Starting phenix.real_space_refine on Tue Mar 3 22:54:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7un6_26614/03_2026/7un6_26614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7un6_26614/03_2026/7un6_26614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7un6_26614/03_2026/7un6_26614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7un6_26614/03_2026/7un6_26614.map" model { file = "/net/cci-nas-00/data/ceres_data/7un6_26614/03_2026/7un6_26614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7un6_26614/03_2026/7un6_26614.cif" } resolution = 3.3 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= -0.002 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5808 2.51 5 N 1533 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9042 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5186 Classifications: {'peptide': 648} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 610} Chain breaks: 8 Chain: "B" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1965 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain breaks: 1 Chain: "C" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1891 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 2 Time building chain proxies: 1.87, per 1000 atoms: 0.21 Number of scatterers: 9042 At special positions: 0 Unit cell: (90.75, 131.175, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1660 8.00 N 1533 7.00 C 5808 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: 0.68 Conformation dependent library (CDL) restraints added in 307.9 milliseconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 31.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 271 through 275 removed outlier: 4.091A pdb=" N SER A 275 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.179A pdb=" N GLY A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 950 through 968 Processing helix chain 'A' and resid 1060 through 1071 Processing helix chain 'A' and resid 1083 through 1088 Processing helix chain 'A' and resid 1090 through 1118 removed outlier: 3.535A pdb=" N ARG A1117 " --> pdb=" O THR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1146 removed outlier: 3.751A pdb=" N ARG A1128 " --> pdb=" O GLU A1124 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR A1133 " --> pdb=" O GLN A1129 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1283 Processing helix chain 'B' and resid 74 through 122 Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 313 through 333 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.655A pdb=" N TYR B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 123 Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 316 through 333 Processing helix chain 'C' and resid 337 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.272A pdb=" N LEU A 65 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 188 removed outlier: 6.668A pdb=" N ILE A 183 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A 177 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR A 185 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 175 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP A 556 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL A 169 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A 554 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 171 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A 552 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A 173 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 550 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 175 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 548 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 177 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 546 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 557 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS A 566 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TRP A 559 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 564 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 356 removed outlier: 6.662A pdb=" N VAL A 546 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 177 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 548 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 175 