REVERT: B 235 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.4449 (mtp-110) REVERT: A 63 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7140 (mpt) REVERT: A 89 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 132 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 230 LYS cc_start: 0.5143 (OUTLIER) cc_final: 0.3930 (mmmm) REVERT: A 235 ARG cc_start: 0.4699 (OUTLIER) cc_final: 0.2242 (ttm110) REVERT: C 228 HIS cc_start: 0.4969 (OUTLIER) cc_final: 0.4345 (t70) REVERT: C 275 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7198 (pt0) REVERT: D 166 LEU cc_start: 0.8154 (pp) cc_final: 0.7952 (pp) REVERT: D 223 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7865 (mt) REVERT: D 230 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4602 (ttmt) outliers start: 38 outliers final: 12 residues processed: 98 average time/residue: 0.3370 time to fit residues: 36.6974 Evaluate side-chains 86 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 240 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.141663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106855 restraints weight = 9854.293| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.69 r_work: 0.3008 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9383 Z= 0.159 Angle : 0.580 6.792 12782 Z= 0.300 Chirality : 0.042 0.120 1495 Planarity : 0.005 0.055 1540 Dihedral : 6.571 63.767 1232 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.29 % Allowed : 14.76 % Favored : 81.95 % 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: -0.55 (0.26), residues: 1116 helix: 0.45 (0.18), residues: 878 sheet: -4.14 (0.97), residues: 12 loop : -3.24 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.014 0.001 TYR D 121 PHE 0.015 0.001 PHE A 248 TRP 0.008 0.001 TRP A 283 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9379) covalent geometry : angle 0.57974 (12774) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.50269 ( 8) hydrogen bonds : bond 0.04347 ( 624) hydrogen bonds : angle 5.13209 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.352 Fit side-chains REVERT: B 89 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8069 (mp) REVERT: B 235 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.4568 (mtp-110) REVERT: A 63 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7334 (mpt) REVERT: A 89 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 230 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.3987 (mmmm) REVERT: A 235 ARG cc_start: 0.4590 (OUTLIER) cc_final: 0.2147 (ttm110) REVERT: C 32 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.4847 (pp20) REVERT: C 35 ASN cc_start: 0.8191 (m-40) cc_final: 0.7823 (m-40) REVERT: C 228 HIS cc_start: 0.5325 (OUTLIER) cc_final: 0.4414 (t70) REVERT: C 275 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7572 (pt0) REVERT: D 223 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8032 (mt) REVERT: D 230 LYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4525 (ttmt) outliers start: 33 outliers final: 13 residues processed: 99 average time/residue: 0.3461 time to fit residues: 38.4155 Evaluate side-chains 91 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 240 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0070 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 12 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 202 GLN C 101 ASN D 119 ASN D 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.111316 restraints weight = 9733.167| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.68 r_work: 0.3060 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9383 Z= 0.122 Angle : 0.538 6.726 12782 Z= 0.278 Chirality : 0.040 0.122 1495 Planarity : 0.004 0.054 1540 Dihedral : 6.152 54.248 1232 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.00 % Favored : 93.91 % Rotamer: Outliers : 3.59 % Allowed : 15.55 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1116 helix: 0.74 (0.18), residues: 883 sheet: -4.42 (0.43), residues: 40 loop : -3.11 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.012 0.001 TYR D 121 PHE 0.012 0.001 PHE A 248 TRP 0.008 0.001 TRP A 283 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9379) covalent geometry : angle 0.53837 (12774) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.46740 ( 8) hydrogen bonds : bond 0.03910 ( 624) hydrogen bonds : angle 4.86540 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.362 