Starting phenix.real_space_refine on Thu Sep 18 03:52:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gge_51329/09_2025/9gge_51329.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gge_51329/09_2025/9gge_51329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gge_51329/09_2025/9gge_51329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gge_51329/09_2025/9gge_51329.map" model { file = "/net/cci-nas-00/data/ceres_data/9gge_51329/09_2025/9gge_51329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gge_51329/09_2025/9gge_51329.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.977 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 41 5.49 5 S 80 5.16 5 C 8706 2.51 5 N 2426 2.21 5 O 2601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13855 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7398 Classifications: {'peptide': 929} Link IDs: {'PTRANS': 62, 'TRANS': 866} Chain breaks: 5 Chain: "B" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2826 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 332} Chain breaks: 4 Chain: "C" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2823 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 331} Chain breaks: 4 Chain: "P" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.19, per 1000 atoms: 0.23 Number of scatterers: 13855 At special positions: 0 Unit cell: (101.016, 93.564, 145.728, 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) Ca 1 19.99 S 80 16.00 P 41 15.00 O 2601 8.00 N 2426 7.00 C 8706 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: 0.93 Conformation dependent library (CDL) restraints added in 564.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3028 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 13 sheets defined 48.1% alpha, 13.1% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.543A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.642A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 317 Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.673A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 350 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.796A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.823A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 5.172A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 554 Processing helix chain 'A' and resid 555 through 558 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.694A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 786 through 810 removed outlier: 3.690A pdb=" N ALA A 791 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 792 " --> pdb=" O GLY A 788 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 942 through 955 removed outlier: 3.504A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 987 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.672A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1169 removed outlier: 3.541A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 removed outlier: 3.696A pdb=" N VAL A1177 " --> pdb=" O PRO A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 3.987A pdb=" N ARG A1208 " --> pdb=" O THR A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 removed outlier: 3.839A pdb=" N GLU A1225 " --> pdb=" O TYR A1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.010A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.120A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.589A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.644A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.210A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 392 through 409 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 4.203A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.643A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 removed outlier: 4.590A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 622 through 625 Processing sheet with id=AA5, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 6.782A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 889 " --> pdb=" O VAL A1137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.573A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'B' and resid 413 through 416 removed outlier: 6.758A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY B 416 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU B 385 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 127 removed outlier: 5.590A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.650A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.013A pdb=" N LYS C 329 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.126A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3528 1.33 - 1.45: 2910 1.45 - 1.57: 7643 1.57 - 1.69: 79 1.69 - 1.81: 126 Bond restraints: 