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 550 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A 173 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A 552 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 171 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A 554 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL A 169 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP A 556 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.753A pdb=" N GLU A 297 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LYS A 223 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 299 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 221 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A 301 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN A 219 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 215 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280 removed outlier: 5.963A pdb=" N TRP A 278 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 231 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 215 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN A 219 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A 301 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 221 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 299 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LYS A 223 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU A 297 " --> pdb=" O LYS A 223 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 306 current: chain 'A' and resid 337 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 631 through 635 removed outlier: 6.530A pdb=" N TRP A 621 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 631 through 635 removed outlier: 6.530A pdb=" N TRP A 621 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 616 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 609 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS A 620 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL A 607 " --> pdb=" O LYS A 620 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 622 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY A 605 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU A 624 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 603 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N VAL A 603 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP A 592 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681 Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 932 removed outlier: 3.873A pdb=" N PHE A 978 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU A 984 " --> pdb=" O PHE A 978 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY A 991 " --> pdb=" O GLY A1000 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY A1000 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 196 through 203 removed outlier: 4.035A pdb=" N LEU B 214 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 231 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 234 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 254 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ARG B 236 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 252 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 278 Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 203 Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 235 removed outlier: 5.790A pdb=" N ARG C 234 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 270 through 278 353 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2928 1.34 - 1.46: 1983 1.46 - 1.58: 4281 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 9253 Sorted by residual: bond pdb=" C PHE A 584 " pdb=" N CYS A 585 " ideal model delta sigma weight residual 1.329 1.248 0.081 1.86e-02 2.89e+03 1.87e+01 bond pdb=" CG LEU C 81 " pdb=" CD2 LEU C 81 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" CB VAL C 201 " pdb=" CG2 VAL C 201 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.99e-01 bond pdb=" CB GLU A1081 " pdb=" CG GLU A1081 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.93e-01 bond pdb=" CB ILE B 192 " pdb=" CG1 ILE B 192 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 8.33e-01 ... (remaining 9248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 12111 1.45 - 2.90: 316 2.90 - 4.35: 74 4.35 - 5.81: 5 5.81 - 7.26: 4 Bond angle restraints: 12510 Sorted by residual: angle pdb=" N GLU A 691 " pdb=" CA GLU A 691 " pdb=" C GLU A 691 " ideal model delta sigma weight residual 111.07 115.58 -4.51 1.07e+00 8.73e-01 1.78e+01 angle pdb=" CA GLU A1081 " pdb=" CB GLU A1081 " pdb=" CG GLU A1081 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" N GLN B 111 " pdb=" CA GLN B 111 " pdb=" C GLN B 111 " ideal model delta sigma weight residual 113.77 109.79 3.98 1.32e+00 5.74e-01 9.09e+00 angle pdb=" N VAL A 692 " pdb=" CA VAL A 692 " pdb=" C VAL A 692 " ideal model delta sigma weight residual 107.75 111.45 -3.70 1.46e+00 4.69e-01 6.41e+00 angle pdb=" C ILE A 973 " pdb=" N MET A 974 " pdb=" CA MET A 974 " ideal model delta sigma weight residual 121.80 117.67 4.13 1.71e+00 3.42e-01 5.82e+00 ... (remaining 12505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5060 17.81 - 35.62: 413 35.62 - 53.43: 61 53.43 - 71.24: 17 71.24 - 89.05: 14 Dihedral angle restraints: 5565 sinusoidal: 2315 harmonic: 3250 Sorted by residual: dihedral pdb=" CA GLU A 691 " pdb=" C GLU A 691 " pdb=" N VAL A 692 " pdb=" CA VAL A 692 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ASN C 221 " pdb=" C ASN C 221 " pdb=" N GLU C 222 " pdb=" CA GLU C 222 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ILE A 973 " pdb=" C ILE A 973 " pdb=" N MET A 974 " pdb=" CA MET A 974 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 979 0.039 - 0.078: 263 0.078 - 0.117: 103 0.117 - 0.156: 24 0.156 - 0.195: 1 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CB ILE B 192 " pdb=" CA ILE B 192 " pdb=" CG1 ILE B 192 " pdb=" CG2 ILE B 192 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA PHE C 216 " pdb=" N PHE C 216 " pdb=" C PHE C 216 " pdb=" CB PHE C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE B 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1367 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 154 " -0.177 9.50e-02 1.11e+02 7.93e-02 4.03e+00 pdb=" NE ARG A 154 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 154 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 154 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 154 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 111 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO B 112 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 622 " 0.009 2.00e-02 2.50e+03 1.06e-02 1.97e+00 pdb=" CG PHE A 622 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 622 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 622 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 622 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 622 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 622 " 0.001 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 50 2.48 - 3.09: 6799 3.09 - 3.69: 13564 3.69 - 4.30: 19819 4.30 - 4.90: 32624 Nonbonded interactions: 72856 Sorted by model distance: nonbonded pdb=" OH TYR C 233 " pdb=" OD1 ASP C 323 " model vdw 1.879 3.040 nonbonded pdb=" OG SER A 287 " pdb=" OD2 ASP C 248 " model vdw 1.955 3.040 nonbonded pdb=" OH TYR A 997 " pdb=" O LEU A1029 " model vdw 1.985 3.040 nonbonded pdb=" OH TYR A 70 " pdb=" OE1 GLU A 129 " model vdw 2.082 3.040 nonbonded pdb=" OH TYR B 233 " pdb=" OD1 ASP B 323 " model vdw 2.126 3.040 ... (remaining 72851 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 'B' and (resid 73 through 126 or resid 166 through 306 or resid 315 throu \ gh 349)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.060 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 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 : 0.004 0.081 9253 Z= 0.177 Angle : 0.600 7.257 12510 Z= 0.331 Chirality : 0.044 0.195 1370 Planarity : 0.004 0.079 1608 Dihedral : 13.875 89.046 3455 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.89 (0.25), residues: 1090 helix: 0.66 (0.30), residues: 293 sheet: -1.50 (0.32), residues: 218 loop : -0.80 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.018 0.001 TYR A1034 PHE 0.024 0.002 PHE A 622 TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9253) covalent geometry : angle 0.59986 (12510) hydrogen bonds : bond 0.13714 ( 344) hydrogen bonds : angle 6.66654 ( 990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.4564 (t80) cc_final: 0.3850 (p90) REVERT: A 193 GLN cc_start: 0.6544 (mm110) cc_final: 0.6295 (mt0) REVERT: A 206 TYR cc_start: 0.5558 (t80) cc_final: 0.5086 (t80) REVERT: A 616 THR cc_start: 0.7799 (p) cc_final: 0.7590 (t) REVERT: B 94 LYS cc_start: 0.6343 (mttp) cc_final: 0.5796 (mmtm) REVERT: B 117 ARG cc_start: 0.6195 (ttp-170) cc_final: 0.3046 (tmm160) REVERT: B 202 LYS cc_start: 0.6898 (mttm) cc_final: 0.6518 (mmmt) REVERT: B 332 GLU cc_start: 0.5227 (pt0) cc_final: 0.5007 (pt0) REVERT: B 337 ARG cc_start: 0.6925 (mtp180) cc_final: 0.6220 (mtt-85) REVERT: C 76 ARG cc_start: 0.6178 (ttm170) cc_final: 0.5442 (tpt170) REVERT: C 202 LYS cc_start: 0.6848 (mtpp) cc_final: 0.6250 (mmtt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1004 time to fit residues: 25.4381 Evaluate side-chains 116 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 346 GLN A1101 ASN B 85 GLN B 226 ASN C 100 HIS C 221 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.283073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.234575 restraints weight = 8505.883| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 2.97 r_work: 0.4336 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9253 Z= 0.157 Angle : 0.649 7.890 12510 Z= 0.337 Chirality : 0.046 0.180 1370 Planarity : 0.005 0.068 1608 Dihedral : 5.128 27.347 1201 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.59 % Allowed : 8.23 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.57 (0.25), residues: 1090 helix: 0.74 (0.30), residues: 293 sheet: -1.36 (0.31), residues: 218 loop : -0.48 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 117 TYR 0.016 0.002 TYR A1002 PHE 0.035 0.002 PHE C 212 TRP 0.010 0.001 TRP B 171 HIS 0.007 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9253) covalent geometry : angle 0.64932 (12510) hydrogen bonds : bond 0.04695 ( 344) hydrogen bonds : angle 5.37001 ( 990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.6820 (mt) cc_final: 0.6534 (tp) REVERT: A 550 THR cc_start: 0.5038 (t) cc_final: 0.3981 (p) REVERT: A 558 MET cc_start: 0.8096 (ttt) cc_final: 0.7876 (ttp) REVERT: A 561 ASP cc_start: 0.7932 (p0) cc_final: 0.7667 (p0) REVERT: B 117 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.5973 (ttp-170) REVERT: B 337 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7550 (mtt-85) REVERT: C 76 ARG cc_start: 0.6433 (ttm170) cc_final: 0.5636 (tpt170) REVERT: C 98 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7589 (mt-10) REVERT: C 115 ASP cc_start: 0.7103 (m-30) cc_final: 0.6857 (m-30) REVERT: C 170 PHE cc_start: 0.6473 (t80) cc_final: 0.6101 (t80) REVERT: C 202 LYS cc_start: 0.6870 (mtpp) cc_final: 0.6598 (mmtt) REVERT: C 216 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6647 (m-10) outliers start: 16 outliers final: 7 residues processed: 132 average time/residue: 0.0761 time to fit residues: 14.6707 Evaluate side-chains 113 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 216 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.280610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.231511 restraints weight = 8440.564| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 2.77 r_work: 0.4323 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9253 Z= 0.148 Angle : 0.599 7.667 12510 Z= 0.310 Chirality : 0.045 0.165 1370 Planarity : 0.004 0.060 1608 Dihedral : 4.951 25.559 1201 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.59 % Allowed : 10.81 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.45 (0.25), residues: 1090 helix: 0.69 (0.29), residues: 300 sheet: -1.15 (0.32), residues: 218 loop : -0.37 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.018 0.002 TYR A 206 PHE 0.040 0.002 PHE C 212 TRP 0.010 0.001 TRP B 171 HIS 0.006 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9253) covalent geometry : angle 0.59928 (12510) hydrogen bonds : bond 0.04477 ( 344) hydrogen bonds : angle 5.14681 ( 990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.6800 (mt) cc_final: 0.6536 (mt) REVERT: A 552 MET cc_start: 0.5353 (ptm) cc_final: 0.4163 (mmt) REVERT: A 561 ASP cc_start: 0.7804 (p0) cc_final: 0.7508 (p0) REVERT: B 226 ASN cc_start: 0.5516 (m-40) cc_final: 0.4772 (t0) REVERT: B 231 LYS cc_start: 0.7592 (tttm) cc_final: 