Fit side-chains REVERT: B 89 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7899 (mp) REVERT: B 235 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.4340 (mtp85) REVERT: A 89 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7798 (mp) REVERT: A 230 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.4172 (mmmm) REVERT: A 235 ARG cc_start: 0.4668 (OUTLIER) cc_final: 0.1991 (ttm110) REVERT: A 256 TYR cc_start: 0.8631 (m-80) cc_final: 0.8313 (m-80) REVERT: C 32 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.4878 (pp20) REVERT: C 35 ASN cc_start: 0.8230 (m-40) cc_final: 0.7829 (m-40) REVERT: C 228 HIS cc_start: 0.5333 (OUTLIER) cc_final: 0.4397 (t70) REVERT: C 275 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7502 (pt0) REVERT: D 194 LEU cc_start: 0.7790 (tp) cc_final: 0.7562 (tm) REVERT: D 230 LYS cc_start: 0.5214 (OUTLIER) cc_final: 0.4575 (ttmt) outliers start: 36 outliers final: 10 residues processed: 113 average time/residue: 0.3168 time to fit residues: 40.3422 Evaluate side-chains 95 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 230 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 106 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 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 = 0.3581 r_free = 0.3581 target = 0.144796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110263 restraints weight = 9736.307| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.68 r_work: 0.3042 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9383 Z= 0.132 Angle : 0.553 8.559 12782 Z= 0.282 Chirality : 0.041 0.125 1495 Planarity : 0.004 0.058 1540 Dihedral : 6.033 54.648 1232 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 3.29 % Allowed : 16.65 % Favored : 80.06 % 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: -0.12 (0.26), residues: 1116 helix: 0.80 (0.18), residues: 883 sheet: -4.37 (0.44), residues: 40 loop : -3.01 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.013 0.001 TYR D 121 PHE 0.013 0.001 PHE A 248 TRP 0.008 0.001 TRP A 283 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9379) covalent geometry : angle 0.55346 (12774) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.48122 ( 8) hydrogen bonds : bond 0.04004 ( 624) hydrogen bonds : angle 4.87430 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.312 Fit side-chains REVERT: B 89 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 235 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.4439 (mtp85) REVERT: A 89 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7800 (mp) REVERT: A 230 LYS cc_start: 0.5564 (OUTLIER) cc_final: 0.4102 (mmmm) REVERT: A 235 ARG cc_start: 0.4728 (OUTLIER) cc_final: 0.1845 (ttm110) REVERT: C 32 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.4840 (pp20) REVERT: C 35 ASN cc_start: 0.8297 (m-40) cc_final: 0.7945 (m-40) REVERT: C 145 GLN cc_start: 0.7319 (tp-100) cc_final: 0.6995 (tp-100) REVERT: C 228 HIS cc_start: 0.5258 (OUTLIER) cc_final: 0.4289 (t70) REVERT: C 275 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7406 (pt0) REVERT: C 297 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8231 (pp) REVERT: D 194 LEU cc_start: 0.7798 (tp) cc_final: 0.7572 (tm) REVERT: D 223 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7898 (mp) REVERT: D 230 LYS cc_start: 0.5216 (OUTLIER) cc_final: 0.4587 (ttmt) outliers start: 33 outliers final: 13 residues processed: 110 average time/residue: 0.2811 time to fit residues: 35.0166 Evaluate side-chains 102 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN A 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.144555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109895 restraints weight = 9722.685| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.69 r_work: 0.3067 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9383 Z= 0.137 Angle : 0.556 7.780 12782 Z= 0.283 Chirality : 0.041 0.117 1495 Planarity : 0.004 0.056 1540 Dihedral : 5.901 54.614 1232 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 3.49 % Allowed : 17.05 % Favored : 79.46 % 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: -0.04 (0.26), residues: 1116 helix: 0.93 (0.18), residues: 864 sheet: -4.21 (0.47), residues: 40 loop : -3.08 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 70 TYR 0.014 0.001 TYR D 121 PHE 0.014 0.001 PHE A 248 TRP 0.008 0.001 TRP A 283 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9379) covalent