Starting phenix.real_space_refine on Thu Mar 13 18:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7un6_26614/03_2025/7un6_26614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7un6_26614/03_2025/7un6_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_2025/7un6_26614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7un6_26614/03_2025/7un6_26614.map" model { file = "/net/cci-nas-00/data/ceres_data/7un6_26614/03_2025/7un6_26614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7un6_26614/03_2025/7un6_26614.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.31, per 1000 atoms: 0.70 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: 2.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.16 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: 2.58 Time building geometry restraints manager: 2.87 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: 2.290 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: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- 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= 0.243 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 : 11.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS A 577 PHE 0.024 0.002 PHE A 622 TYR 0.018 0.001 TYR A1034 ARG 0.007 0.000 ARG A 154 *********************** 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 : 1.038 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: 0.2316 time to fit residues: 57.7462 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 : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0030 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 A1018 HIS A1101 ASN A1129 GLN B 85 GLN B 226 ASN C 100 HIS C 221 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.280554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.231431 restraints weight = 8429.375| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 2.99 r_work: 0.4297 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9253 Z= 0.274 Angle : 0.683 8.158 12510 Z= 0.353 Chirality : 0.047 0.181 1370 Planarity : 0.005 0.069 1608 Dihedral : 5.238 27.565 1201 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.88 % Allowed : 8.73 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1090 helix: 0.50 (0.29), residues: 300 sheet: -1.37 (0.31), residues: 218 loop : -0.52 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.006 0.001 HIS A 577 PHE 0.037 0.002 PHE C 212 TYR 0.016 0.002 TYR A1002 ARG 0.006 0.001 ARG C 117 *********************** 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 141 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.6871 (mt) cc_final: 0.6519 (mt) REVERT: A 558 MET cc_start: 0.8138 (ttt) cc_final: 0.7886 (ttp) REVERT: A 561 ASP cc_start: 0.8000 (p0) cc_final: 0.7755 (p0) REVERT: B 231 LYS cc_start: 0.7621 (tttm) cc_final: 0.7208 (mtpp) REVERT: B 337 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7570 (mtt-85) REVERT: C 76 ARG cc_start: 0.6482 (ttm170) cc_final: 0.5643 (tpt170) REVERT: C 170 PHE cc_start: 0.6422 (t80) cc_final: 0.6056 (t80) REVERT: C 202 LYS cc_start: 0.6926 (mtpp) cc_final: 0.6611 (mmtt) outliers start: 19 outliers final: 9 residues processed: 134 average time/residue: 0.1714 time to fit residues: 33.8759 Evaluate side-chains 113 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 102 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.278866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.229638 restraints weight = 8565.401| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 3.09 r_work: 0.4273 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9253 Z= 0.267 Angle : 0.621 7.371 12510 Z= 0.320 Chirality : 0.045 0.161 1370 Planarity : 0.005 0.063 1608 Dihedral : 5.066 25.973 1201 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.59 % Allowed : 11.81 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1090 helix: 0.57 (0.29), residues: 300 sheet: -1.22 (0.32), residues: 215 loop : -0.41 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.006 0.001 HIS C 328 PHE 0.043 0.002 PHE C 212 TYR 0.017 0.002 TYR A 206 ARG 0.004 0.000 ARG B 117 *********************** 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 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.941 Fit side-chains REVERT: A 140 LEU cc_start: 0.6849 (mt) cc_final: 0.6566 (mt) REVERT: A 185 TYR cc_start: 0.6696 (t80) cc_final: 0.4187 (p90) REVERT: A 558 MET cc_start: 0.8149 (ttt) cc_final: 0.7924 (ttp) REVERT: A 561 ASP cc_start: 0.7902 (p0) cc_final: 0.7434 (p0) REVERT: B 226 ASN cc_start: 0.5626 (m-40) cc_final: 0.4753 (t0) REVERT: B 231 LYS cc_start: 0.7703 (tttm) cc_final: 0.7210 (mtpp) REVERT: B 337 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7592 (mtt-85) REVERT: C 76 