Starting phenix.real_space_refine on Thu Jun 12 10:11:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gge_51329/06_2025/9gge_51329.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gge_51329/06_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_51329/06_2025/9gge_51329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gge_51329/06_2025/9gge_51329.map" model { file = "/net/cci-nas-00/data/ceres_data/9gge_51329/06_2025/9gge_51329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gge_51329/06_2025/9gge_51329.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.64, per 1000 atoms: 0.62 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: 3.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.12 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: 5.43 Time building geometry restraints manager: 3.93 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: 1.410 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.150 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (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 TRP 0.007 0.001 TRP A 748 HIS 0.003 0.000 HIS C 258 PHE 0.014 0.001 PHE B 403 TYR 0.009 0.001 TYR A1108 ARG 0.002 0.000 ARG A 802 Details of bonding type rmsd hydrogen bonds : bond 0.17588 ( 673) hydrogen bonds : angle 7.47731 ( 1883) covalent geometry : bond 0.00274 (14286) covalent geometry : angle 0.53101 (19527) *********************** 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 : 1.352 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: 1.2592 time to fit residues: 432.9127 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 : 1.338 ------------------------------------------------------------------------------- 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 138 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 736 ASN A 758 ASN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.201931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.172167 restraints weight = 15303.859| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.95 r_work: 0.4066 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3970 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 14286 Z= 0.321 Angle : 0.727 8.794 19527 Z= 0.377 Chirality : 0.049 0.242 2099 Planarity : 0.006 0.060 2369 Dihedral : 14.301 124.216 2194 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.66 % Allowed : 11.17 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1596 helix: 0.70 (0.19), residues: 690 sheet: 0.24 (0.32), residues: 256 loop : -0.25 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 241 HIS 0.013 0.002 HIS A 945 PHE 0.026 0.003 PHE A1129 TYR 0.020 0.003 TYR B 291 ARG 0.009 0.001 ARG A 807 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 673) hydrogen bonds : angle 5.73599 ( 1883) covalent geometry : bond 0.00758 (14286) covalent geometry : angle 0.72716 (19527) *********************** 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 258 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5805 (mt-10) cc_final: 0.4990 (pp20) REVERT: A 87 ILE cc_start: 0.6302 (mm) cc_final: 0.6051 (mt) REVERT: A 105 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.4329 (pp20) REVERT: A 145 LYS cc_start: 0.7755 (tttp) cc_final: 0.7168 (tmmt) REVERT: A 189 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6904 (mm) REVERT: A 191 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6583 (tp30) REVERT: A 375 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6258 (pm20) REVERT: A 473 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7106 (mp) REVERT: A 475 SER cc_start: 0.7237 (m) cc_final: 0.6889 (p) REVERT: A 736 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7120 (t0) REVERT: A 963 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7448 (tm-30) REVERT: A 1146 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.5462 (ptm160) REVERT: B 372 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7364 (mt) REVERT: B 462 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5374 (mmm) REVERT: B 465 MET cc_start: 0.6605 (mtm) cc_final: 0.5933 (mpp) REVERT: C 89 ASP cc_start: 0.6875 (m-30) cc_final: 0.6674 (m-30) REVERT: C 233 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6447 (mt-10) REVERT: C 397 GLN cc_start: 0.7722 (tp40) cc_final: 0.7351 (tp-100) REVERT: C 463 LYS cc_start: 0.7691 (mttt) cc_final: 0.7329 (mtpm) outliers start: 66 outliers final: 24 residues processed: 234 average time/residue: 1.1437 time to fit residues: 295.8164 Evaluate side-chains 194 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU 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 292 LEU Chi-restraints excluded: chain A residue 462 SER 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 606 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1141 VAL 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 462 MET Chi-restraints excluded: chain B residue 468 ILE 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 440 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 736 ASN A1202 