geometry : angle 0.55597 (12774) SS BOND : bond 0.00038 ( 4) SS BOND : angle 0.45596 ( 8) hydrogen bonds : bond 0.04047 ( 624) hydrogen bonds : angle 4.90432 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 time to evaluate : 0.309 Fit side-chains REVERT: B 89 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 235 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.4426 (mtp85) REVERT: A 63 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7190 (mpt) REVERT: A 89 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7832 (mp) REVERT: A 230 LYS cc_start: 0.5665 (OUTLIER) cc_final: 0.4177 (mmmm) REVERT: C 32 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.4623 (pp20) REVERT: C 145 GLN cc_start: 0.7209 (tp-100) cc_final: 0.6901 (tp-100) REVERT: C 228 HIS cc_start: 0.5185 (OUTLIER) cc_final: 0.4271 (t70) REVERT: C 297 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8249 (pp) REVERT: D 223 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 230 LYS cc_start: 0.5203 (OUTLIER) cc_final: 0.4581 (ttmt) outliers start: 35 outliers final: 14 residues processed: 105 average time/residue: 0.2415 time to fit residues: 28.8910 Evaluate side-chains 99 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS D 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.107952 restraints weight = 9615.847| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.69 r_work: 0.3002 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.004 0.033 9383 Z= 0.153 Angle : 0.570 7.799 12782 Z= 0.289 Chirality : 0.042 0.134 1495 Planarity : 0.004 0.059 1540 Dihedral : 5.692 55.155 1228 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 3.09 % Allowed : 17.35 % Favored : 79.56 % 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: -0.16 (0.26), residues: 1116 helix: 0.75 (0.18), residues: 881 sheet: -4.07 (0.51), residues: 40 loop : -2.96 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.017 0.001 TYR D 121 PHE 0.015 0.001 PHE A 248 TRP 0.009 0.001 TRP B 252 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9379) covalent geometry : angle 0.57026 (12774) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.48147 ( 8) hydrogen bonds : bond 0.04192 ( 624) hydrogen bonds : angle 4.96867 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.345 Fit side-chains REVERT: B 89 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 235 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.4493 (mtp180) REVERT: A 63 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7238 (mpt) REVERT: A 89 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 190 TYR cc_start: 0.8353 (m-80) cc_final: 0.8142 (m-80) REVERT: A 230 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.4187 (mmmm) REVERT: C 32 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.4721 (pp20) REVERT: C 145 GLN cc_start: 0.7166 (tp-100) cc_final: 0.6857 (tp-100) REVERT: C 228 HIS cc_start: 0.5094 (OUTLIER) cc_final: 0.4132 (t70) REVERT: C 297 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8265 (pp) REVERT: D 223 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7789 (mp) REVERT: D 230 LYS cc_start: 0.5162 (OUTLIER) cc_final: 0.4529 (ttmt) outliers start: 31 outliers final: 15 residues processed: 100 average time/residue: 0.2821 time to fit residues: 32.1938 Evaluate side-chains 98 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110672 restraints weight = 9685.665| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.70 r_work: 0.3072 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9383 Z= 0.127 Angle : 0.545 6.746 12782 Z= 0.277 Chirality : 0.040 0.124 1495 Planarity : 0.004 0.055 1540 Dihedral : 5.594 54.280 1228 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 2.59 % Allowed : 18.34 % Favored : 79.06 % 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: 0.19 (0.27), residues: 1116 helix: 0.97 (0.18), residues: 872 sheet: -3.94 (0.55), residues: 40 loop : -2.54 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.015 0.001 TYR D 121 PHE 0.012 0.001 PHE A 248 TRP 0.010 0.001 TRP B 252 HIS 0.003 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9379) covalent geometry : angle 0.54498 (12774) SS BOND : bond 0.00020 ( 4) SS BOND : angle 0.49916 ( 8) hydrogen bonds : bond 0.03929 ( 624) hydrogen bonds : angle 4.84213 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: B 89 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 