Starting phenix.real_space_refine on Thu Jul 2 15:08:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zn5_14801/07_2026/7zn5_14801.cif" } resolution = 3.7 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= 1.000 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: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 18 5.16 5 C 5500 2.51 5 N 1562 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9046 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3533 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3525 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 430, 3525 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3601 Chain: "B" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3566 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Time building chain proxies: 2.50, per 1000 atoms: 0.28 Number of scatterers: 9046 At special positions: 0 Unit cell: (146.685, 98.679, 89.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 97 15.00 O 1869 8.00 N 1562 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.74 Conformation dependent library (CDL) restraints added in 324.4 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 46.8% alpha, 9.6% beta 13 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 4.267A pdb=" N TYR A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.580A pdb=" N VAL A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.773A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.700A pdb=" N LEU A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.153A pdb=" N HIS A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 254 through 268 removed outlier: 4.117A pdb=" N HIS A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.927A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 381 removed outlier: 3.870A pdb=" N LYS A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 426 through 429 removed outlier: 3.547A pdb=" N SER A 429 " --> pdb=" O SER A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 450 through 463 Processing helix chain 'B' and resid 15 through 31 removed outlier: 4.349A pdb=" N TYR B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 52 through 67 removed outlier: 3.615A pdb=" N VAL B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.814A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 removed outlier: 3.659A pdb=" N GLY B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.543A pdb=" N VAL B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 removed outlier: 4.374A pdb=" N THR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.976A pdb=" N HIS B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.693A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 382 removed outlier: 3.789A pdb=" N LYS B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 450 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.822A pdb=" N PHE A 109 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR A 423 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N LYS A 421 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY A 442 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR A 423 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 440 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 388 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175 removed outlier: 6.698A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A 276 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 241 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL A 194 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TYR A 240 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 196 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR A 195 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE A 219 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 197 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.552A pdb=" N GLY A 225 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.597A pdb=" N GLY B 175 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 239 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASP B 276 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B 241 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 194 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 240 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 196 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.874A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 440 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2318 1.34 - 1.45: 2259 1.45 - 1.57: 4657 1.57 - 1.69: 190 1.69 - 1.81: 32 Bond restraints: 9456 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.544 0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.545 0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C4 LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.464 1.615 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 9451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 12984 2.23 - 4.45: 194 4.45 - 6.68: 28 6.68 - 8.90: 3 8.90 - 11.13: 6 Bond angle restraints: 13215 Sorted by residual: angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT D 40 " pdb=" C4 DT D 40 " pdb=" O4 DT D 40 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT C 7 " pdb=" C4 DT C 7 " pdb=" O4 DT C 7 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 19 " pdb=" C4 DT