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN C 96 HIS C 313 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.206373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177379 restraints weight = 15209.744| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.87 r_work: 0.4129 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14286 Z= 0.131 Angle : 0.535 7.106 19527 Z= 0.282 Chirality : 0.040 0.155 2099 Planarity : 0.005 0.052 2369 Dihedral : 13.833 83.826 2192 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.89 % Allowed : 12.65 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1596 helix: 1.14 (0.20), residues: 694 sheet: 0.42 (0.33), residues: 241 loop : -0.12 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 241 HIS 0.009 0.001 HIS C 313 PHE 0.013 0.001 PHE C 403 TYR 0.022 0.002 TYR C 432 ARG 0.007 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 673) hydrogen bonds : angle 5.20885 ( 1883) covalent geometry : bond 0.00284 (14286) covalent geometry : angle 0.53534 (19527) *********************** 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 235 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 1.553 Fit side-chains REVERT: A 105 GLU cc_start: 0.4879 (OUTLIER) cc_final: 0.4192 (pp20) REVERT: A 189 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6739 (mm) REVERT: A 191 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6460 (tp30) REVERT: A 200 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6693 (mm-30) REVERT: A 311 LEU cc_start: 0.7985 (mt) cc_final: 0.7707 (mp) REVERT: A 375 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6157 (pm20) REVERT: A 382 MET cc_start: 0.7244 (tpp) cc_final: 0.6989 (tpp) REVERT: A 473 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6913 (mp) REVERT: A 475 SER cc_start: 0.7010 (m) cc_final: 0.6596 (t) REVERT: A 736 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7254 (t0) REVERT: A 833 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6477 (mm-30) REVERT: A 963 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7376 (tm-30) REVERT: A 1107 ASP cc_start: 0.7648 (m-30) cc_final: 0.7279 (m-30) REVERT: A 1146 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5420 (ptm-80) REVERT: B 427 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7296 (pp30) REVERT: B 465 MET cc_start: 0.6638 (mtm) cc_final: 0.5968 (mpp) REVERT: C 89 ASP cc_start: 0.6969 (m-30) cc_final: 0.6717 (m-30) REVERT: C 203 ARG cc_start: 0.6429 (mtm180) cc_final: 0.5887 (mmp-170) REVERT: C 408 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: C 445 GLU cc_start: 0.6542 (mp0) cc_final: 0.6325 (mp0) outliers start: 55 outliers final: 19 residues processed: 217 average time/residue: 1.1133 time to fit residues: 268.7296 Evaluate side-chains 184 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 467 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 833 GLU 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 405 GLU Chi-restraints excluded: chain B residue 411 ILE 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 408 GLU Chi-restraints excluded: chain C residue 440 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 6 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.201828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.172073 restraints weight = 15206.874| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.93 r_work: 0.4066 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3967 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14286 Z= 0.248 Angle : 0.648 9.201 19527 Z= 0.337 Chirality : 0.046 0.260 2099 Planarity : 0.006 0.053 2369 Dihedral : 13.881 84.950 2189 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.02 % Allowed : 12.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1596 helix: 0.76 (0.19), residues: 691 sheet: 0.15 (0.31), residues: 241 loop : -0.27 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 241 HIS 0.018 0.001 HIS A 945 PHE 0.021 0.002 PHE A1129 TYR 0.018 0.002 TYR B 291 ARG 0.005 0.001 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 673) hydrogen bonds : angle 5.43570 ( 1883) covalent geometry : bond 0.00581 (14286) covalent geometry : angle 0.64831 (19527) *********************** 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 240 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 169 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.6203 (mm) cc_final: 0.5943 (mt) REVERT: A 105 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4269 (pp20) REVERT: A 191 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6560 (tp30) REVERT: A 375 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6202 (pm20) REVERT: A 473 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7034 (mp) REVERT: A 475 SER cc_start: 0.6901 (m) cc_final: 0.6509 (t) REVERT: A 541 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.6156 (mt0) REVERT: A 833 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6643 (mm-30) REVERT: A 963 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7442 (tm-30) REVERT: A 1146 