0.7258 (mtpp) REVERT: B 337 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7556 (mtt-85) REVERT: C 76 ARG cc_start: 0.6529 (ttm170) cc_final: 0.5640 (tpt170) REVERT: C 202 LYS cc_start: 0.6832 (mtpp) cc_final: 0.6458 (mmtt) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 0.0724 time to fit residues: 13.9839 Evaluate side-chains 123 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.274866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.224981 restraints weight = 8692.773| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 3.58 r_work: 0.4175 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9253 Z= 0.200 Angle : 0.634 7.238 12510 Z= 0.327 Chirality : 0.046 0.174 1370 Planarity : 0.005 0.054 1608 Dihedral : 5.035 25.365 1201 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.48 % Allowed : 12.50 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.50 (0.25), residues: 1090 helix: 0.54 (0.29), residues: 301 sheet: -1.05 (0.33), residues: 216 loop : -0.41 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 117 TYR 0.014 0.002 TYR B 106 PHE 0.047 0.002 PHE C 212 TRP 0.013 0.002 TRP A 278 HIS 0.009 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9253) covalent geometry : angle 0.63382 (12510) hydrogen bonds : bond 0.04618 ( 344) hydrogen bonds : angle 5.18125 ( 990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.347 Fit side-chains REVERT: A 185 TYR cc_start: 0.6703 (t80) cc_final: 0.4167 (p90) REVERT: A 552 MET cc_start: 0.5356 (ptm) cc_final: 0.4233 (mmt) REVERT: A 561 ASP cc_start: 0.7946 (p0) cc_final: 0.7687 (p0) REVERT: A 623 LYS cc_start: 0.8421 (ptpt) cc_final: 0.8006 (ptpp) REVERT: B 231 LYS cc_start: 0.7827 (tttm) cc_final: 0.7411 (mtpp) REVERT: C 76 ARG cc_start: 0.6806 (ttm170) cc_final: 0.5781 (tpt170) REVERT: C 202 LYS cc_start: 0.6865 (mtpp) cc_final: 0.6489 (mptt) REVERT: C 224 PHE cc_start: 0.3951 (OUTLIER) cc_final: 0.2788 (p90) REVERT: C 233 TYR cc_start: 0.7629 (m-10) cc_final: 0.7290 (m-80) outliers start: 25 outliers final: 17 residues processed: 136 average time/residue: 0.0783 time to fit residues: 15.6528 Evaluate side-chains 122 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 224 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 193 GLN ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.276990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.226925 restraints weight = 8667.865| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 3.45 r_work: 0.4212 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9253 Z= 0.150 Angle : 0.583 7.492 12510 Z= 0.299 Chirality : 0.044 0.195 1370 Planarity : 0.004 0.045 1608 Dihedral : 4.884 23.697 1201 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.31 (0.26), residues: 1090 helix: 0.71 (0.30), residues: 295 sheet: -0.98 (0.33), residues: 216 loop : -0.26 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.011 0.001 TYR A1002 PHE 0.040 0.002 PHE C 212 TRP 0.014 0.001 TRP B 171 HIS 0.007 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9253) covalent geometry : angle 0.58251 (12510) hydrogen bonds : bond 0.04311 ( 344) hydrogen bonds : angle 5.02971 ( 990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.310 Fit side-chains REVERT: A 185 TYR cc_start: 0.6523 (t80) cc_final: 0.4251 (p90) REVERT: A 304 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5849 (pp) REVERT: A 552 MET cc_start: 0.5360 (ptm) cc_final: 0.4244 (mmt) REVERT: A 561 ASP cc_start: 0.7939 (p0) cc_final: 0.7663 (p0) REVERT: A 623 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7989 (ptpp) REVERT: A 657 ASP cc_start: 0.5906 (OUTLIER) cc_final: 0.4639 (m-30) REVERT: A 962 MET cc_start: 0.7512 (mtm) cc_final: 0.7142 (mmt) REVERT: B 231 LYS cc_start: 0.7679 (tttm) cc_final: 0.7279 (mtpp) REVERT: B 305 GLU cc_start: 0.7202 (mp0) cc_final: 0.6686 (mp0) REVERT: C 76 ARG cc_start: 0.6739 (ttm170) cc_final: 0.5900 (tpt170) REVERT: C 202 LYS cc_start: 0.6811 (mtpp) cc_final: 0.6472 (mptt) REVERT: C 233 TYR cc_start: 0.7488 (m-10) cc_final: 0.7233 (m-80) REVERT: C 253 MET cc_start: 0.5971 (mmm) cc_final: 0.4794 (ptp) outliers start: 28 outliers final: 22 residues processed: 134 average time/residue: 0.0702 time to fit residues: 14.0681 Evaluate side-chains 128 