ARG cc_start: 0.6635 (ttm170) cc_final: 0.5711 (tpt170) REVERT: C 202 LYS cc_start: 0.6851 (mtpp) cc_final: 0.6513 (mmtt) REVERT: C 216 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7097 (m-10) outliers start: 16 outliers final: 11 residues processed: 125 average time/residue: 0.1663 time to fit residues: 31.3055 Evaluate side-chains 119 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1127 ILE 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 73 VAL Chi-restraints excluded: chain C residue 205 ASP 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 109 optimal weight: 0.9980 chunk 46 optimal weight: 0.0030 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 99 optimal weight: 0.0060 overall best weight: 0.6008 ------------------------------------------------------------------------------- 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 A 193 GLN ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.279913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.230232 restraints weight = 8578.562| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 3.48 r_work: 0.4246 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9253 Z= 0.198 Angle : 0.571 7.511 12510 Z= 0.294 Chirality : 0.044 0.161 1370 Planarity : 0.004 0.052 1608 Dihedral : 4.843 22.964 1201 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.48 % Allowed : 13.19 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1090 helix: 0.80 (0.30), residues: 295 sheet: -1.07 (0.33), residues: 215 loop : -0.22 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.011 0.001 HIS A 83 PHE 0.039 0.002 PHE C 212 TYR 0.013 0.001 TYR A 206 ARG 0.004 0.000 ARG B 117 *********************** 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 136 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.063 Fit side-chains REVERT: A 82 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 185 TYR cc_start: 0.6600 (t80) cc_final: 0.4188 (p90) REVERT: A 193 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: A 552 MET cc_start: 0.5297 (ptm) cc_final: 0.4209 (mmt) REVERT: A 561 ASP cc_start: 0.7851 (p0) cc_final: 0.7592 (p0) REVERT: A 623 LYS cc_start: 0.8443 (ptpt) cc_final: 0.8030 (ptpp) REVERT: B 226 ASN cc_start: 0.6162 (m110) cc_final: 0.5052 (t0) REVERT: B 231 LYS cc_start: 0.7514 (tttm) cc_final: 0.7075 (mtpp) REVERT: B 337 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7584 (mtt-85) REVERT: C 76 ARG cc_start: 0.6666 (ttm170) cc_final: 0.5714 (tpt170) REVERT: C 202 LYS cc_start: 0.6811 (mtpp) cc_final: 0.6513 (mptt) REVERT: C 233 TYR cc_start: 0.7429 (m-10) cc_final: 0.7201 (m-80) REVERT: C 253 MET cc_start: 0.5935 (mmm) cc_final: 0.4748 (ptp) outliers start: 25 outliers final: 17 residues processed: 130 average time/residue: 0.1795 time to fit residues: 34.6404 Evaluate side-chains 124 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 193 GLN 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 1273 LEU Chi-restraints excluded: chain B residue 201 VAL 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 216 PHE Chi-restraints excluded: chain C residue 217 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1032 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.276784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.226252 restraints weight = 8603.805| |-----------------------------------------------------------------------------| r_work (start): 0.4607 rms_B_bonded: 3.42 r_work: 0.4208 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9253 Z= 0.249 Angle : 0.583 7.400 12510 Z= 0.301 Chirality : 0.044 0.158 1370 Planarity : 0.004 0.044 1608 Dihedral : 4.874 23.540 1201 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.68 % Allowed : 14.68 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1090 helix: 0.77 (0.30), residues: 294 sheet: -1.01 (0.33), residues: 214 loop : -0.22 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.007 0.001 HIS C 328 PHE 0.038 0.002 PHE C 212 TYR 0.012 0.001 TYR B 106 ARG 0.004 0.000 ARG B 117 *********************** 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 146 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.004 Fit side-chains REVERT: A 185 TYR cc_start: 0.6520 (t80) cc_final: 0.4239 (p90) REVERT: A 304 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5856 (pp) REVERT: A 552 MET cc_start: 0.5214 (ptm) cc_final: 0.4193 (mmt) REVERT: A 561 ASP cc_start: 0.7905 (p0) cc_final: 0.7638 (p0) REVERT: A 623 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8005 (ptpp) REVERT: A 657 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.4654 (m-30) REVERT: B 231 LYS cc_start: 0.7567 (tttm) cc_final: 0.7118 (mtpp) REVERT: C 76 ARG cc_start: 0.6791 (ttm170) cc_final: 