14286 Sorted by residual: bond pdb=" C6 DCP A1302 " pdb=" N1 DCP A1302 " ideal model delta sigma weight residual 1.375 1.334 0.041 1.20e-02 6.94e+03 1.14e+01 bond pdb=" C4 DCP A1302 " pdb=" C5 DCP A1302 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 9.90e+00 bond pdb=" O1B DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.10e-02 8.26e+03 8.59e+00 bond pdb=" CA PHE A 273 " pdb=" C PHE A 273 " ideal model delta sigma weight residual 1.524 1.490 0.034 1.26e-02 6.30e+03 7.15e+00 bond pdb=" O1A DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.477 1.501 -0.024 1.00e-02 1.00e+04 5.98e+00 ... (remaining 14281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 19496 3.86 - 7.72: 29 7.72 - 11.58: 0 11.58 - 15.44: 1 15.44 - 19.30: 1 Bond angle restraints: 19527 Sorted by residual: angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 136.83 122.32 14.51 1.00e+00 1.00e+00 2.11e+02 angle pdb=" N ASP B 459 " pdb=" CA ASP B 459 " pdb=" C ASP B 459 " ideal model delta sigma weight residual 111.24 117.56 -6.32 1.29e+00 6.01e-01 2.40e+01 angle pdb=" N ILE A 215 " pdb=" CA ILE A 215 " pdb=" C ILE A 215 " ideal model delta sigma weight residual 107.37 113.95 -6.58 1.48e+00 4.57e-01 1.98e+01 angle pdb=" N SER A 272 " pdb=" CA SER A 272 " pdb=" C SER A 272 " ideal model delta sigma weight residual 111.36 106.82 4.54 1.09e+00 8.42e-01 1.74e+01 ... (remaining 19522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7842 17.65 - 35.30: 426 35.30 - 52.96: 108 52.96 - 70.61: 31 70.61 - 88.26: 5 Dihedral angle restraints: 8412 sinusoidal: 3722 harmonic: 4690 Sorted by residual: dihedral pdb=" CA VAL A 196 " pdb=" C VAL A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB ARG A 964 " pdb=" CG ARG A 964 " pdb=" CD ARG A 964 " pdb=" NE ARG A 964 " ideal model delta sinusoidal sigma weight residual -60.00 -118.15 58.15 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB ARG A 386 " pdb=" CG ARG A 386 " pdb=" CD ARG A 386 " pdb=" NE ARG A 386 " ideal model delta sinusoidal sigma weight residual -60.00 -114.54 54.54 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 8409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1353 0.028 - 0.056: 502 0.056 - 0.084: 123 0.084 - 0.112: 100 0.112 - 0.140: 21 Chirality restraints: 2099 Sorted by residual: chirality pdb=" CA VAL C 338 " pdb=" N VAL C 338 " pdb=" C VAL C 338 " pdb=" CB VAL C 338 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE C 211 " pdb=" N ILE C 211 " pdb=" C ILE C 211 " pdb=" CB ILE C 211 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE A 744 " pdb=" N ILE A 744 " pdb=" C ILE A 744 " pdb=" CB ILE A 744 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2096 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 405 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C GLU B 405 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU B 405 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 406 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1199 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A1200 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1200 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1200 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 73 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.023 5.00e-02 4.00e+02 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 21 2.37 - 3.00: 7075 3.00 - 3.64: 20720 3.64 - 4.27: 33054 4.27 - 4.90: 54545 Nonbonded interactions: 115415 Sorted by model distance: nonbonded pdb="CA CA A1301 " pdb=" O1B DCP A1302 " model vdw 1.742 2.510 nonbonded pdb=" O VAL A 891 " pdb="CA CA A1301 " model vdw 1.826 2.510 nonbonded pdb=" OD2 ASP A1135 " pdb="CA CA A1301 " model vdw 2.167 2.510 nonbonded pdb=" O SER C 117 " pdb=" NH1 ARG C 122 " model vdw 2.213 3.120 nonbonded pdb=" NE1 TRP B 263 " pdb=" OE1 GLU B 301 " model vdw 2.237 3.120 ... (remaining 115410 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 67 through 137 or resid 178 through 387 or resid 391 throu \ gh 482)) selection = (chain 'C' and (resid 67 through 137 or resid 178 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.003 0.042 14286 Z= 0.156 Angle : 0.531 19.295 19527 Z= 0.340 Chirality : 0.037 0.140 2099 Planarity : 0.004 0.047 2369 Dihedral : 12.112 88.260 5384 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.49 % Allowed : 3.39 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 0.99 (0.21), residues: 1596 helix: 1.43 (0.20), residues: 682 sheet: 0.57 (0.36), residues: 211 loop : 0.01 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 802 TYR 0.009 0.001 TYR A1108 PHE 0.014 0.001 PHE B 403 TRP 0.007 0.001 TRP A 748 HIS 0.003 0.000 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00274 (14286) covalent