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 221 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 155 HIS A 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.277240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.228439 restraints weight = 8733.781| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 3.54 r_work: 0.4198 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9253 Z= 0.146 Angle : 0.574 7.659 12510 Z= 0.296 Chirality : 0.044 0.231 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.813 23.022 1201 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.08 % Allowed : 14.98 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.24 (0.26), residues: 1090 helix: 0.73 (0.30), residues: 295 sheet: -0.94 (0.33), residues: 216 loop : -0.19 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.013 0.001 TYR C 223 PHE 0.045 0.002 PHE C 212 TRP 0.013 0.001 TRP A 278 HIS 0.013 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9253) covalent geometry : angle 0.57393 (12510) hydrogen bonds : bond 0.04215 ( 344) hydrogen bonds : angle 4.94362 ( 990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.271 Fit side-chains REVERT: A 185 TYR cc_start: 0.6512 (t80) cc_final: 0.4165 (p90) REVERT: A 304 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5844 (pp) REVERT: A 552 MET cc_start: 0.5297 (ptm) cc_final: 0.4189 (mmt) REVERT: A 561 ASP cc_start: 0.7941 (p0) cc_final: 0.7670 (p0) REVERT: A 623 LYS cc_start: 0.8378 (ptpt) cc_final: 0.7954 (ptpp) REVERT: A 657 ASP cc_start: 0.5845 (OUTLIER) cc_final: 0.4426 (m-30) REVERT: A 962 MET cc_start: 0.7564 (mtm) cc_final: 0.7108 (mmt) REVERT: B 231 LYS cc_start: 0.7609 (tttm) cc_final: 0.7191 (mtpp) REVERT: C 76 ARG cc_start: 0.6835 (ttm170) cc_final: 0.5902 (tpt170) REVERT: C 202 LYS cc_start: 0.6837 (mtpp) cc_final: 0.6460 (mptt) REVERT: C 224 PHE cc_start: 0.3785 (OUTLIER) cc_final: 0.2659 (p90) REVERT: C 233 TYR cc_start: 0.7603 (m-10) cc_final: 0.7251 (m-80) REVERT: C 253 MET cc_start: 0.6018 (mmm) cc_final: 0.4831 (ptp) outliers start: 31 outliers final: 24 residues processed: 131 average time/residue: 0.0755 time to fit residues: 14.5418 Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 224 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 41 optimal weight: 0.0010 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 39 optimal weight: 0.0040 chunk 21 optimal weight: 4.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.280170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.231153 restraints weight = 8685.723| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 3.40 r_work: 0.4263 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9253 Z= 0.113 Angle : 0.542 7.831 12510 Z= 0.280 Chirality : 0.043 0.210 1370 Planarity : 0.004 0.044 1608 Dihedral : 4.682 21.801 1201 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.17 % Allowed : 15.08 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.26), residues: 1090 helix: 0.80 (0.30), residues: 295 sheet: -0.82 (0.34), residues: 205 loop : -0.05 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 154 TYR 0.013 0.001 TYR B 223 PHE 0.036 0.002 PHE C 212 TRP 0.012 0.001 TRP B 171 HIS 0.010 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9253) covalent geometry : angle 0.54216 (12510) hydrogen bonds : bond 0.04050 ( 344) hydrogen bonds : angle 4.83003 ( 990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6396 (t80) cc_final: 0.4145 (p90) REVERT: A 200 TYR cc_start: 0.7587 (m-80) cc_final: 0.7375 (m-80) REVERT: A 304 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5980 (pp) REVERT: A 552 MET cc_start: 0.5218 (ptm) cc_final: 0.4124 (mmt) REVERT: A 561 ASP cc_start: 0.7818 (p0) cc_final: 0.7569 (p0) REVERT: A 623 LYS cc_start: 0.8333 (ptpt) cc_final: 0.7929 (ptpp) REVERT: A 657 ASP cc_start: 0.5662 (OUTLIER) cc_final: 0.4894 (m-30) REVERT: A 962 MET cc_start: 0.7454 (mtm) cc_final: 0.7043 (mmt) REVERT: B 117 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.6100 (ttp80) REVERT: B 226 ASN cc_start: 0.6324 (m110) cc_final: 0.4895 (t0) REVERT: B 231 LYS cc_start: 0.7422 (tttm) cc_final: 0.7030 (mtpp) REVERT: B 305 GLU cc_start: 0.7124 (mp0) cc_final: 0.6563 (mp0) REVERT: C 76 ARG cc_start: 0.6658 (ttm170) cc_final: 0.5755 (tpt170) REVERT: C 202 LYS cc_start: 0.6783 (mtpp) cc_final: 0.6336 (mmtt) REVERT: C 233 TYR cc_start: 0.7387 (m-10) cc_final: 0.7125 (m-80) REVERT: C 253 MET cc_start: 0.5881 (mmm) cc_final: 0.4664 (ptp) outliers start: 32 outliers final: 22 residues processed: 139 average time/residue: 0.0789 time to fit residues: 15.6133 Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 155 HIS A 193 GLN ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.277533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.229604 restraints weight = 8651.322| |-----------------------------------------------------------------------------| r_work (start): 0.4645 rms_B_bonded: 3.29 r_work: 0.4255 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9253 Z= 0.133 Angle : 0.560 8.091 12510 Z= 0.290 Chirality : 0.044 0.221 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.684 21.910 1201 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.47 % Allowed : 14.78 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.02 (0.26), residues: 1090 helix: 0.83 (0.30), residues: 295 sheet: -0.74 (0.35), residues: 208 loop : -0.05 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 154 TYR 0.011 0.001 TYR B 223 PHE 0.032 0.002 PHE C 212 TRP 0.010 0.001 TRP A1136 HIS 0.007 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9253) covalent geometry : angle 0.56007 (12510) hydrogen bonds : bond 0.04061 ( 344) hydrogen bonds : angle 4.84145 ( 990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6371 (t80) cc_final: 0.4152 (p90) REVERT: A 200 TYR cc_start: 0.7570 (m-80) cc_final: 0.7350 (m-80) REVERT: A 552 MET cc_start: 0.5199 (ptm) cc_final: 0.4127 (mmt) REVERT: A 561 ASP cc_start: 0.7850 (p0) cc_final: 0.7600 (p0) REVERT: A 623 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7902 (ptpp) REVERT: A 657 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.4983 (m-30) REVERT: A 962 MET cc_start: 0.7464 (mtm) cc_final: 0.7030 (mmt) REVERT: B 117 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.6327 (tmm-80) REVERT: C 76 ARG cc_start: 0.6720 (ttm170) cc_final: 0.5873 (tpt170) REVERT: C 202 LYS cc_start: 0.6781 (mtpp) cc_final: 0.6385 (mmtt) REVERT: C 233 TYR cc_start: 0.7457 (m-10) cc_final: 0.7198 (m-80) REVERT: C 253 MET cc_start: 0.5899 (mmm) cc_final: 0.4704 (ptp) REVERT: C 330 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6741 (tt) outliers start: 35 outliers final: 24 residues processed: 135 average time/residue: 0.0781 time to fit residues: 15.3981 Evaluate side-chains 134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 0.0050 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 155 HIS A 193 GLN ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.278606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.229706 restraints weight = 8675.074| |-----------------------------------------------------------------------------| r_work (start): 0.4642 rms_B_bonded: 3.27 r_work: 0.4255 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9253 Z= 0.124 Angle : 0.557 8.260 12510 Z= 0.288 Chirality : 0.044 0.215 1370 Planarity : 0.004 0.045 1608 Dihedral : 4.651 22.394 1201 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.98 % Allowed : 15.18 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.02 (0.26), residues: 1090 helix: 0.86 (0.30), residues: 295 sheet: -0.80 (0.34), residues: 214 loop : -0.03 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 154 TYR 0.018 0.001 TYR C 223 PHE 0.031 0.002 PHE C 212 TRP 0.011 0.001 TRP B 171 HIS 0.008 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9253) covalent geometry : angle 0.55744 (12510) hydrogen bonds : bond 0.03987 ( 344) hydrogen bonds : angle 4.80148 ( 990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6323 (t80) cc_final: 0.4169 (p90) REVERT: A 200 TYR cc_start: 0.7555 (m-80) cc_final: 0.7319 (m-80) REVERT: A 552 MET cc_start: 0.5314 (ptm) cc_final: 0.4174 (mmt) REVERT: A 561 ASP cc_start: 0.7832 (p0) cc_final: 0.7575 (p0) REVERT: A 623 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7871 (ptpp) REVERT: A 657 ASP cc_start: 0.5763 (OUTLIER) cc_final: 0.5006 (m-30) REVERT: A 962 MET cc_start: 0.7485 (mtm) cc_final: 0.7064 (mmt) REVERT: B 117 ARG cc_start: 0.7355 (ttp-170) cc_final: 0.6149 (ttp80) REVERT: B 179 