Starting phenix.real_space_refine on Wed Mar 4 01:02:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r3q_4719/03_2026/6r3q_4719.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r3q_4719/03_2026/6r3q_4719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2026/6r3q_4719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2026/6r3q_4719.map" model { file = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2026/6r3q_4719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2026/6r3q_4719.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 6130 2.51 5 N 1599 2.21 5 O 1727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 9529 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6687 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 20, 'TRANS': 820} Chain breaks: 6 Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2809 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.21, per 1000 atoms: 0.23 Number of scatterers: 9529 At special positions: 0 Unit cell: (162.8, 105.006, 105.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 3 15.00 Mg 1 11.99 O 1727 8.00 N 1599 7.00 C 6130 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: 0.78 Conformation dependent library (CDL) restraints added in 460.2 milliseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.725A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.750A pdb=" N THR A 112 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 removed outlier: 3.577A pdb=" N ALA A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 219 through 237 removed outlier: 4.227A pdb=" N SER A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 261 removed outlier: 3.552A pdb=" N TYR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 336 removed outlier: 3.615A pdb=" N PHE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.185A pdb=" N GLU A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.899A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 785 through 807 Processing helix chain 'A' and resid 817 through 844 removed outlier: 4.155A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 859 removed outlier: 3.529A pdb=" N TRP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 882 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 892 through 907 Processing helix chain 'A' and resid 916 through 935 removed outlier: 3.842A pdb=" N ARG A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 978 through 1037 removed outlier: 3.596A pdb=" N ALA A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1047 removed outlier: 3.723A pdb=" N VAL A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1069 No H-bonds generated for 'chain 'A' and resid 1067 through 1069' Processing helix chain 'A' and resid 1079 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1133 through 1156 removed outlier: 4.092A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 3.958A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1218 Processing helix chain 'A' and resid 1219 through 1221 No H-bonds generated for 'chain 'A' and resid 1219 through 1221' Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.681A pdb=" N ASP B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 89 through 112 removed outlier: 3.881A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.042A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.637A pdb=" N ARG B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 236 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.886A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 388 removed outlier: 3.558A pdb=" N ILE B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 441 removed outlier: 7.312A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 441 removed outlier: 7.312A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 570 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.401A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A1052 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A1177 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A1054 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A1175 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A1056 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1173 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.401A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A1052 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A1177 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A1054 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A1175 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A1056 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1173 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 214 removed outlier: 5.626A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1752 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: 1.25 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1897 1.32 - 1.44: 2347 1.44 - 1.57: 5380 1.57 - 1.69: 5 1.69 - 1.81: 106 Bond restraints: 9735 Sorted by residual: bond pdb=" C LYS A 549 " pdb=" N VAL A 550 " ideal model delta sigma weight residual 1.332 1.286 0.046 1.73e-02 3.34e+03 6.96e+00 bond pdb=" CD LYS A1107 " pdb=" CE LYS A1107 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.73e+00 bond pdb=" CG LEU A1164 " pdb=" CD2 LEU A1164 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.65e+00 bond pdb=" SD MET A 469 " pdb=" CE MET A 469 " ideal model delta sigma weight residual 1.791 1.732 0.059 2.50e-02 1.60e+03 5.48e+00 bond pdb=" CB TRP A 510 " pdb=" CG TRP A 510 