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5585 (mtp180) REVERT: A 1219 ASP cc_start: 0.6149 (t0) cc_final: 0.5896 (t0) REVERT: B 372 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7353 (mt) REVERT: B 462 MET cc_start: 0.5578 (OUTLIER) cc_final: 0.5235 (mmm) REVERT: C 89 ASP cc_start: 0.7040 (m-30) cc_final: 0.6787 (m-30) REVERT: C 233 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6480 (mt-10) REVERT: C 397 GLN cc_start: 0.7754 (tp40) cc_final: 0.7389 (tp-100) REVERT: C 408 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: C 419 GLU cc_start: 0.7507 (tt0) cc_final: 0.7303 (tt0) REVERT: C 432 TYR cc_start: 0.7405 (m-80) cc_final: 0.7065 (m-10) REVERT: C 463 LYS cc_start: 0.7701 (mttt) cc_final: 0.7158 (mtpt) outliers start: 71 outliers final: 30 residues processed: 211 average time/residue: 1.1095 time to fit residues: 259.5507 Evaluate side-chains 202 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 232 ARG 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 780 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 1095 SER Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1141 VAL 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 462 MET 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 421 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 ASN A 811 GLN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.202461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.172818 restraints weight = 15357.021| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.89 r_work: 0.4084 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3986 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14286 Z= 0.210 Angle : 0.603 7.548 19527 Z= 0.315 Chirality : 0.044 0.378 2099 Planarity : 0.005 0.055 2369 Dihedral : 13.875 85.244 2189 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.95 % Allowed : 13.14 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1596 helix: 0.73 (0.19), residues: 697 sheet: 0.02 (0.31), residues: 251 loop : -0.31 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 241 HIS 0.017 0.001 HIS A 945 PHE 0.019 0.002 PHE A1129 TYR 0.025 0.002 TYR A1166 ARG 0.008 0.001 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 673) hydrogen bonds : angle 5.34364 ( 1883) covalent geometry : bond 0.00489 (14286) covalent geometry : angle 0.60297 (19527) *********************** 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 246 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 176 time to evaluate : 1.373 Fit side-chains REVERT: A 87 ILE cc_start: 0.6151 (mm) cc_final: 0.5756 (mm) REVERT: A 105 GLU cc_start: 0.5092 (OUTLIER) cc_final: 0.4327 (pp20) REVERT: A 191 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: A 200 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 311 LEU cc_start: 0.7997 (mt) cc_final: 0.7717 (mp) REVERT: A 375 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6237 (pm20) REVERT: A 473 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6953 (mp) REVERT: A 475 SER cc_start: 0.6883 (m) cc_final: 0.6516 (t) REVERT: A 541 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6168 (mt0) REVERT: A 736 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7234 (t0) REVERT: A 833 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: A 963 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7433 (tm-30) REVERT: A 985 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6370 (mtp) REVERT: A 1144 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7284 (mm-30) REVERT: A 1146 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5627 (mtp180) REVERT: B 372 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7287 (mt) REVERT: B 462 MET cc_start: 0.5503 (OUTLIER) cc_final: 0.5246 (mmm) REVERT: C 89 ASP cc_start: 0.7085 (m-30) cc_final: 0.6832 (m-30) REVERT: C 203 ARG cc_start: 0.6559 (mtm180) cc_final: 0.6316 (mtm180) REVERT: C 233 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6455 (mt-10) REVERT: C 397 GLN cc_start: 0.7765 (tp40) cc_final: 0.7371 (tp-100) REVERT: C 408 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: C 463 LYS cc_start: 0.7720 (mttt) cc_final: 0.7216 (mtpt) outliers start: 70 outliers final: 31 residues processed: 220 average time/residue: 1.1617 time to fit residues: 284.2986 Evaluate side-chains 205 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 232 ARG 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 603 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 780 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 1083 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 1137 VAL Chi-restraints excluded: chain A residue 1144 GLU 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 372 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 462 MET 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 462 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 153 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 287 ASN B 397 GLN C 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.204220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.175114 