geometry : angle 0.53101 (19527) hydrogen bonds : bond 0.17588 ( 673) hydrogen bonds : angle 7.47731 ( 1883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 309 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.6224 (mt-10) cc_final: 0.5911 (pp20) REVERT: A 145 LYS cc_start: 0.7642 (tttp) cc_final: 0.7352 (tmmt) REVERT: A 311 LEU cc_start: 0.8062 (mt) cc_final: 0.7800 (mp) REVERT: A 375 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6726 (pm20) REVERT: A 1107 ASP cc_start: 0.6918 (m-30) cc_final: 0.6246 (m-30) REVERT: A 1186 ASP cc_start: 0.6003 (t0) cc_final: 0.5798 (t0) REVERT: B 462 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5802 (mmm) REVERT: B 465 MET cc_start: 0.6679 (mtm) cc_final: 0.6226 (mpp) outliers start: 7 outliers final: 3 residues processed: 314 average time/residue: 0.5854 time to fit residues: 200.6662 Evaluate side-chains 196 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 758 ASN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN C 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.209032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.179839 restraints weight = 15126.256| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 1.88 r_work: 0.4155 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4058 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14286 Z= 0.155 Angle : 0.557 7.073 19527 Z= 0.291 Chirality : 0.041 0.150 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.949 107.501 2194 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.82 % Allowed : 11.66 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 1.10 (0.21), residues: 1596 helix: 1.50 (0.20), residues: 695 sheet: 0.58 (0.34), residues: 239 loop : 0.07 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1190 TYR 0.020 0.002 TYR A1166 PHE 0.017 0.002 PHE A1129 TRP 0.014 0.001 TRP B 241 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00351 (14286) covalent geometry : angle 0.55701 (19527) hydrogen bonds : bond 0.04078 ( 673) hydrogen bonds : angle 5.35695 ( 1883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5784 (mt-10) cc_final: 0.4908 (pp20) REVERT: A 87 ILE cc_start: 0.6337 (mm) cc_final: 0.6065 (mt) REVERT: A 105 GLU cc_start: 0.4926 (OUTLIER) cc_final: 0.4156 (pp20) REVERT: A 145 LYS cc_start: 0.7727 (tttp) cc_final: 0.7140 (tmmt) REVERT: A 189 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6610 (mm) REVERT: A 191 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6493 (tp30) REVERT: A 200 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6663 (mm-30) REVERT: A 231 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5692 (tp30) REVERT: A 311 LEU cc_start: 0.7902 (mt) cc_final: 0.7600 (mp) REVERT: A 375 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6152 (pm20) REVERT: A 473 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6915 (mp) REVERT: A 475 SER cc_start: 0.7125 (m) cc_final: 0.6829 (p) REVERT: A 833 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6454 (mm-30) REVERT: A 1107 ASP cc_start: 0.7657 (m-30) cc_final: 0.7225 (m-30) REVERT: A 1133 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7131 (mm) REVERT: A 1146 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.5995 (ptt90) REVERT: B 462 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.5324 (mmm) REVERT: B 465 MET cc_start: 0.6483 (mtm) cc_final: 0.5863 (mpp) outliers start: 54 outliers final: 18 residues processed: 234 average time/residue: 0.5421 time to fit residues: 139.6316 Evaluate side-chains 188 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 54 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** 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 = 0.4520 r_free = 0.4520 target = 0.205444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.176041 restraints weight = 15317.021| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.96 r_work: 0.4105 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14286 Z= 0.186 Angle : 0.579 8.117 19527 Z= 0.301 Chirality : 0.043 0.266 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.757 83.041 2192 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.45 % Allowed : 11.94 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 0.85 (0.21), residues: 1596 helix: 1.22 (0.19), residues: 700 sheet: 0.55 (0.33), residues: 241 loop : -0.01 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 361 TYR 0.016 0.002 TYR A 178 PHE 0.015 0.002 PHE A1129 TRP 0.016 0.001 TRP B 241 HIS 0.010 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00431 (14286) covalent geometry : angle 0.57920 (19527) hydrogen bonds : bond 0.04100 ( 673) hydrogen bonds : angle 5.30590 ( 1883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.5003 (OUTLIER) cc_final: 0.4255 (pp20) REVERT: A 189 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6709 (mm) REVERT: A 191 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6477 (tp30) REVERT: A 200 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6747 (mm-30) REVERT: A 311 LEU cc_start: 0.8006 (mt) cc_final: 0.7706 (mp) REVERT: A 375 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6148 (pm20) REVERT: A 473 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6931 (mp) REVERT: A 475 SER cc_start: 0.7085 (m) cc_final: 0.6680 (t) REVERT: A 833 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6509 (mm-30) REVERT: A 963 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7304 (tm-30) REVERT: A 1058 PHE cc_start: 0.4531 (OUTLIER) cc_final: 0.3188 (t80) REVERT: A 1107 ASP cc_start: 0.7612 (m-30) cc_final: 0.7223 (m-30) REVERT: A 1146 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5471 (ptm-80) REVERT: B 372 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7234 (mt) REVERT: B 427 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7213 (pp30) REVERT: C 89 ASP cc_start: 0.6985 (m-30) cc_final: 0.6724 (m-30) REVERT: C 233 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6432 (mt-10) REVERT: C 408 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: C 445 GLU cc_start: 0.6566 (mp0) cc_final: 0.6351 (mp0) outliers start: 63 outliers final: 24 residues processed: 214 average time/residue: 0.4970 time to fit residues: 118.1515 Evaluate side-chains 185 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1058 PHE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.0030 chunk 154 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 GLN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.208042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.179092 restraints weight = 15143.837| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.81 r_work: 0.4155 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14286 Z= 0.117 Angle : 0.511 8.125 19527 Z= 0.267 Chirality : 0.040 0.266 2099 Planarity : 0.004 0.054 2369 Dihedral : 13.662 83.948 2189 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.89 % Allowed : 13.36 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 1.08 (0.21), residues: 1596 helix: 1.43 (0.19), residues: 705 sheet: 0.63 (0.33), residues: 241 loop : 0.08 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 361 TYR 0.022 0.002 TYR A1166 PHE 0.012 0.001 PHE C 403 TRP 0.015 0.001 TRP B 241 HIS 0.017 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00256 (14286) covalent geometry : angle 0.51104 (19527) hydrogen bonds : bond 0.03301 ( 673) hydrogen bonds : angle 5.01823 ( 1883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.6295 (mm) cc_final: 0.6031 (mt) REVERT: A 105 GLU cc_start: 0.5029 (OUTLIER) cc_final: 0.4313 (pp20) REVERT: A 189 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6749 (mp) REVERT: A 191 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6413 (tp30) REVERT: A 200 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6679 (mm-30) REVERT: A 231 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5587 (tp30) REVERT: A 311 LEU cc_start: 0.7951 (mt) cc_final: 0.7663 (mp) REVERT: A 375 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6130 (pm20) REVERT: A 382 MET cc_start: 0.7163 (tpp) cc_final: 0.6799 (tpp) REVERT: A 473 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6896 (mp) REVERT: A 475 SER cc_start: 0.6979 (m) cc_final: 0.6628 (t) REVERT: A 541 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6229 (mt0) REVERT: A 596 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: A 603 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7825 (mtp) REVERT: A 833 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6454 (mm-30) REVERT: A 919 MET cc_start: 0.6709 (mtt) cc_final: 0.6503 (mtt) REVERT: A 1107 ASP cc_start: 0.7490 (m-30) cc_final: 0.7145 (m-30) REVERT: A 1146 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.5480 (mtp180) REVERT: B 427 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7145 (pp30) REVERT: C 89 ASP cc_start: 0.6972 (m-30) cc_final: 0.6733 (m-30) REVERT: C 203 ARG cc_start: 0.6430 (mtm180) cc_final: 0.6203 (mtm180) REVERT: C 233 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6369 (mt-10) REVERT: C 408 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7188 (tt0) outliers start: 55 outliers final: 18 residues processed: 207 average time/residue: 0.5170 time to fit residues: 117.8083 Evaluate side-chains 180 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** B 74 GLN ** 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 = 0.4541 r_free = 0.4541 target = 0.207485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.178173 