235 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.4403 (mtp85) REVERT: A 89 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7780 (mp) REVERT: A 230 LYS cc_start: 0.5635 (OUTLIER) cc_final: 0.4247 (mmmm) REVERT: A 256 TYR cc_start: 0.8614 (m-80) cc_final: 0.8315 (m-80) REVERT: C 32 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.4728 (pp20) REVERT: C 35 ASN cc_start: 0.8359 (m-40) cc_final: 0.7990 (m-40) REVERT: C 145 GLN cc_start: 0.7171 (tp-100) cc_final: 0.6905 (tp-100) REVERT: C 228 HIS cc_start: 0.5099 (OUTLIER) cc_final: 0.4125 (t70) REVERT: C 297 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8155 (pp) REVERT: D 223 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7842 (mp) REVERT: D 230 LYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4544 (ttmt) outliers start: 26 outliers final: 13 residues processed: 106 average time/residue: 0.2923 time to fit residues: 35.2248 Evaluate side-chains 103 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.0070 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 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 = 0.3569 r_free = 0.3569 target = 0.143519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108439 restraints weight = 9704.743| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.71 r_work: 0.3037 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9383 Z= 0.152 Angle : 0.572 7.662 12782 Z= 0.289 Chirality : 0.042 0.172 1495 Planarity : 0.004 0.057 1540 Dihedral : 5.601 54.764 1228 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 2.49 % Allowed : 18.74 % Favored : 78.76 % 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: 0.10 (0.26), residues: 1116 helix: 0.90 (0.18), residues: 870 sheet: -3.90 (0.56), residues: 40 loop : -2.54 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.017 0.001 TYR D 121 PHE 0.015 0.001 PHE A 248 TRP 0.009 0.001 TRP A 283 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9379) covalent geometry : angle 0.57180 (12774) SS BOND : bond 0.00030 ( 4) SS BOND : angle 0.50608 ( 8) hydrogen bonds : bond 0.04154 ( 624) hydrogen bonds : angle 4.91896 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 89 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 235 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.4418 (mtp180) REVERT: A 89 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7870 (mp) REVERT: A 190 TYR cc_start: 0.8341 (m-80) cc_final: 0.8108 (m-80) REVERT: A 230 LYS cc_start: 0.5611 (OUTLIER) cc_final: 0.4252 (mmmm) REVERT: C 32 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.4780 (pp20) REVERT: C 145 GLN cc_start: 0.7174 (tp-100) cc_final: 0.6890 (tp-100) REVERT: C 228 HIS cc_start: 0.5153 (OUTLIER) cc_final: 0.4178 (t70) REVERT: C 297 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8297 (pp) REVERT: C 300 ILE cc_start: 0.8592 (mp) cc_final: 0.8353 (mt) REVERT: D 223 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7844 (mp) REVERT: D 230 LYS cc_start: 0.5183 (OUTLIER) cc_final: 0.4541 (ttmt) outliers start: 25 outliers final: 15 residues processed: 95 average time/residue: 0.3139 time to fit residues: 33.5381 Evaluate side-chains 97 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** D 35 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 = 0.3582 r_free = 0.3582 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109275 restraints weight = 9646.063| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.72 r_work: 0.3029 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9383 Z= 0.146 Angle : 0.564 7.572 12782 Z= 0.286 Chirality : 0.042 0.169 1495 Planarity : 0.004 0.054 1540 Dihedral : 5.588 54.577 1228 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 2.59 % Allowed : 18.64 % Favored : 78.76 % 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: 0.14 (0.27), residues: 1116 helix: 0.93 (0.18), residues: 869 sheet: -3.82 (0.57), residues: 40 loop : -2.49 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.016 0.001 TYR D 121 PHE 0.014 0.001 PHE A 248 TRP 0.009 0.001 TRP B 252 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9379) covalent geometry : angle 0.56415 (12774) SS BOND : bond 0.00025 ( 4) SS BOND : angle 0.50438 ( 8) hydrogen bonds : bond 0.04124 ( 624) hydrogen bonds : angle 4.92185 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.22 seconds wall clock time: 40 minutes 54.75 seconds (2454.75 seconds total)