C 19 " pdb=" O4 DT C 19 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 13210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.21: 4923 28.21 - 56.42: 464 56.42 - 84.63: 30 84.63 - 112.84: 2 112.84 - 141.06: 1 Dihedral angle restraints: 5420 sinusoidal: 2863 harmonic: 2557 Sorted by residual: dihedral pdb=" CA ARG A 74 " pdb=" C ARG A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C4' DA D 33 " pdb=" C3' DA D 33 " pdb=" O3' DA D 33 " pdb=" P DA D 34 " ideal model delta sinusoidal sigma weight residual 220.00 78.94 141.06 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" CA PRO A 73 " pdb=" C PRO A 73 " pdb=" N ARG A 74 " pdb=" CA ARG A 74 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 883 0.032 - 0.064: 331 0.064 - 0.096: 176 0.096 - 0.128: 54 0.128 - 0.159: 6 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CA ARG B 138 " pdb=" N ARG B 138 " pdb=" C ARG B 138 " pdb=" CB ARG B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA GLU B 154 " pdb=" N GLU B 154 " pdb=" C GLU B 154 " pdb=" CB GLU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1447 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " -0.156 2.00e-02 2.50e+03 2.55e-01 6.53e+02 pdb=" NZ LLP A 309 " 0.341 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " 0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " -0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " 0.089 2.00e-02 2.50e+03 8.51e-02 7.24e+01 pdb=" NZ LLP B 309 " -0.091 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " 0.081 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 168 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 169 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.027 5.00e-02 4.00e+02 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 804 2.74 - 3.28: 8566 3.28 - 3.82: 15123 3.82 - 4.36: 16992 4.36 - 4.90: 27837 Nonbonded interactions: 69322 Sorted by model distance: nonbonded pdb=" OG SER A 254 " pdb=" OD1 ASN A 256 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 162 " pdb=" OE2 GLU A 281 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLN B 184 " pdb=" OH TYR B 330 " model vdw 2.262 3.040 nonbonded pdb=" O HIS B 145 " pdb=" OG SER B 339 " model vdw 2.265 3.040 nonbonded pdb=" O THR B 131 " pdb=" ND2 ASN B 136 " model vdw 2.302 3.120 ... (remaining 69317 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 15 through 442 or resid 444 through 464)) selection = (chain 'B' and (resid 15 through 442 or resid 444 through 464)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.720 Find NCS groups from input model: 0.100 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 0.182 9456 Z= 0.418 Angle : 0.702 11.128 13215 Z= 0.508 Chirality : 0.043 0.159 1450 Planarity : 0.009 0.255 1348 Dihedral : 18.868 141.055 3784 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.13 % Allowed : 0.52 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.18 (0.30), residues: 852 helix: 1.18 (0.28), residues: 374 sheet: 0.15 (0.52), residues: 106 loop : -0.97 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.019 0.001 TYR A 82 PHE 0.011 0.001 PHE A 128 TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.42 ( 9456) covalent geometry : angle 0.70173 / 0.51 (13215) hydrogen bonds : bond 0.16656 / 10.58 ( 324) hydrogen bonds : angle 6.50322 / 4.51 ( 910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8787 (pt) cc_final: 0.8580 (mt) REVERT: A 270 ASN cc_start: 0.7690 (t0) cc_final: 0.7392 (t0) REVERT: B 270 ASN cc_start: 0.7313 (t0) cc_final: 0.6885 (t0) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.0967 time to fit residues: 13.3129 Evaluate side-chains 66 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN A 183 GLN B 53 GLN B 142 ASN B 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.133707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097955 restraints weight = 15902.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101181 restraints weight = 8119.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103334 restraints weight = 5071.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104797 restraints weight = 3649.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105758 restraints weight = 2916.967| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9456 Z= 0.176 Angle : 0.656 6.984 13215 Z= 0.376 Chirality : 0.046 0.243 1450 Planarity : 0.005 0.050 1348 Dihedral : 20.564 142.140 2050 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.83 % Allowed : 7.44 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.07 (0.29), residues: 852 helix: 1.08 (0.27), residues: 378 sheet: -0.30 (0.49), residues: 113 loop : -0.91 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 138 TYR 0.023 0.002 TYR B 21 PHE 0.011 0.002 PHE A 151 TRP 0.017 0.001 TRP B 264 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 ( 9456) covalent geometry : angle 0.65635 / 0.38 (13215) hydrogen bonds : bond 0.05807 / 3.57 ( 324) hydrogen bonds : angle 4.22258 / 2.85 ( 910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7608 (pt0) REVERT: A 237 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5960 (m-30) REVERT: A 270 ASN cc_start: 0.7862 (t0) cc_final: 0.7400 (t0) REVERT: B 70 GLU cc_start: 0.8533 (tp30) cc_final: 0.8166 (pm20) REVERT: B 268 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7175 (t-90) REVERT: B 270 ASN cc_start: 0.7509 (t0) cc_final: 0.6948 (t0) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.0800 time to fit residues: 8.8348 Evaluate side-chains 68 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 142 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.134427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098636 restraints weight = 15972.