restraints weight = 15235.096| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 1.89 r_work: 0.4138 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14286 Z= 0.129 Angle : 0.511 7.719 19527 Z= 0.268 Chirality : 0.040 0.202 2099 Planarity : 0.005 0.055 2369 Dihedral : 13.587 84.293 2189 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.03 % Allowed : 13.50 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 1.07 (0.21), residues: 1596 helix: 1.42 (0.19), residues: 706 sheet: 0.60 (0.32), residues: 243 loop : 0.08 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 361 TYR 0.022 0.002 TYR A1166 PHE 0.014 0.001 PHE C 403 TRP 0.016 0.001 TRP B 241 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00290 (14286) covalent geometry : angle 0.51129 (19527) hydrogen bonds : bond 0.03359 ( 673) hydrogen bonds : angle 4.96395 ( 1883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 170 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.5099 (OUTLIER) cc_final: 0.4424 (pp20) REVERT: A 189 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6747 (mp) REVERT: A 191 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6401 (tp30) REVERT: A 200 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 231 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5559 (tp30) REVERT: A 311 LEU cc_start: 0.7948 (mt) cc_final: 0.7650 (mp) REVERT: A 375 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6107 (pm20) REVERT: A 382 MET cc_start: 0.7179 (tpp) cc_final: 0.6760 (tpp) REVERT: A 473 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6961 (mp) REVERT: A 475 SER cc_start: 0.6944 (m) cc_final: 0.6600 (t) REVERT: A 541 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6227 (mt0) REVERT: A 833 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6423 (mm-30) REVERT: A 985 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6133 (mtp) REVERT: A 1107 ASP cc_start: 0.7455 (m-30) cc_final: 0.7055 (m-30) REVERT: A 1146 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5506 (mtp180) REVERT: B 85 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5601 (mp10) REVERT: B 89 ASP cc_start: 0.7393 (t0) cc_final: 0.7122 (t0) REVERT: B 427 GLN cc_start: 0.7385 (tm-30) cc_final: 0.7143 (pp30) REVERT: B 468 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6095 (tt) REVERT: C 89 ASP cc_start: 0.7004 (m-30) cc_final: 0.6744 (m-30) REVERT: C 233 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6444 (mt-10) REVERT: C 253 ASP cc_start: 0.6951 (m-30) cc_final: 0.6735 (m-30) REVERT: C 408 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7250 (tt0) outliers start: 57 outliers final: 21 residues processed: 207 average time/residue: 0.4754 time to fit residues: 109.2580 Evaluate side-chains 187 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 140 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 736 ASN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.206907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.177803 restraints weight = 15208.251| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 1.87 r_work: 0.4127 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14286 Z= 0.134 Angle : 0.528 12.822 19527 Z= 0.274 Chirality : 0.040 0.243 2099 Planarity : 0.004 0.054 2369 Dihedral : 13.564 84.356 2188 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.46 % Allowed : 14.70 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 1.03 (0.21), residues: 1596 helix: 1.39 (0.20), residues: 702 sheet: 0.57 (0.32), residues: 243 loop : 0.07 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.023 0.002 TYR A1166 PHE 0.019 0.002 PHE A1092 TRP 0.016 0.001 TRP B 241 HIS 0.008 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00302 (14286) covalent geometry : angle 0.52827 (19527) hydrogen bonds : bond 0.03363 ( 673) hydrogen bonds : angle 4.96134 ( 1883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.491 Fit side-chains REVERT: A 87 ILE cc_start: 0.6269 (mm) cc_final: 0.6002 (mt) REVERT: A 105 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.4479 (pp20) REVERT: A 189 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6757 (mp) REVERT: A 191 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6304 (tp30) REVERT: A 200 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6703 (mm-30) REVERT: A 311 LEU cc_start: 0.7968 (mt) cc_final: 0.7644 (mp) REVERT: A 375 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6061 (pm20) REVERT: A 382 MET cc_start: 0.7173 (tpp) cc_final: 0.6829 (tpp) REVERT: A 473 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7011 (mp) REVERT: A 475 SER cc_start: 0.6833 (m) cc_final: 0.6475 (t) REVERT: A 541 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6221 (mt0) REVERT: A 833 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6429 (mm-30) REVERT: A 985 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6212 (mtp) REVERT: A 1107 ASP cc_start: 0.7473 (m-30) cc_final: 0.7177 (m-30) REVERT: A 1146 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5549 (mtp180) REVERT: B 85 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.5588 (mp10) REVERT: B 89 ASP cc_start: 0.7411 (t0) cc_final: 0.7142 (t0) REVERT: B 372 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7197 (mt) REVERT: B 465 MET cc_start: 0.6573 (mtp) cc_final: 0.6322 (mtt) REVERT: B 468 ILE cc_start: 0.6390 (OUTLIER) cc_final: 0.6008 (tt) REVERT: C 203 ARG cc_start: 0.6588 (mtm180) cc_final: 0.6347 (mtm180) REVERT: C 233 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: C 408 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: C 436 SER cc_start: 0.5908 (p) cc_final: 0.5699 (m) outliers start: 49 outliers final: 23 residues processed: 197 average time/residue: 0.4718 time to fit residues: 103.3577 Evaluate side-chains 188 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.205914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176307 restraints weight = 15218.315| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.87 r_work: 0.4112 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14286 Z= 0.162 Angle : 0.555 9.001 19527 Z= 0.289 Chirality : 0.041 0.250 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.597 84.487 2188 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.24 % Allowed : 14.56 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 0.92 (0.21), residues: 1596 helix: 1.31 (0.20), residues: 701 sheet: 0.49 (0.32), residues: 246 loop : 0.00 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 344 TYR 0.022 0.002 TYR A1166 PHE 0.035 0.002 PHE A 969 TRP 0.018 0.001 TRP B 241 HIS 0.013 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00371 (14286) covalent geometry : angle 0.55458 (19527) hydrogen bonds : bond 0.03565 ( 673) hydrogen bonds : angle 5.05621 ( 1883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.403 Fit side-chains REVERT: A 105 GLU cc_start: 0.5252 (OUTLIER) cc_final: 0.4472 (pp20) REVERT: A 189 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6715 (mp) REVERT: A 191 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6295 (tp30) REVERT: A 200 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6723 (mm-30) REVERT: A 311 LEU cc_start: 0.7926 (mt) cc_final: 0.7564 (mp) REVERT: A 375 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6046 (pm20) REVERT: A 382 MET cc_start: 0.7147 (tpp) cc_final: 0.6735 (tpp) REVERT: A 473 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7005 (mp) REVERT: A 475 SER cc_start: 0.6760 (m) cc_final: 0.6409 (t) REVERT: A 541 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6248 (mt0) REVERT: A 736 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.7077 (t0) REVERT: A 833 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6440 (mm-30) REVERT: A 963 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7202 (tm-30) REVERT: A 985 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6232 (mtp) REVERT: A 1107 ASP cc_start: 0.7549 (m-30) cc_final: 0.7264 (m-30) REVERT: A 1146 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5530 (mtp180) REVERT: B 89 ASP cc_start: 0.7488 (t0) cc_final: 0.7223 (t0) REVERT: B 412 SER cc_start: 0.5858 (m) cc_final: 0.5641 (p) REVERT: B 465 MET cc_start: 0.6598 (mtp) cc_final: 0.6335 (mtt) REVERT: B 468 ILE cc_start: 0.6406 (OUTLIER) cc_final: 0.6078 (tt) REVERT: C 203 ARG cc_start: 0.6498 (mtm180) cc_final: 0.6041 (mtm180) REVERT: C 233 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6414 (mt-10) REVERT: C 253 ASP cc_start: 0.6867 (m-30) cc_final: 0.6627 (m-30) REVERT: C 408 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7385 (tt0) outliers start: 60 outliers final: 29 residues processed: 208 average time/residue: 0.5216 time to fit residues: 119.8106 Evaluate side-chains 197 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 23 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 736 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.201881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.172042 restraints weight = 15240.351| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.85 r_work: 0.4074 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14286 Z= 0.261 Angle : 0.677 8.437 19527 Z= 0.351 Chirality : 0.046 0.242 2099 Planarity : 0.006 0.054 2369 Dihedral : 13.812 85.006 2188 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.82 % Allowed : 15.34 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 0.26 (0.20), residues: 1596 helix: 0.73 (0.19), residues: 