0.5919 (tpt170) REVERT: C 202 LYS cc_start: 0.6826 (mtpp) cc_final: 0.6429 (mmtt) REVERT: C 224 PHE cc_start: 0.3883 (OUTLIER) cc_final: 0.2535 (p90) REVERT: C 233 TYR cc_start: 0.7480 (m-10) cc_final: 0.7214 (m-80) REVERT: C 253 MET cc_start: 0.6021 (mmm) cc_final: 0.4875 (ptp) outliers start: 27 outliers final: 19 residues processed: 138 average time/residue: 0.2207 time to fit residues: 45.5407 Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 224 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 A 680 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.275500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.226321 restraints weight = 8474.192| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 3.28 r_work: 0.4236 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3326 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= 0.226 Angle : 0.571 7.697 12510 Z= 0.295 Chirality : 0.044 0.158 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.790 22.344 1201 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.98 % Allowed : 14.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1090 helix: 0.73 (0.30), residues: 295 sheet: -0.99 (0.33), residues: 214 loop : -0.14 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.012 0.001 HIS A 83 PHE 0.046 0.002 PHE C 212 TYR 0.011 0.001 TYR C 223 ARG 0.003 0.000 ARG B 117 *********************** 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 144 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.975 Fit side-chains REVERT: A 185 TYR cc_start: 0.6455 (t80) cc_final: 0.4166 (p90) REVERT: A 552 MET cc_start: 0.5163 (ptm) cc_final: 0.4109 (mmt) REVERT: A 561 ASP cc_start: 0.7872 (p0) cc_final: 0.7596 (p0) REVERT: A 623 LYS cc_start: 0.8393 (ptpt) cc_final: 0.7981 (ptpp) REVERT: A 657 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.4569 (m-30) REVERT: A 962 MET cc_start: 0.7322 (mmm) cc_final: 0.6945 (mmt) REVERT: B 231 LYS cc_start: 0.7479 (tttm) cc_final: 0.7033 (mtpp) REVERT: B 305 GLU cc_start: 0.7312 (mp0) cc_final: 0.6721 (mp0) REVERT: C 76 ARG cc_start: 0.6757 (ttm170) cc_final: 0.5725 (tpt170) REVERT: C 98 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7657 (mt-10) REVERT: C 202 LYS cc_start: 0.6800 (mtpp) cc_final: 0.6378 (mmtt) REVERT: C 224 PHE cc_start: 0.3727 (OUTLIER) cc_final: 0.2254 (p90) REVERT: C 233 TYR cc_start: 0.7506 (m-10) cc_final: 0.7248 (m-80) REVERT: C 253 MET cc_start: 0.5989 (mmm) cc_final: 0.4859 (ptp) outliers start: 30 outliers final: 23 residues processed: 136 average time/residue: 0.2681 time to fit residues: 53.4090 Evaluate side-chains 135 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.995 ------------------------------------------------------------------------------- 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 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 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 56 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 96 optimal weight: 0.0980 chunk 87 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN C 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.276643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.227004 restraints weight = 8728.302| |-----------------------------------------------------------------------------| r_work (start): 0.4613 rms_B_bonded: 3.52 r_work: 0.4201 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9253 Z= 0.238 Angle : 0.574 7.872 12510 Z= 0.296 Chirality : 0.044 0.158 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.828 22.881 1201 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.27 % Allowed : 14.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1090 helix: 0.71 (0.30), residues: 295 sheet: -0.96 (0.33), residues: 214 loop : -0.11 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.014 0.001 HIS A 155 PHE 0.042 0.002 PHE C 212 TYR 0.012 0.001 TYR B 106 ARG 0.010 0.000 ARG A 154 *********************** 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 145 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.970 Fit side-chains REVERT: A 185 TYR cc_start: 0.6467 (t80) cc_final: 0.4175 (p90) REVERT: A 200 TYR cc_start: 0.7689 (m-80) cc_final: 0.7421 (m-80) REVERT: A 552 MET cc_start: 0.5179 (ptm) cc_final: 0.4110 (mmt) REVERT: A 561 ASP cc_start: 0.7895 (p0) cc_final: 0.7632 (p0) REVERT: A 623 LYS cc_start: 0.8378 (ptpt) cc_final: 0.7959 (ptpp) REVERT: A 645 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6281 (tt) REVERT: A 657 ASP cc_start: 0.5913 (OUTLIER) cc_final: 0.4639 (m-30) REVERT: A 962 MET cc_start: 0.7474 (mmm) cc_final: 0.7089 (mmt) REVERT: B 231 LYS cc_start: 0.7505 (tttm) cc_final: 0.7022 (mtpp) REVERT: C 76 ARG cc_start: 0.6837 (ttm170) cc_final: 