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 4.94e+00 ... (remaining 9730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 12608 2.68 - 5.35: 475 5.35 - 8.03: 60 8.03 - 10.71: 20 10.71 - 13.38: 8 Bond angle restraints: 13171 Sorted by residual: angle pdb=" N LEU A 875 " pdb=" CA LEU A 875 " pdb=" C LEU A 875 " ideal model delta sigma weight residual 109.81 121.90 -12.09 2.21e+00 2.05e-01 2.99e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 122.97 118.46 4.51 9.80e-01 1.04e+00 2.12e+01 angle pdb=" C VAL B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 ... (remaining 13166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 5253 15.24 - 30.48: 382 30.48 - 45.72: 127 45.72 - 60.95: 15 60.95 - 76.19: 10 Dihedral angle restraints: 5787 sinusoidal: 2329 harmonic: 3458 Sorted by residual: dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 144.43 35.57 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual 180.00 -148.87 -31.13 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA CYS A 910 " pdb=" C CYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 5784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1308 0.109 - 0.218: 161 0.218 - 0.328: 13 0.328 - 0.437: 0 0.437 - 0.546: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CB VAL A 986 " pdb=" CA VAL A 986 " pdb=" CG1 VAL A 986 " pdb=" CG2 VAL A 986 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CG LEU B 99 " pdb=" CB LEU B 99 " pdb=" CD1 LEU B 99 " pdb=" CD2 LEU B 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1481 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 385 " -0.016 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE A 385 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 385 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 385 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 385 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 385 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 385 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " -0.030 2.00e-02 2.50e+03 2.66e-02 1.24e+01 pdb=" CG PHE A 232 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO B 115 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.041 5.00e-02 4.00e+02 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 142 2.64 - 3.21: 8594 3.21 - 3.77: 15256 3.77 - 4.34: 19710 4.34 - 4.90: 32248 Nonbonded interactions: 75950 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" OG SER B 54 " pdb="MG MG B 502 " model vdw 2.113 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.119 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.124 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.205 3.040 ... (remaining 75945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.370 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.011 0.082 9735 Z= 0.483 Angle : 1.245 13.383 13171 Z= 0.651 Chirality : 0.072 0.546 1484 Planarity : 0.008 0.074 1655 Dihedral : 12.612 76.192 3549 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.20), residues: 1164 helix: -2.14 (0.15), residues: 684 sheet: -2.03 (0.43), residues: 136 loop : -2.85 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 342 TYR 0.050 0.004 TYR A 446 PHE 0.060 0.005 PHE A 232 TRP 0.027 0.004 TRP A 918 HIS 0.016 0.003 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.01126 ( 9735) covalent geometry : angle 1.24461 (13171) hydrogen bonds : bond 0.14151 ( 569) hydrogen bonds : angle 7.18277 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7842 (t80) cc_final: 0.7457 (t80) REVERT: A 138 MET cc_start: 0.6930 (ttt) cc_final: 0.6257 (ttt) REVERT: A 152 PHE cc_start: 0.6885 (t80) cc_final: 0.6632 (t80) REVERT: A 182 LEU cc_start: 0.8690 (mp) cc_final: 0.8428 (mp) REVERT: A 286 LEU cc_start: 0.8847 (mt) cc_final: 0.8630 (mt) REVERT: A 333 MET cc_start: 0.8765 (mmt) cc_final: 0.8547 (mmp) REVERT: A 987 PHE cc_start: 0.8294 (m-80) cc_final: 0.8056 (m-80) REVERT: A 1006 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.6473 (mmp-170) REVERT: B 174 CYS cc_start: 0.7864 (p) cc_final: 0.7382 (p) outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.0881 time to fit residues: 22.4814 Evaluate side-chains 102 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 HIS A1055 HIS A1154 ASN A1169 ASN A1231 ASN B 31 GLN B 98 ASN B 239 ASN B 264 ASN B 357 HIS B 362 HIS B 371 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.104420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083377 restraints weight = 25931.524| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.03 r_work: 0.3305 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 0.042 9735 Z= 0.168 Angle : 0.707 12.804 13171 Z= 0.357 Chirality : 0.045 0.202 1484 Planarity : 0.005 0.066 1655 Dihedral : 5.733 35.340 1300 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.84 % Allowed : 11.24 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1164 helix: -0.09 (0.19), residues: 686 sheet: -1.99 (0.41), residues: 137 loop : -2.33 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 920 TYR 0.027 0.002 TYR A 446 PHE 0.018 0.002 PHE A 232 TRP 0.016 0.002 TRP A1159 HIS 0.004 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9735) covalent geometry : angle 0.70748 (13171) hydrogen bonds : bond 0.05054 ( 569) hydrogen bonds : angle 4.86357 ( 1752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8034 (t80) cc_final: 0.7392 (t80) REVERT: A 138 MET cc_start: 0.7393 (ttt) cc_final: 0.7126 (ttm) REVERT: A 232 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8588 (m-10) REVERT: A 239 