699 sheet: 0.18 (0.30), residues: 253 loop : -0.30 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 325 TYR 0.021 0.002 TYR C 291 PHE 0.034 0.003 PHE A 969 TRP 0.023 0.002 TRP B 241 HIS 0.009 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00615 (14286) covalent geometry : angle 0.67712 (19527) hydrogen bonds : bond 0.04480 ( 673) hydrogen bonds : angle 5.40699 ( 1883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.5250 (OUTLIER) cc_final: 0.4492 (pp20) REVERT: A 191 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6446 (tp30) REVERT: A 200 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6816 (mm-30) REVERT: A 311 LEU cc_start: 0.7957 (mt) cc_final: 0.7615 (mp) REVERT: A 375 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6197 (pm20) REVERT: A 382 MET cc_start: 0.7296 (tpp) cc_final: 0.6838 (tpp) REVERT: A 473 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6916 (mp) REVERT: A 475 SER cc_start: 0.6839 (m) cc_final: 0.6512 (t) REVERT: A 541 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6225 (mt0) REVERT: A 833 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6508 (mm-30) REVERT: A 963 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7293 (tm-30) REVERT: A 985 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6320 (mtp) REVERT: A 1107 ASP cc_start: 0.7649 (m-30) cc_final: 0.7391 (m-30) REVERT: A 1146 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.5626 (mtp180) REVERT: A 1219 ASP cc_start: 0.6033 (t0) cc_final: 0.5750 (t0) REVERT: B 89 ASP cc_start: 0.7520 (t0) cc_final: 0.7246 (t0) REVERT: B 372 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7217 (mt) REVERT: B 468 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6240 (tt) REVERT: C 233 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: C 341 ASP cc_start: 0.6591 (t0) cc_final: 0.6344 (t0) REVERT: C 397 GLN cc_start: 0.7733 (tp40) cc_final: 0.7354 (tp-100) REVERT: C 408 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: C 463 LYS cc_start: 0.7673 (mttt) cc_final: 0.7278 (mtpm) outliers start: 54 outliers final: 28 residues processed: 201 average time/residue: 0.5104 time to fit residues: 113.1595 Evaluate side-chains 200 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 74 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN C 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.206982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.177520 restraints weight = 15250.688| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.83 r_work: 0.4142 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14286 Z= 0.123 Angle : 0.534 9.268 19527 Z= 0.282 Chirality : 0.040 0.217 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.674 85.056 2188 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.18 % Allowed : 16.47 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 0.78 (0.21), residues: 1596 helix: 1.25 (0.20), residues: 701 sheet: 0.36 (0.31), residues: 246 loop : -0.12 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 325 TYR 0.013 0.001 TYR A 363 PHE 0.022 0.001 PHE A 969 TRP 0.018 0.001 TRP B 241 HIS 0.005 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00273 (14286) covalent geometry : angle 0.53391 (19527) hydrogen bonds : bond 0.03305 ( 673) hydrogen bonds : angle 5.02512 ( 1883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.6261 (mm) cc_final: 0.5753 (mt) REVERT: A 105 GLU cc_start: 0.5280 (OUTLIER) cc_final: 0.4540 (pp20) REVERT: A 189 ILE cc_start: 0.7163 (mm) cc_final: 0.6803 (mp) REVERT: A 191 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6390 (tp30) REVERT: A 311 LEU cc_start: 0.7973 (mt) cc_final: 0.7661 (mp) REVERT: A 375 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6137 (pm20) REVERT: A 382 MET cc_start: 0.7272 (tpp) cc_final: 0.6862 (tpp) REVERT: A 475 SER cc_start: 0.6827 (m) cc_final: 0.6514 (t) REVERT: A 541 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6203 (mt0) REVERT: A 793 GLU cc_start: 0.6156 (mt-10) cc_final: 0.5669 (tt0) REVERT: A 833 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6478 (mm-30) REVERT: A 963 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7255 (tm-30) REVERT: A 985 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6346 (mtp) REVERT: A 1107 ASP cc_start: 0.7444 (m-30) cc_final: 0.7140 (m-30) REVERT: A 1144 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: A 1146 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5602 (mtp180) REVERT: B 89 ASP cc_start: 0.7447 (t0) cc_final: 0.7207 (t0) REVERT: B 400 GLN cc_start: 0.6785 (tp-100) cc_final: 0.6388 (tp40) REVERT: C 203 ARG cc_start: 0.6590 (mtm180) cc_final: 0.6228 (mtm180) REVERT: C 253 ASP cc_start: 0.6914 (m-30) cc_final: 0.6656 (m-30) REVERT: C 408 