ASP cc_start: 0.7446 (m-30) cc_final: 0.7121 (t0) REVERT: B 226 ASN cc_start: 0.6357 (m110) cc_final: 0.4922 (t0) REVERT: B 305 GLU cc_start: 0.7149 (mp0) cc_final: 0.6516 (mp0) REVERT: C 76 ARG cc_start: 0.6701 (ttm170) cc_final: 0.5820 (tpt170) REVERT: C 184 MET cc_start: 0.4955 (mtm) cc_final: 0.4673 (mtm) REVERT: C 196 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5438 (tp) REVERT: C 202 LYS cc_start: 0.6720 (mtpp) cc_final: 0.6306 (mmtt) REVERT: C 224 PHE cc_start: 0.3568 (OUTLIER) cc_final: 0.2464 (p90) REVERT: C 233 TYR cc_start: 0.7439 (m-10) cc_final: 0.7179 (m-80) REVERT: C 253 MET cc_start: 0.5912 (mmm) cc_final: 0.4732 (ptp) REVERT: C 330 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6730 (tt) outliers start: 30 outliers final: 25 residues processed: 131 average time/residue: 0.0731 time to fit residues: 14.2642 Evaluate side-chains 134 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 0.0000 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 193 GLN B 188 HIS B 294 ASN ** C 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.270310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.224329 restraints weight = 8708.868| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 3.46 r_work: 0.4099 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9253 Z= 0.268 Angle : 0.682 7.757 12510 Z= 0.359 Chirality : 0.048 0.325 1370 Planarity : 0.005 0.056 1608 Dihedral : 5.105 23.102 1201 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.78 % Allowed : 15.18 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.50 (0.25), residues: 1090 helix: 0.45 (0.30), residues: 300 sheet: -1.01 (0.34), residues: 218 loop : -0.36 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 331 TYR 0.021 0.002 TYR C 223 PHE 0.040 0.003 PHE C 212 TRP 0.014 0.002 TRP A 209 HIS 0.037 0.003 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 9253) covalent geometry : angle 0.68158 (12510) hydrogen bonds : bond 0.04679 ( 344) hydrogen bonds : angle 5.25196 ( 990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6509 (t80) cc_final: 0.4195 (p90) REVERT: A 200 TYR cc_start: 0.7691 (m-80) cc_final: 0.7383 (m-80) REVERT: A 552 MET cc_start: 0.5416 (ptm) cc_final: 0.4318 (mmt) REVERT: A 623 LYS cc_start: 0.8379 (ptpt) cc_final: 0.7947 (ptpp) REVERT: A 657 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.4819 (m-30) REVERT: A 962 MET cc_start: 0.7579 (mtm) cc_final: 0.7163 (mmt) REVERT: C 76 ARG cc_start: 0.6988 (ttm170) cc_final: 0.6038 (tpt170) REVERT: C 184 MET cc_start: 0.5344 (mtm) cc_final: 0.4994 (mtm) REVERT: C 202 LYS cc_start: 0.6982 (mtpp) cc_final: 0.6605 (mptt) REVERT: C 224 PHE cc_start: 0.3774 (OUTLIER) cc_final: 0.2571 (p90) REVERT: C 233 TYR cc_start: 0.7754 (m-10) cc_final: 0.7409 (m-80) REVERT: C 253 MET cc_start: 0.6237 (mmm) cc_final: 0.5005 (ptp) REVERT: C 330 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7123 (tt) outliers start: 28 outliers final: 21 residues processed: 135 average time/residue: 0.0725 time to fit residues: 14.6767 Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1111 SER Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS C 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.276526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.226796 restraints weight = 8633.846| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 3.52 r_work: 0.4221 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9253 Z= 0.137 Angle : 0.597 10.405 12510 Z= 0.307 Chirality : 0.045 0.245 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.843 25.122 1201 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.48 % Allowed : 16.47 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 (0.26), residues: 1090 helix: 0.70 (0.30), residues: 294 sheet: -0.86 (0.35), residues: 208 loop : -0.16 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 154 TYR 0.017 0.001 TYR C 223 PHE 0.039 0.002 PHE C 95 TRP 0.015 0.002 TRP A 308 HIS 0.012 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9253) covalent geometry : angle 0.59651 (12510) hydrogen bonds : bond 0.04113 ( 344) hydrogen bonds : angle 4.95246 ( 990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.81 seconds wall clock time: 39 minutes 6.25 seconds (2346.25 seconds total)