restraints weight = 15365.626| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.84 r_work: 0.4104 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14286 Z= 0.155 Angle : 0.559 8.159 19527 Z= 0.294 Chirality : 0.041 0.247 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.800 85.358 2189 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.95 % Allowed : 13.92 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1596 helix: 0.96 (0.19), residues: 700 sheet: 0.12 (0.31), residues: 246 loop : -0.19 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 241 HIS 0.015 0.001 HIS A 945 PHE 0.027 0.002 PHE A 969 TYR 0.023 0.002 TYR A1166 ARG 0.006 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 673) hydrogen bonds : angle 5.18051 ( 1883) covalent geometry : bond 0.00351 (14286) covalent geometry : angle 0.55862 (19527) *********************** 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 247 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.6157 (mm) cc_final: 0.5718 (mm) REVERT: A 105 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4452 (pp20) REVERT: A 189 ILE cc_start: 0.7149 (mm) cc_final: 0.6799 (mp) REVERT: A 191 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6388 (tt0) REVERT: A 200 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6808 (mm-30) REVERT: A 231 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5771 (tp30) REVERT: A 311 LEU cc_start: 0.7972 (mt) cc_final: 0.7683 (mp) REVERT: A 375 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6225 (pm20) REVERT: A 382 MET cc_start: 0.7350 (tpp) cc_final: 0.6948 (tpp) REVERT: A 473 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6922 (mp) REVERT: A 475 SER cc_start: 0.6857 (m) cc_final: 0.6505 (t) REVERT: A 541 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6201 (mt0) REVERT: A 736 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.7007 (t0) REVERT: A 833 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: A 963 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7460 (tm-30) REVERT: A 985 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6378 (mtp) REVERT: A 1107 ASP cc_start: 0.7717 (m-30) cc_final: 0.7366 (m-30) REVERT: A 1144 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: A 1146 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.5589 (mtp180) REVERT: A 1163 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6116 (tpt) REVERT: A 1219 ASP cc_start: 0.6029 (t0) cc_final: 0.5801 (t0) REVERT: B 462 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.5103 (mmm) REVERT: C 233 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: C 397 GLN cc_start: 0.7708 (tp40) cc_final: 0.7313 (tp-100) REVERT: C 408 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: C 463 LYS cc_start: 0.7704 (mttt) cc_final: 0.7214 (mtpt) outliers start: 70 outliers final: 29 residues processed: 219 average time/residue: 1.6142 time to fit residues: 392.5563 Evaluate side-chains 203 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 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 232 ARG 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 736 ASN Chi-restraints excluded: chain A residue 780 GLN 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 1144 GLU Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 462 MET 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 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 421 MET Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 462 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 3 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 287 ASN B 397 GLN C 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.204819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.175136 restraints weight = 15352.159| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.86 r_work: 0.4109 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14286 Z= 0.148 Angle : 0.550 8.910 19527 Z= 0.289 Chirality : 0.041 0.260 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.732 85.393 2188 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.45 % Allowed : 14.84 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1596 helix: 1.08 (0.19), residues: 702 sheet: 0.15 (0.31), residues: 246 loop : -0.11 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 241 HIS 0.010 0.001 HIS A 945 PHE 0.045 0.002 PHE A 969 TYR 0.023 0.002 TYR A1166 ARG 0.007 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 673) hydrogen bonds : angle 5.12299 ( 1883) covalent geometry : bond 0.00335 (14286) covalent geometry : angle 0.55030 (19527) *********************** 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 231 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 1.337 Fit side-chains REVERT: A 87 ILE cc_start: 0.6157 (mm) cc_final: 0.5671 (mm) REVERT: A 105 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4372 (pp20) REVERT: A 189 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6756 (mp) REVERT: A 191 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6363 (tt0) REVERT: A 200 