HIS cc_start: 0.8386 (t-90) cc_final: 0.8069 (t-90) REVERT: A 248 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7950 (tp) REVERT: A 795 THR cc_start: 0.8872 (t) cc_final: 0.8661 (m) REVERT: A 896 MET cc_start: 0.8256 (mtm) cc_final: 0.8014 (mtp) REVERT: A 1002 GLU cc_start: 0.8093 (pp20) cc_final: 0.7832 (tm-30) REVERT: A 1006 ARG cc_start: 0.7188 (ttm-80) cc_final: 0.6705 (mmp-170) REVERT: A 1164 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8854 (pt) REVERT: B 110 MET cc_start: 0.8189 (mmt) cc_final: 0.7796 (mmt) REVERT: B 174 CYS cc_start: 0.8112 (p) cc_final: 0.7707 (p) outliers start: 40 outliers final: 16 residues processed: 163 average time/residue: 0.0759 time to fit residues: 19.1243 Evaluate side-chains 130 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 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 = 0.3841 r_free = 0.3841 target = 0.105207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084294 restraints weight = 25962.828| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.05 r_work: 0.3313 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9735 Z= 0.132 Angle : 0.657 13.805 13171 Z= 0.322 Chirality : 0.043 0.170 1484 Planarity : 0.004 0.059 1655 Dihedral : 5.111 32.596 1300 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.65 % Allowed : 13.93 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1164 helix: 0.88 (0.20), residues: 682 sheet: -1.74 (0.42), residues: 133 loop : -2.03 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.021 0.002 TYR A 446 PHE 0.018 0.001 PHE A 897 TRP 0.013 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9735) covalent geometry : angle 0.65651 (13171) hydrogen bonds : bond 0.04357 ( 569) hydrogen bonds : angle 4.33704 ( 1752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 232 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8565 (m-10) REVERT: A 248 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7926 (tp) REVERT: A 385 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8119 (p90) REVERT: A 1002 GLU cc_start: 0.8009 (pp20) cc_final: 0.7772 (tp30) REVERT: A 1006 ARG cc_start: 0.7116 (ttm-80) cc_final: 0.6670 (mmp-170) REVERT: B 99 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9312 (tp) outliers start: 38 outliers final: 18 residues processed: 155 average time/residue: 0.0768 time to fit residues: 18.5251 Evaluate side-chains 129 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.102660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081363 restraints weight = 26463.692| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.04 r_work: 0.3252 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9735 Z= 0.194 Angle : 0.699 13.837 13171 Z= 0.344 Chirality : 0.045 0.178 1484 Planarity : 0.004 0.056 1655 Dihedral : 5.031 33.408 1298 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.80 % Allowed : 14.51 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1164 helix: 1.05 (0.20), residues: 687 sheet: -1.69 (0.42), residues: 135 loop : -2.04 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 920 TYR 0.022 0.002 TYR A 446 PHE 0.018 0.002 PHE A 232 TRP 0.014 0.002 TRP A1159 HIS 0.006 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 9735) covalent geometry : angle 0.69903 (13171) hydrogen bonds : bond 0.04583 ( 569) hydrogen bonds : angle 4.28851 ( 1752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.378 Fit side-chains REVERT: A 138 MET cc_start: 0.7475 (ttt) cc_final: 0.7127 (ttm) REVERT: A 232 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8732 (m-10) REVERT: A 248 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7944 (tp) REVERT: A 568 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7428 (p) REVERT: A 841 MET cc_start: 0.5998 (ttp) cc_final: 0.5753 (ptm) REVERT: A 1002 GLU cc_start: 0.8103 (pp20) cc_final: 0.7614 (tm-30) REVERT: A 1006 ARG cc_start: 0.7237 (ttm-80) cc_final: 0.6726 (mmp-170) REVERT: B 99 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9320 (tp) outliers start: 50 outliers final: 29 residues processed: 152 average time/residue: 0.0766 time to fit residues: 18.0936 Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 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 191 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.105048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084269 restraints weight = 26398.838| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.03 r_work: 0.3308 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9735 Z= 0.129 Angle : 0.655 14.803 13171 Z= 0.314 Chirality : 0.043 0.194 1484 Planarity : 0.004 0.045 1655 Dihedral : 4.738 30.267 1298 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.55 % Allowed : 16.04 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1164 helix: 1.43 (0.20), residues: 687 sheet: -1.51 (0.42), residues: 133 loop : -1.70 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 920 TYR 0.019 0.001 TYR A 446 PHE 0.015 0.001 PHE A 232 TRP 0.012 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9735) covalent geometry : angle 0.65465 (13171) hydrogen bonds : bond 0.04168 ( 569) hydrogen bonds : angle 4.09117 ( 1752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.372 Fit side-chains REVERT: A 138 MET cc_start: 0.7576 (ttt) cc_final: 0.7299 (ttm) REVERT: A 232 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: A 248 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7938 (tp) REVERT: A 347 MET cc_start: 0.8126 (mmp) cc_final: 0.7818 (mmt) REVERT: A 522 