0.5968 (tpt170) REVERT: C 202 LYS cc_start: 0.6832 (mtpp) cc_final: 0.6445 (mptt) REVERT: C 224 PHE cc_start: 0.3783 (OUTLIER) cc_final: 0.2398 (p90) REVERT: C 253 MET cc_start: 0.6035 (mmm) cc_final: 0.4917 (ptp) REVERT: C 330 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6850 (tt) outliers start: 33 outliers final: 21 residues processed: 136 average time/residue: 0.2058 time to fit residues: 40.6810 Evaluate side-chains 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 106 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.4560 ------------------------------------------------------------------------------- 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 = 0.5035 r_free = 0.5035 target = 0.279466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.229560 restraints weight = 8690.965| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 3.41 r_work: 0.4259 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9253 Z= 0.184 Angle : 0.548 8.101 12510 Z= 0.284 Chirality : 0.043 0.164 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.712 23.202 1201 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.17 % Allowed : 14.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1090 helix: 0.81 (0.30), residues: 295 sheet: -0.85 (0.34), residues: 210 loop : 0.02 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.008 0.001 HIS C 328 PHE 0.043 0.002 PHE C 212 TYR 0.017 0.001 TYR C 223 ARG 0.005 0.000 ARG A 154 *********************** 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 139 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6375 (t80) cc_final: 0.4162 (p90) REVERT: A 200 TYR cc_start: 0.7599 (m-80) cc_final: 0.7359 (m-80) REVERT: A 552 MET cc_start: 0.5079 (ptm) cc_final: 0.4033 (mmt) REVERT: A 561 ASP cc_start: 0.7845 (p0) cc_final: 0.7587 (p0) REVERT: A 623 LYS cc_start: 0.8323 (ptpt) cc_final: 0.7913 (ptpp) REVERT: A 645 ILE cc_start: 0.6565 (OUTLIER) cc_final: 0.6289 (tt) REVERT: A 657 ASP cc_start: 0.5837 (OUTLIER) cc_final: 0.4506 (m-30) REVERT: A 962 MET cc_start: 0.7439 (mmm) cc_final: 0.7131 (mmt) REVERT: B 117 ARG cc_start: 0.7393 (ttp-170) cc_final: 0.6186 (ttp80) REVERT: B 179 ASP cc_start: 0.7510 (m-30) cc_final: 0.7161 (t0) REVERT: B 226 ASN cc_start: 0.6347 (m110) cc_final: 0.4947 (t0) REVERT: B 231 LYS cc_start: 0.7326 (tttm) cc_final: 0.6848 (mtpp) REVERT: B 305 GLU cc_start: 0.7242 (mp0) cc_final: 0.6636 (mp0) REVERT: C 76 ARG cc_start: 0.6713 (ttm170) cc_final: 0.5860 (tpt170) REVERT: C 202 LYS cc_start: 0.6794 (mtpp) cc_final: 0.6443 (mptt) REVERT: C 224 PHE cc_start: 0.3715 (OUTLIER) cc_final: 0.2124 (p90) REVERT: C 233 TYR cc_start: 0.7510 (m-80) cc_final: 0.7282 (m-80) REVERT: C 253 MET cc_start: 0.5981 (mmm) cc_final: 0.4811 (ptp) REVERT: C 330 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6807 (tt) outliers start: 32 outliers final: 21 residues processed: 132 average time/residue: 0.1963 time to fit residues: 37.8733 Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 155 HIS Chi-restraints excluded: chain A residue 159 THR 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 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 224 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 3 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.277582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.227993 restraints weight = 8592.177| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 3.30 r_work: 0.4231 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9253 Z= 0.212 Angle : 0.562 8.236 12510 Z= 0.291 Chirality : 0.044 0.159 1370 Planarity : 0.004 0.048 1608 Dihedral : 4.719 23.024 1201 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1090 helix: 0.81 (0.30), residues: 295 sheet: -0.83 (0.34), residues: 210 loop : 0.03 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.007 0.001 HIS C 328 PHE 0.040 0.002 PHE C 95 TYR 0.018 0.001 TYR C 223 ARG 0.007 0.000 ARG A 154 *********************** 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 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6332 (t80) cc_final: 0.4189 (p90) REVERT: A 200 TYR cc_start: 0.7628 (m-80) cc_final: 0.7377 (m-80) REVERT: A 552 MET cc_start: 0.5190 (ptm) cc_final: 0.4073 (mmt) REVERT: A 561 ASP cc_start: 0.7879 (p0) cc_final: 0.7632 (p0) REVERT: A 623 LYS cc_start: 0.8314 (ptpt) cc_final: 0.7896 (ptpp) REVERT: A 645 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6285 (tt) REVERT: A 657 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.4607 (m-30) REVERT: A 962 MET cc_start: 0.7465 (mmm) cc_final: 0.7133 (mmt) REVERT: B 117 ARG cc_start: 0.7496 (ttp-170) cc_final: 0.6302 (ttp80) REVERT: B 179 ASP cc_start: 0.7542 (m-30) cc_final: 0.7199 (t0) REVERT: B 226 ASN cc_start: 0.6420 (m110) cc_final: 0.5180 (t0) REVERT: B 231 LYS cc_start: 0.7400 (tttm) cc_final: 0.6937 (mtpp) REVERT: C 76 ARG cc_start: 0.6758 (ttm170) cc_final: 0.5898 (tpt170) REVERT: C 202 LYS cc_start: 0.6839 (mtpp) cc_final: 0.6490 (mptt) REVERT: C 224 PHE cc_start: 0.3705 (OUTLIER) cc_final: 0.2110 (p90) REVERT: C 233 TYR cc_start: 0.7554 (m-80) cc_final: 0.7314 (m-80) REVERT: C 253 MET cc_start: 0.6015 (mmm) cc_final: 0.4855 (ptp) REVERT: C 330 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6840 (tt) outliers start: 28 outliers final: 20 residues processed: 125 average time/residue: 0.3077 time to fit residues: 56.3036 Evaluate side-chains 126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 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 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 17 optimal weight: 0.0170 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 overall best weight: 0.4820 ------------------------------------------------------------------------------- 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 = 0.5032 r_free = 0.5032 target = 0.279581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.231396 restraints weight = 8689.812| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 3.36 r_work: 0.4274 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9253 Z= 0.180 Angle : 0.536 7.181 12510 Z= 0.280 Chirality : 0.043 0.154 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.623 23.520 1201 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.78 % Allowed : 15.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1090 helix: 0.87 (0.30), residues: 295 sheet: -0.80 (0.34), residues: 216 loop : 0.08 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 171 HIS 0.009 0.001 HIS A 83 PHE 0.043 0.002 PHE C 212 TYR 0.015 0.001 TYR C 223 ARG 0.009 0.000 ARG A 154 ********************** 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 135 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 82 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7836 (mp) REVERT: A 185 TYR cc_start: 0.6285 (t80) cc_final: 0.4235 (p90) REVERT: A 200 TYR cc_start: 0.7455 (m-80) cc_final: 0.7233 (m-80) REVERT: A 552 MET cc_start: 0.5161 (ptm) cc_final: 0.4061 (mmt) REVERT: A 561 ASP cc_start: 0.7806 (p0) cc_final: 0.7539 (p0) REVERT: A 623 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7899 (ptpp) REVERT: A 657 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.4355 (m-30) REVERT: A 962 MET cc_start: 0.7425 (mmm) cc_final: 0.7089 (mmt) REVERT: B 117 ARG cc_start: 0.7347 (ttp-170) cc_final: 0.6309 (tmm-80) REVERT: B 179 ASP cc_start: 0.7482 (m-30) cc_final: 0.7149 (t0) REVERT: B 226 ASN cc_start: 0.6312 (m110) cc_final: 0.5134 (t0) REVERT: B 231 LYS cc_start: 0.7304 (tttm) cc_final: 0.6853 (mtpp) REVERT: B 305 GLU cc_start: 0.7298 (mp0) cc_final: 0.6677 (mp0) REVERT: C 76 ARG cc_start: 0.6692 (ttm170) cc_final: 0.5861 (tpt170) REVERT: C 202 LYS cc_start: 0.6763 (mtpp) cc_final: 0.6414 (mptt) REVERT: C 224 PHE cc_start: 0.3624 (OUTLIER) cc_final: 0.2135 (p90) REVERT: C 233 TYR cc_start: 0.7498 (m-80) cc_final: 0.7242 (m-80) REVERT: C 253 MET cc_start: 0.5841 (mmm) cc_final: 0.4679 (ptp) REVERT: C 330 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6805 (tt) outliers start: 28 outliers final: 21 residues processed: 129 average time/residue: 0.2010 time to fit residues: 37.6628 Evaluate side-chains 129 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 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 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 217 HIS 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 86 optimal weight: 0.0470 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 48 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 C 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.280084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.230538 restraints weight = 8608.935| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 3.37 r_work: 0.4262 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9253 Z= 0.165 Angle : 0.528 7.166 12510 Z= 0.274 Chirality : 0.043 0.156 1370 Planarity : 0.004 0.043 1608 Dihedral : 4.550 23.528 1201 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.58 % Allowed : 15.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1090 helix: 0.94 (0.30), residues: 295 sheet: -0.83 (0.33), residues: 226 loop : 0.17 (0.28), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.013 0.001 HIS A 83 PHE 0.035 0.002 PHE C 95 TYR 0.014 0.001 TYR C 223 ARG 0.006 0.000 ARG A 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5160.72 seconds wall clock time: 92 minutes 21.57 seconds (5541.57 seconds total)