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 230 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6159 (tt0) REVERT: A 231 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5788 (tp30) REVERT: A 311 LEU cc_start: 0.7974 (mt) cc_final: 0.7652 (mp) REVERT: A 375 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6115 (pm20) REVERT: A 382 MET cc_start: 0.7285 (tpp) cc_final: 0.6893 (tpp) REVERT: A 473 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6900 (mp) REVERT: A 475 SER cc_start: 0.6801 (m) cc_final: 0.6452 (t) REVERT: A 541 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6224 (mt0) REVERT: A 736 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6764 (t0) REVERT: A 833 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6522 (mm-30) REVERT: A 963 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7337 (tm-30) REVERT: A 1107 ASP cc_start: 0.7650 (m-30) cc_final: 0.7320 (m-30) REVERT: A 1144 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: A 1146 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.5531 (mtp180) REVERT: A 1163 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6032 (tpt) REVERT: B 372 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7228 (mt) REVERT: B 462 MET cc_start: 0.5246 (OUTLIER) cc_final: 0.4955 (mmm) REVERT: C 203 ARG cc_start: 0.6620 (mtm180) cc_final: 0.6373 (mtm180) REVERT: C 233 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6523 (mt-10) REVERT: C 408 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: C 463 LYS cc_start: 0.7636 (mttt) cc_final: 0.7051 (mtpt) outliers start: 63 outliers final: 31 residues processed: 209 average time/residue: 1.1805 time to fit residues: 272.5381 Evaluate side-chains 205 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 231 GLU 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 473 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 780 GLN 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 1095 SER Chi-restraints excluded: chain A residue 1103 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 A residue 1163 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 462 MET 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 421 MET Chi-restraints excluded: chain C residue 440 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 128 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 397 GLN C 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.205939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.176548 restraints weight = 15311.919| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 1.85 r_work: 0.4127 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3049 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= 0.133 Angle : 0.540 8.616 19527 Z= 0.284 Chirality : 0.041 0.240 2099 Planarity : 0.005 0.053 2369 Dihedral : 13.688 85.300 2188 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.10 % Allowed : 15.83 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1596 helix: 1.19 (0.20), residues: 703 sheet: 0.22 (0.31), residues: 244 loop : -0.07 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 241 HIS 0.008 0.001 HIS A 945 PHE 0.043 0.002 PHE A 969 TYR 0.024 0.002 TYR A1166 ARG 0.010 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 673) hydrogen bonds : angle 5.06017 ( 1883) covalent geometry : bond 0.00297 (14286) covalent geometry : angle 0.53981 (19527) *********************** 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 225 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 3.161 Fit side-chains REVERT: A 87 ILE cc_start: 0.6155 (mm) cc_final: 0.5641 (mm) REVERT: A 105 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4426 (pp20) REVERT: A 189 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6722 (mp) REVERT: A 200 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6720 (mm-30) REVERT: A 230 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6142 (tt0) REVERT: A 231 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5722 (tp30) REVERT: A 311 LEU cc_start: 0.7912 (mt) cc_final: 0.7620 (mp) REVERT: A 375 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6092 (pm20) REVERT: A 382 MET cc_start: 0.7276 (tpp) cc_final: 0.6910 (tpp) REVERT: A 473 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6920 (mp) REVERT: A 475 SER cc_start: 0.6718 (m) cc_final: 0.6377 (t) REVERT: A 541 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6201 (mt0) REVERT: A 736 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6478 (t0) REVERT: A 833 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6470 (mm-30) REVERT: A 963 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7280 (tm-30) REVERT: A 1107 ASP cc_start: 0.7626 (m-30) cc_final: 0.7310 (m-30) REVERT: A 1144 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: A 1146 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5544 (mtp180) REVERT: A 1219 ASP cc_start: 0.5946 (t0) cc_final: 0.5721 (t0) REVERT: B 89 ASP cc_start: 0.7404 (t0) cc_final: 0.7180 (t0) REVERT: B 372 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7198 (mt) REVERT: B 407 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5728 (mp) REVERT: B 462 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4890 (mmm) REVERT: C 203 ARG cc_start: 0.6520 (mtm180) cc_final: 0.6257 (mtm180) REVERT: C 233 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6522 (mt-10) REVERT: C 253 ASP cc_start: 0.6867 (m-30) cc_final: 0.6652 (m-30) REVERT: C 408 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: C 432 TYR cc_start: 0.7175 (m-80) cc_final: 0.6964 (m-80) REVERT: C 463 LYS cc_start: 0.7626 (mttt) cc_final: 0.7060 (mtpt) outliers start: 58 outliers final: 31 residues processed: 206 average time/residue: 1.5597 time to fit residues: 355.9618 Evaluate side-chains 207 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 232 ARG 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 473 LEU Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 780 GLN 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 1095 SER Chi-restraints excluded: chain A residue 1103 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 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 463 LYS 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 421 MET Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 125 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 397 GLN C 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.198317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.168215 restraints weight = 15204.932| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.89 r_work: 0.4027 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14286 Z= 0.247 Angle : 0.653 9.801 19527 Z= 0.340 Chirality : 0.046 0.238 2099 Planarity : 0.005 0.053 2369 Dihedral : 13.830 85.378 2188 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.89 % Allowed : 16.40 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1596 helix: 0.75 (0.19), residues: 700 sheet: 0.04 (0.30), residues: 246 loop : -0.30 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 241 HIS 0.005 0.001 HIS A 971 PHE 0.024 0.002 PHE A1092 TYR 0.023 0.002 TYR A1166 ARG 0.009 0.001 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 673) hydrogen bonds : angle 5.35969 ( 1883) covalent geometry : bond 0.00577 (14286) covalent geometry : angle 0.65340 (19527) *********************** 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 218 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.576 Fit side-chains REVERT: A 87 ILE cc_start: 0.6130 (mm) cc_final: 0.5706 (mm) REVERT: A 105 GLU cc_start: 0.5199 (OUTLIER) cc_final: 0.4469 (pp20) REVERT: A 191 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6458 (tp30) REVERT: A 200 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6798 (mm-30) REVERT: A 311 LEU cc_start: 0.7919 (mt) cc_final: 0.7621 (mp) REVERT: A 375 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6051 (pm20) REVERT: A 473 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6930 (mp) REVERT: A 475 SER cc_start: 0.6805 (m) cc_final: 0.6481 (t) REVERT: A 541 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6249 (mt0) REVERT: A 736 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6871 (t0) REVERT: A 833 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6582 (mm-30) REVERT: A 963 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7330 (tm-30) REVERT: A 1144 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: A 1146 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5577 (mtp180) REVERT: A 1219 ASP cc_start: 0.6068 (t0) cc_final: 0.5804 (t0) REVERT: B 372 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7245 (mt) REVERT: B 407 LEU cc_start: 0.6069 (OUTLIER) cc_final: 0.5769 (mp) REVERT: B 462 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.5038 (mmm) REVERT: B 468 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6025 (tt) REVERT: C 203 ARG cc_start: 0.6545 (mtm180) cc_final: 0.6075 (mtm180) REVERT: C 233 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6335 (mt-10) REVERT: C 309 HIS cc_start: 0.5958 (m-70) cc_final: 0.5725 (m90) REVERT: C 397 GLN cc_start: 0.7753 (tp40) cc_final: 0.7318 (tp-100) REVERT: C 408 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: C 463 LYS cc_start: 0.7708 (mttt) cc_final: 0.7146 (mtpt) outliers start: 55 outliers final: 28 residues processed: 203 average time/residue: 1.2766 time to fit residues: 287.5468 Evaluate side-chains 201 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 232 ARG 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 736 ASN Chi-restraints excluded: chain A residue 780 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 1095 SER Chi-restraints excluded: chain A residue 1103 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 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 462 MET 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 421 MET Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 138 optimal weight: 0.0070 chunk 161 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- 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 ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 397 GLN C 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.201358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.171106 restraints weight = 15178.289| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.85 r_work: 0.4052 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14286 Z= 0.151 Angle : 0.572 11.282 19527 Z= 0.300 Chirality : 0.041 0.232 2099 Planarity : 0.005 0.054 2369 Dihedral : 13.765 85.213 2188 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.46 % Allowed : 17.03 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1596 helix: 0.97 (0.20), residues: 704 sheet: 0.13 (0.31), residues: 244 loop : -0.18 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 263 HIS 0.005 0.001 HIS B 96 PHE 0.021 0.001 PHE A1092 TYR 0.016 0.002 TYR C 291 ARG 0.009 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 673) hydrogen bonds : angle 5.16772 ( 1883) covalent geometry : bond 0.00344 (14286) covalent geometry : angle 0.57205 (19527) ********************** 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 216 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 1.573 Fit side-chains REVERT: A 105 GLU cc_start: 0.5151 (OUTLIER) cc_final: 0.4437 (pp20) REVERT: A 189 ILE cc_start: 0.7118 (mm) cc_final: 0.6766 (mp) REVERT: A 191 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6361 (tp30) REVERT: A 200 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6723 (mm-30) REVERT: A 230 GLU cc_start: 0.6380 (mt-10) cc_final: 0.6110 (tt0) REVERT: A 311 LEU cc_start: 0.7876 (mt) cc_final: 0.7569 (mp) REVERT: A 375 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6017 (pm20) REVERT: A 382 MET cc_start: 0.7069 (tpp) cc_final: 0.6803 (tpp) REVERT: A 473 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6907 (mp) REVERT: A 475 SER cc_start: 0.6629 (m) cc_final: 0.6301 (t) REVERT: A 541 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.6161 (mt0) REVERT: A 736 ASN cc_start: 0.6802 (OUTLIER) cc_final: 0.6525 (t0) REVERT: A 833 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6496 (mm-30) REVERT: A 963 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7294 (tm-30) REVERT: A 1107 ASP cc_start: 0.7694 (m-30) cc_final: 0.7411 (m-30) REVERT: A 1144 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: A 1146 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.5545 (mtp180) REVERT: A 1219 ASP cc_start: 0.6026 (t0) cc_final: 0.5803 (t0) REVERT: B 89 ASP cc_start: 0.7533 (t0) cc_final: 0.7254 (t0) REVERT: B 372 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7178 (mt) REVERT: B 407 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5657 (mp) REVERT: B 462 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.4836 (mmm) REVERT: B 468 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.6085 (tt) REVERT: C 203 ARG cc_start: 0.6536 (mtm180) cc_final: 0.6082 (mtm180) REVERT: C 233 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: C 253 ASP cc_start: 0.6792 (m-30) cc_final: 0.6537 (m-30) REVERT: C 397 GLN cc_start: 0.7672 (tp40) cc_final: 0.7224 (tp-100) REVERT: C 408 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: C 463 LYS cc_start: 0.7632 (mttt) cc_final: 0.7105 (mtpt) outliers start: 49 outliers final: 30 residues processed: 201 average time/residue: 1.1990 time to fit residues: 266.0434 Evaluate side-chains 205 residues out of total 1415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 232 ARG 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 780 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 1095 SER Chi-restraints excluded: chain A residue 1103 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 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain B residue 465 MET 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 421 MET Chi-restraints excluded: chain C residue 440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 397 GLN C 258 HIS C 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.204364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.174789 restraints weight = 15193.582| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.81 r_work: 0.4085 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14286 Z= 0.120 Angle : 0.539 11.369 19527 Z= 0.284 Chirality : 0.040 0.218 2099 Planarity : 0.005 0.053 2369 Dihedral : 13.694 85.224 2188 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.04 % Allowed : 17.67 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1596 helix: 1.22 (0.20), residues: 704 sheet: 0.25 (0.32), residues: 236 loop : -0.03 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 263 HIS 0.006 0.001 HIS A 945 PHE 0.019 0.001 PHE A1092 TYR 0.032 0.002 TYR A1166 ARG 0.013 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 673) hydrogen bonds : angle 4.99885 ( 1883) covalent geometry : bond 0.00264 (14286) covalent geometry : angle 0.53939 (19527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11194.54 seconds wall clock time: 196 minutes 2.74 seconds (11762.74 seconds total)