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101894 restraints weight = 8220.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104068 restraints weight = 5167.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.105532 restraints weight = 3730.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106418 restraints weight = 2985.812| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9456 Z= 0.136 Angle : 0.569 6.153 13215 Z= 0.338 Chirality : 0.042 0.159 1450 Planarity : 0.005 0.050 1348 Dihedral : 20.691 142.016 2050 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.48 % Allowed : 9.40 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.29), residues: 852 helix: 1.17 (0.27), residues: 378 sheet: -0.23 (0.49), residues: 113 loop : -0.80 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 TYR 0.014 0.001 TYR B 17 PHE 0.008 0.001 PHE A 151 TRP 0.006 0.001 TRP B 264 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 ( 9456) covalent geometry : angle 0.56946 / 0.34 (13215) hydrogen bonds : bond 0.04576 / 2.89 ( 324) hydrogen bonds : angle 3.98575 / 2.67 ( 910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8034 (tm-30) REVERT: A 237 ASP cc_start: 0.6112 (OUTLIER) cc_final: 0.5900 (m-30) REVERT: A 270 ASN cc_start: 0.7764 (t0) cc_final: 0.7273 (t0) REVERT: B 70 GLU cc_start: 0.8466 (tp30) cc_final: 0.8177 (pm20) REVERT: B 268 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.7158 (t-90) REVERT: B 270 ASN cc_start: 0.7533 (t0) cc_final: 0.7145 (t0) outliers start: 19 outliers final: 11 residues processed: 79 average time/residue: 0.0692 time to fit residues: 7.8699 Evaluate side-chains 72 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN B 183 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099250 restraints weight = 15918.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102517 restraints weight = 8124.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104735 restraints weight = 5072.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106204 restraints weight = 3646.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.107030 restraints weight = 2911.082| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9456 Z= 0.124 Angle : 0.546 5.905 13215 Z= 0.326 Chirality : 0.041 0.144 1450 Planarity : 0.005 0.050 1348 Dihedral : 20.818 143.843 2050 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.96 % Allowed : 10.70 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.32 (0.30), residues: 852 helix: 1.27 (0.27), residues: 378 sheet: -0.09 (0.49), residues: 114 loop : -0.78 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 138 TYR 0.014 0.001 TYR B 17 PHE 0.015 0.001 PHE B 119 TRP 0.006 0.001 TRP B 264 HIS 0.008 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 ( 9456) covalent geometry : angle 0.54550 / 0.33 (13215) hydrogen bonds : bond 0.03948 / 2.49 ( 324) hydrogen bonds : angle 3.81505 / 2.56 ( 910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 237 ASP cc_start: 0.5993 (OUTLIER) cc_final: 0.5758 (m-30) REVERT: A 270 ASN cc_start: 0.7695 (t0) cc_final: 0.7205 (t0) REVERT: B 70 GLU cc_start: 0.8469 (tp30) cc_final: 0.8229 (pm20) REVERT: B 268 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.7039 (t-90) REVERT: B 270 ASN cc_start: 0.7534 (t0) cc_final: 0.7108 (t0) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.0779 time to fit residues: 8.1459 Evaluate side-chains 74 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 0.0070 chunk 63 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 0.0030 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 0.8810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.135433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099352 restraints weight = 15759.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102615 restraints weight = 8123.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104812 restraints weight = 5093.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.106191 restraints weight = 3670.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.107219 restraints weight = 2943.772| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9456 Z= 0.127 Angle : 0.541 6.387 13215 Z= 0.324 Chirality : 0.041 0.143 1450 Planarity : 0.005 0.050 1348 Dihedral : 20.902 144.668 2050 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.87 % Allowed : 10.44 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.34 (0.30), residues: 852 helix: 1.28 (0.27), residues: 378 sheet: -0.03 (0.50), residues: 112 loop : -0.78 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.012 0.001 TYR B 17 PHE 0.011 0.001 PHE B 119 TRP 0.004 0.001 TRP A 264 HIS 0.012 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 ( 9456) covalent geometry : angle 0.54111 / 0.32 (13215) hydrogen bonds : bond 0.03823 / 2.43 ( 324) hydrogen bonds : angle 3.74951 / 2.51 ( 910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5761 (m-30) REVERT: A 270 ASN cc_start: 0.7716 (t0) cc_final: 0.7205 (t0) REVERT: B 70 GLU cc_start: 0.8463 (tp30) cc_final: 0.8184 (pm20) REVERT: B 270 ASN cc_start: 0.7549 (t0) cc_final: 0.7123 (t0) outliers start: 22 outliers final: 18 residues processed: 77 average time/residue: 0.0804 time to fit residues: 8.8284 Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.128401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092165 restraints weight = 16274.