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: A 568 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7345 (p) REVERT: A 1002 GLU cc_start: 0.8046 (pp20) cc_final: 0.7807 (tp30) REVERT: A 1006 ARG cc_start: 0.7143 (ttm-80) cc_final: 0.6663 (mmp-170) REVERT: B 99 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9343 (tp) outliers start: 37 outliers final: 22 residues processed: 138 average time/residue: 0.0726 time to fit residues: 15.7821 Evaluate side-chains 135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 114 optimal weight: 0.0060 chunk 36 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.106005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085283 restraints weight = 26258.247| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.05 r_work: 0.3330 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9735 Z= 0.122 Angle : 0.660 15.414 13171 Z= 0.311 Chirality : 0.042 0.186 1484 Planarity : 0.004 0.041 1655 Dihedral : 4.531 29.849 1298 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.03 % Allowed : 15.66 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1164 helix: 1.64 (0.20), residues: 688 sheet: -1.42 (0.43), residues: 126 loop : -1.61 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.018 0.001 TYR A 446 PHE 0.014 0.001 PHE A 232 TRP 0.010 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9735) covalent geometry : angle 0.65954 (13171) hydrogen bonds : bond 0.04035 ( 569) hydrogen bonds : angle 3.96244 ( 1752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.384 Fit side-chains REVERT: A 138 MET cc_start: 0.7551 (ttt) cc_final: 0.7302 (ttm) REVERT: A 232 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: A 248 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7970 (tp) REVERT: A 522 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: A 537 LYS cc_start: 0.8484 (ptpp) cc_final: 0.8085 (ptmm) REVERT: A 1006 ARG cc_start: 0.7094 (ttm-80) cc_final: 0.5246 (tpt170) REVERT: B 99 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9342 (tp) outliers start: 42 outliers final: 22 residues processed: 147 average time/residue: 0.0733 time to fit residues: 17.0597 Evaluate side-chains 135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 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 = 0.3777 r_free = 0.3777 target = 0.101315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079888 restraints weight = 26683.898| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.02 r_work: 0.3224 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9735 Z= 0.252 Angle : 0.755 15.037 13171 Z= 0.370 Chirality : 0.047 0.201 1484 Planarity : 0.004 0.044 1655 Dihedral : 4.999 33.220 1298 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.80 % Allowed : 16.04 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1164 helix: 1.25 (0.19), residues: 685 sheet: -1.66 (0.42), residues: 135 loop : -1.79 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 920 TYR 0.024 0.002 TYR A 446 PHE 0.020 0.002 PHE A 232 TRP 0.017 0.002 TRP A 918 HIS 0.006 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 9735) covalent geometry : angle 0.75489 (13171) hydrogen bonds : bond 0.04815 ( 569) hydrogen bonds : angle 4.26683 ( 1752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.389 Fit side-chains REVERT: A 138 MET cc_start: 0.7553 (ttt) cc_final: 0.7240 (ttm) REVERT: A 232 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8807 (m-10) REVERT: A 248 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 347 MET cc_start: 0.8291 (mmp) cc_final: 0.7946 (mmt) REVERT: A 522 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: A 859 ILE cc_start: 0.5182 (OUTLIER) cc_final: 0.4956 (tp) REVERT: A 1002 GLU cc_start: 0.7839 (tp30) cc_final: 0.7374 (tp30) REVERT: A 1006 ARG cc_start: 0.7340 (ttm-80) cc_final: 0.6926 (mmp-170) REVERT: B 99 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9357 (tp) REVERT: B 266 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8904 (tt) outliers start: 50 outliers final: 32 residues processed: 147 average time/residue: 0.0719 time to fit residues: 16.7858 Evaluate side-chains 140 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 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 = 0.3836 r_free = 0.3836 target = 0.104846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083814 restraints weight = 26392.073| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.04 r_work: 0.3300 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9735 Z= 0.132 Angle : 0.683 15.763 13171 Z= 0.323 Chirality : 0.043 0.168 1484 Planarity : 0.004 0.043 1655 Dihedral : 4.601 28.667 1297 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.75 % Allowed : 17.96 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1164 helix: 1.65 (0.20), residues: 685 sheet: -1.43 (0.43), residues: 126 loop : -1.64 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 920 TYR 0.019 0.001 TYR A 446 PHE 0.017 0.001 PHE A 160 TRP 0.011 0.001 TRP A 918 HIS 0.005 0.001 HIS A 530 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9735) covalent geometry : angle 0.68276 (13171) hydrogen bonds : bond 0.04148 ( 569) hydrogen bonds : angle 3.99694 ( 1752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 232 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8599 (m-10) REVERT: A 248 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7953 (tp) REVERT: A 347 MET cc_start: 0.8155 (mmp) cc_final: 0.7767 (mmt) REVERT: A 522 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: A 1002 GLU cc_start: 0.7823 (tp30) cc_final: 0.7461 (tp30) REVERT: A 1006 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.5240 (tpt170) REVERT: A 1164 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8783 (pt) REVERT: B 99 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9346 (tp) REVERT: B 255 MET cc_start: 0.8515 (mtp) cc_final: 0.8243 (mtp) REVERT: B 266 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8697 (tt) outliers start: 39 outliers final: 26 residues processed: 143 average time/residue: 0.0762 time to fit residues: 16.7294 Evaluate side-chains 141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 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 = 0.3842 r_free = 0.3842 target = 0.105319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084425 restraints weight = 26266.467| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.05 r_work: 0.3313 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9735 Z= 0.129 Angle : 0.674 16.897 13171 Z= 0.318 Chirality : 0.042 0.171 1484 Planarity : 0.004 0.045 1655 Dihedral : 4.408 28.528 1297 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.84 % Allowed : 17.58 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1164 helix: 1.78 (0.20), residues: 687 sheet: -1.38 (0.42), residues: 126 loop : -1.54 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.018 0.001 TYR A 446 PHE 0.015 0.001 PHE A 897 TRP 0.011 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9735) covalent geometry : angle 0.67446 (13171) hydrogen bonds : bond 0.04061 ( 569) hydrogen bonds : angle 3.92050 ( 1752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 115 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 232 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8667 (m-10) REVERT: A 248 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 347 MET cc_start: 0.8155 (mmp) cc_final: 0.7839 (mmt) REVERT: A 522 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: A 537 LYS cc_start: 0.8446 (ptpp) cc_final: 0.7962 (ptpp) REVERT: A 1002 GLU cc_start: 0.7868 (tp30) cc_final: 0.7500 (tp30) REVERT: A 1006 ARG cc_start: 0.7034 (ttm-80) cc_final: 0.5199 (tpt170) REVERT: B 35 GLN cc_start: 0.8504 (tp40) cc_final: 0.7299 (tm-30) REVERT: B 99 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9343 (tp) REVERT: B 266 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8700 (tt) outliers start: 40 outliers final: 31 residues processed: 146 average time/residue: 0.0757 time to fit residues: 16.9372 Evaluate side-chains 146 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 77 optimal weight: 0.0570 chunk 57 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.107181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.086631 restraints weight = 26082.446| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.08 r_work: 0.3361 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9735 Z= 0.120 Angle : 0.698 17.332 13171 Z= 0.321 Chirality : 0.042 0.177 1484 Planarity : 0.004 0.039 1655 Dihedral : 4.272 26.241 1297 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.69 % Allowed : 19.50 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1164 helix: 1.94 (0.20), residues: 688 sheet: -1.27 (0.43), residues: 126 loop : -1.44 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.018 0.001 TYR A 446 PHE 0.019 0.001 PHE A 160 TRP 0.012 0.001 TRP A 995 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9735) covalent geometry : angle 0.69798 (13171) hydrogen bonds : bond 0.03889 ( 569) hydrogen bonds : angle 3.85390 ( 1752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 232 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8668 (m-10) REVERT: A 248 LEU cc_start: 0.8224 (mp) cc_final: 0.7950 (tp) REVERT: A 522 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: A 537 LYS cc_start: 0.8398 (ptpp) cc_final: 0.7905 (ptpp) REVERT: A 1002 GLU cc_start: 0.7842 (tp30) cc_final: 0.7345 (tp30) REVERT: A 1006 ARG cc_start: 0.6885 (ttm-80) cc_final: 0.5120 (tpt170) REVERT: B 35 GLN cc_start: 0.8526 (tp40) cc_final: 0.7305 (tm-30) REVERT: B 99 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9330 (tp) REVERT: B 266 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8687 (tt) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.0750 time to fit residues: 16.2197 Evaluate side-chains 137 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 90 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** 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 = 0.3845 r_free = 0.3845 target = 0.105302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084401 restraints weight = 25931.218| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.07 r_work: 0.3318 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9735 Z= 0.140 Angle : 0.683 16.967 13171 Z= 0.321 Chirality : 0.043 0.172 1484 Planarity : 0.004 0.040 1655 Dihedral : 4.311 27.871 1297 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.17 % Allowed : 18.92 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1164 helix: 1.95 (0.20), residues: 685 sheet: -1.22 (0.43), residues: 126 loop : -1.45 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.022 0.001 TYR A 446 PHE 0.024 0.001 PHE A 125 TRP 0.012 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9735) covalent geometry : angle 0.68297 (13171) hydrogen bonds : bond 0.04039 ( 569) hydrogen bonds : angle 3.89062 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.73 seconds wall clock time: 39 minutes 11.88 seconds (2351.88 seconds total)