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: C 477 LYS cc_start: 0.7303 (tttp) cc_final: 0.6850 (ttpp) outliers start: 45 outliers final: 24 residues processed: 200 average time/residue: 0.5361 time to fit residues: 118.1922 Evaluate side-chains 193 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 139 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 160 optimal weight: 0.1980 chunk 131 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A 736 ASN A 945 HIS ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.204349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.174663 restraints weight = 15264.304| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.85 r_work: 0.4108 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14286 Z= 0.181 Angle : 0.593 10.066 19527 Z= 0.310 Chirality : 0.042 0.219 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.715 85.353 2188 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.69 % Allowed : 17.03 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 0.62 (0.21), residues: 1596 helix: 1.10 (0.19), residues: 701 sheet: 0.30 (0.31), residues: 246 loop : -0.19 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 325 TYR 0.017 0.002 TYR C 291 PHE 0.022 0.002 PHE A1092 TRP 0.023 0.002 TRP A 918 HIS 0.009 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00420 (14286) covalent geometry : angle 0.59312 (19527) hydrogen bonds : bond 0.03756 ( 673) hydrogen bonds : angle 5.15578 ( 1883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.6248 (mm) cc_final: 0.5993 (mt) REVERT: A 105 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.4588 (pp20) REVERT: A 189 ILE cc_start: 0.7208 (mm) cc_final: 0.6841 (mp) REVERT: A 191 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: A 311 LEU cc_start: 0.7995 (mt) cc_final: 0.7661 (mp) REVERT: A 375 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6151 (pm20) REVERT: A 382 MET cc_start: 0.7254 (tpp) cc_final: 0.6854 (tpp) REVERT: A 475 SER cc_start: 0.6829 (m) cc_final: 0.6524 (t) REVERT: A 541 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6176 (mt0) REVERT: A 793 GLU cc_start: 0.6201 (mt-10) cc_final: 0.5710 (tt0) REVERT: A 833 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6517 (mm-30) REVERT: A 963 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7305 (tm-30) REVERT: A 985 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6354 (mtp) REVERT: A 1107 ASP cc_start: 0.7627 (m-30) cc_final: 0.7248 (m-30) REVERT: A 1144 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: A 1146 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5647 (mtp180) REVERT: A 1219 ASP cc_start: 0.5976 (t0) cc_final: 0.5741 (t0) REVERT: B 89 ASP cc_start: 0.7481 (t0) cc_final: 0.7230 (t0) REVERT: B 407 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5869 (mp) REVERT: C 203 ARG cc_start: 0.6625 (mtm180) cc_final: 0.6252 (mtm180) REVERT: C 233 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6524 (mt-10) REVERT: C 253 ASP cc_start: 0.6915 (m-30) cc_final: 0.6690 (m-30) REVERT: C 397 GLN cc_start: 0.7685 (tp40) cc_final: 0.7298 (tp-100) REVERT: C 408 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: C 477 LYS cc_start: 0.7372 (tttp) cc_final: 0.6864 (ttpp) outliers start: 38 outliers final: 25 residues processed: 186 average time/residue: 0.5367 time to fit residues: 109.9989 Evaluate side-chains 191 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.0470 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 945 HIS A 968 GLN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.204154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.174250 restraints weight = 15078.123| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.78 r_work: 0.4083 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14286 Z= 0.124 Angle : 0.542 11.243 19527 Z= 0.285 Chirality : 0.040 0.207 2099 Planarity : 0.005 0.056 2369 Dihedral : 13.676 85.186 2188 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.69 % Allowed : 17.03 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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 aren not related in a simple way. whole: 0.84 (0.21), residues: 1596 helix: 1.31 (0.20), residues: 703 sheet: 0.32 (0.31), residues: 247 loop : -0.06 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 325 TYR 0.013 0.001 TYR C 291 PHE 0.019 0.001 PHE A1092 TRP 0.021 0.001 TRP A 918 HIS 0.004 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00275 (14286) covalent geometry : angle 0.54198 (19527) hydrogen bonds : bond 0.03284 ( 673) hydrogen bonds : angle 4.97373 ( 1883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4654.63 seconds wall clock time: 80 minutes 3.61 seconds (4803.61 seconds total)