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094975 restraints weight = 8838.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096881 restraints weight = 5776.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098211 restraints weight = 4284.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099105 restraints weight = 3478.877| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9456 Z= 0.216 Angle : 0.649 6.035 13215 Z= 0.374 Chirality : 0.045 0.157 1450 Planarity : 0.005 0.051 1348 Dihedral : 21.173 145.262 2050 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.52 % Allowed : 12.01 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.17 (0.29), residues: 852 helix: 0.82 (0.26), residues: 378 sheet: -0.48 (0.48), residues: 117 loop : -0.93 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 32 TYR 0.019 0.002 TYR B 319 PHE 0.020 0.003 PHE B 352 TRP 0.006 0.001 TRP B 124 HIS 0.028 0.002 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 ( 9456) covalent geometry : angle 0.64903 / 0.37 (13215) hydrogen bonds : bond 0.05116 / 3.27 ( 324) hydrogen bonds : angle 4.01023 / 2.72 ( 910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6723 (pp) REVERT: A 270 ASN cc_start: 0.7830 (t0) cc_final: 0.7264 (t0) REVERT: B 17 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6613 (t80) REVERT: B 270 ASN cc_start: 0.7620 (t0) cc_final: 0.7194 (t0) REVERT: B 339 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8174 (t) outliers start: 27 outliers final: 21 residues processed: 80 average time/residue: 0.0710 time to fit residues: 8.2811 Evaluate side-chains 80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 35 TYR Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.0770 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN B 23 HIS B 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.132010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095444 restraints weight = 15970.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098394 restraints weight = 8547.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100421 restraints weight = 5511.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101777 restraints weight = 4045.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102712 restraints weight = 3273.879| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9456 Z= 0.128 Angle : 0.558 6.331 13215 Z= 0.331 Chirality : 0.042 0.153 1450 Planarity : 0.005 0.052 1348 Dihedral : 21.228 146.032 2050 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.00 % Allowed : 13.19 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.29), residues: 852 helix: 1.11 (0.27), residues: 379 sheet: -0.06 (0.50), residues: 110 loop : -0.82 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 283 TYR 0.014 0.001 TYR B 17 PHE 0.012 0.001 PHE B 119 TRP 0.006 0.001 TRP A 124 HIS 0.010 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 ( 9456) covalent geometry : angle 0.55767 / 0.33 (13215) hydrogen bonds : bond 0.03947 / 2.50 ( 324) hydrogen bonds : angle 3.73564 / 2.52 ( 910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7735 (t0) cc_final: 0.7186 (t0) REVERT: B 17 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6572 (t80) REVERT: B 70 GLU cc_start: 0.8456 (tp30) cc_final: 0.8133 (pm20) REVERT: B 270 ASN cc_start: 0.7591 (t0) cc_final: 0.7196 (t0) outliers start: 23 outliers final: 20 residues processed: 78 average time/residue: 0.0742 time to fit residues: 8.3840 Evaluate side-chains 79 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 0.0050 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN B 23 HIS B 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.132433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095756 restraints weight = 16078.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.098746 restraints weight = 8607.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.100798 restraints weight = 5554.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102182 restraints weight = 4073.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103102 restraints weight = 3295.464| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9456 Z= 0.124 Angle : 0.553 8.567 13215 Z= 0.327 Chirality : 0.041 0.160 1450 Planarity : 0.005 0.051 1348 Dihedral : 21.296 146.698 2050 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.00 % Allowed : 13.84 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.30), residues: 852 helix: 1.29 (0.27), residues: 379 sheet: 0.11 (0.51), residues: 111 loop : -0.77 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 138 TYR 0.015 0.001 TYR B 17 PHE 0.011 0.001 PHE B 119 TRP 0.024 0.002 TRP B 124 HIS 0.019 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.12 ( 9456) covalent geometry : angle 0.55281 / 0.33 (13215) hydrogen bonds : bond 0.03748 / 2.37 ( 324) hydrogen bonds : angle 3.65232 / 2.46 ( 910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7700 (t0) cc_final: 0.7124 (t0) REVERT: B 70 GLU cc_start: 0.8455 (tp30) cc_final: 0.8042 (pm20) REVERT: B 270 ASN cc_start: 0.7586 (t0) cc_final: 0.7179 (t0) outliers start: 23 outliers final: 19 residues processed: 77 average time/residue: 0.0712 time to fit residues: 7.7319 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.0050 chunk 81 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN B 23 HIS B 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094034 restraints weight = 16306.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096940 restraints weight = 8782.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098920 restraints weight = 5700.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.100172 restraints weight = 4202.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101161 restraints weight = 3414.734| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9456 Z= 0.168 Angle : 0.584 6.506 13215 Z= 0.341 Chirality : 0.043 0.141 1450 Planarity : 0.005 0.051 1348 Dihedral : 21.420 146.900 2050 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.39 % Allowed : 13.97 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.21 (0.30), residues: 852 helix: 1.10 (0.27), residues: 379 sheet: -0.03 (0.51), residues: 111 loop : -0.79 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.019 0.002 TYR B 17 PHE 0.017 0.002 PHE B 352 TRP 0.010 0.001 TRP B 124 HIS 0.020 0.002 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 9456) covalent geometry : angle 0.58428 / 0.34 (13215) hydrogen bonds : bond 0.04291 / 2.74 ( 324) hydrogen bonds : angle 3.73829 / 2.52 ( 910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7796 (t0) cc_final: 0.7201 (t0) REVERT: B 17 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6652 (t80) REVERT: B 70 GLU cc_start: 0.8495 (tp30) cc_final: 0.8053 (pm20) REVERT: B 270 ASN cc_start: 0.7623 (t0) cc_final: 0.7199 (t0) outliers start: 26 outliers final: 21 residues processed: 74 average time/residue: 0.0764 time to fit residues: 8.0192 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.0030 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093457 restraints weight = 16066.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096328 restraints weight = 8749.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.098285 restraints weight = 5717.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.099620 restraints weight = 4237.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100548 restraints weight = 3442.667| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9456 Z= 0.158 Angle : 0.577 6.673 13215 Z= 0.337 Chirality : 0.042 0.147 1450 Planarity : 0.005 0.051 1348 Dihedral : 21.496 147.148 2050 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.26 % Allowed : 13.84 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.29), residues: 852 helix: 1.06 (0.27), residues: 379 sheet: -0.10 (0.51), residues: 111 loop : -0.81 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.017 0.001 TYR B 17 PHE 0.016 0.002 PHE B 352 TRP 0.013 0.001 TRP B 124 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 9456) covalent geometry : angle 0.57703 / 0.34 (13215) hydrogen bonds : bond 0.04221 / 2.69 ( 324) hydrogen bonds : angle 3.71360 / 2.51 ( 910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASN cc_start: 0.7798 (t0) cc_final: 0.7234 (t0) REVERT: B 17 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6371 (t80) REVERT: B 70 GLU cc_start: 0.8487 (tp30) cc_final: 0.8036 (pm20) REVERT: B 270 ASN cc_start: 0.7637 (t0) cc_final: 0.7167 (t0) outliers start: 25 outliers final: 20 residues processed: 75 average time/residue: 0.0731 time to fit residues: 7.9738 Evaluate side-chains 78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 83 optimal weight: 0.0670 chunk 44 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093836 restraints weight = 15939.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096688 restraints weight = 8697.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098650 restraints weight = 5685.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099988 restraints weight = 4219.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100893 restraints weight = 3431.192| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.230 9456 Z= 0.228 Angle : 0.883 59.189 13215 Z= 0.545 Chirality : 0.049 0.935 1450 Planarity : 0.006 0.077 1348 Dihedral : 21.499 147.147 2050 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.29 % Favored : 94.59 % Rotamer: Outliers : 3.13 % Allowed : 13.97 % Favored : 82.90 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 5.26 % 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: 0.17 (0.29), residues: 852 helix: 1.08 (0.27), residues: 379 sheet: -0.10 (0.51), residues: 111 loop : -0.81 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 233 TYR 0.017 0.001 TYR B 17 PHE 0.015 0.002 PHE B 352 TRP 0.012 0.001 TRP B 124 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.23 ( 9456) covalent geometry : angle 0.88257 / 0.55 (13215) hydrogen bonds : bond 0.04182 / 2.66 ( 324) hydrogen bonds : angle 3.71132 / 2.50 ( 910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.66 seconds wall clock time: 28 minutes 54.56 seconds (1734.56 seconds total)