Starting phenix.real_space_refine on Wed Mar 4 00:37:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dcx_27330/03_2026/8dcx_27330.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dcx_27330/03_2026/8dcx_27330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2026/8dcx_27330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2026/8dcx_27330.map" model { file = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2026/8dcx_27330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2026/8dcx_27330.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6141 2.51 5 N 1655 2.21 5 O 1761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7621 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 886} Chain breaks: 10 Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 2006 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 231} Chain breaks: 1 Time building chain proxies: 1.93, per 1000 atoms: 0.20 Number of scatterers: 9627 At special positions: 0 Unit cell: (84.032, 132.288, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1761 8.00 N 1655 7.00 C 6141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 459.9 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 11 sheets defined 49.8% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.999A pdb=" N ILE A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.672A pdb=" N MET A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.646A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.662A pdb=" N ALA A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 189 removed outlier: 4.117A pdb=" N LYS A 184 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.755A pdb=" N VAL A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.045A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.909A pdb=" N VAL A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 330 " --> pdb=" O LEU A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 488 through 494 removed outlier: 4.095A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 555 through 563 removed outlier: 3.930A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 560 " --> pdb=" O TYR A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.795A pdb=" N LEU A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 570 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.557A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.777A pdb=" N LEU A 602 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 638 removed outlier: 5.327A pdb=" N ILE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLN A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.579A pdb=" N ARG A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 718 removed outlier: 4.111A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 4.173A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 875 through 885 removed outlier: 4.216A pdb=" N ASN A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 889 removed outlier: 4.086A pdb=" N ILE A 889 " --> pdb=" O LYS A 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 889' Processing helix chain 'A' and resid 890 through 911 Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.746A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 removed outlier: 3.662A pdb=" N GLN A 993 " --> pdb=" O LEU A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.135A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 removed outlier: 4.323A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1009' Processing helix chain 'A' and resid 1015 through 1018 Processing helix chain 'A' and resid 1019 through 1026 removed outlier: 3.752A pdb=" N ARG A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 454 through 516 removed outlier: 3.590A pdb=" N GLN B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 582 Proline residue: B 568 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 211 removed outlier: 8.647A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.278A pdb=" N LEU A 339 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLU A 385 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A 337 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU A 387 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG A 335 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR A 389 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA A 333 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE A 338 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU A 476 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.579A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.557A pdb=" N THR A 358 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 751 through 753 removed outlier: 4.236A pdb=" N PHE A 751 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS A 759 " --> pdb=" O SER A 753 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 779 through 782 Processing sheet with id=AA8, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AA9, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386 449 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3137 1.34 - 1.46: 1907 1.46 - 1.58: 4673 1.58 - 1.69: 1 1.69 - 1.81: 110 Bond restraints: 9828 Sorted by residual: bond pdb=" CB PRO B 427 " pdb=" CG PRO B 427 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.77e+00 bond pdb=" N ASP B 387 " pdb=" CA ASP B 387 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.11e+00 bond pdb=" CG PRO B 395 " pdb=" CD PRO B 395 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.64e-01 bond pdb=" CG1 ILE A 894 " pdb=" CD1 ILE A 894 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.61e-01 bond pdb=" CG MET A1004 " pdb=" SD MET A1004 " ideal model delta sigma weight residual 1.803 1.780 0.023 2.50e-02 1.60e+03 8.46e-01 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12896 1.62 - 3.24: 303 3.24 - 4.86: 39 4.86 - 6.48: 6 6.48 - 8.10: 3 Bond angle restraints: 13247 Sorted by residual: angle pdb=" N GLY A 439 " pdb=" CA GLY A 439 " pdb=" C GLY A 439 " ideal model delta sigma weight residual 110.43 114.62 -4.19 1.35e+00 5.49e-01 9.62e+00 angle pdb=" C LEU B 420 " pdb=" N ASP B 421 " pdb=" CA ASP B 421 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.32e+00 angle pdb=" N GLU B 462 " pdb=" CA GLU B 462 " pdb=" CB GLU B 462 " ideal model delta sigma weight residual 110.28 114.90 -4.62 1.55e+00 4.16e-01 8.89e+00 angle pdb=" N GLU A1037 " pdb=" CA GLU A1037 " pdb=" CB GLU A1037 " ideal model delta sigma weight residual 110.28 114.75 -4.47 1.55e+00 4.16e-01 8.32e+00 angle pdb=" CA PRO B 427 " pdb=" N PRO B 427 " pdb=" CD PRO B 427 " ideal model delta sigma weight residual 112.00 108.15 3.85 1.40e+00 5.10e-01 7.55e+00 ... (remaining 13242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5299 18.00 - 36.00: 594 36.00 - 53.99: 85 53.99 - 71.99: 15 71.99 - 89.99: 8 Dihedral angle restraints: 6001 sinusoidal: 2559 harmonic: 3442 Sorted by residual: dihedral pdb=" CA LYS A 440 " pdb=" C LYS A 440 " pdb=" N MET A 441 " pdb=" CA MET A 441 " ideal model delta harmonic sigma weight residual 180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA TYR A 165 " pdb=" C TYR A 165 " pdb=" N VAL A 166 " pdb=" CA VAL A 166 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU A 474 " pdb=" CG GLU A 474 " pdb=" CD GLU A 474 " pdb=" OE1 GLU A 474 " ideal model delta sinusoidal sigma weight residual 0.00 89.28 -89.28 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1208 0.056 - 0.111: 207 0.111 - 0.167: 18 0.167 - 0.223: 2 0.223 - 0.278: 1 Chirality restraints: 1436 Sorted by residual: chirality pdb=" CB ILE A 561 " pdb=" CA ILE A 561 " pdb=" CG1 ILE A 561 " pdb=" CG2 ILE A 561 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU A 793 " pdb=" CB LEU A 793 " pdb=" CD1 LEU A 793 " pdb=" CD2 LEU A 793 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1433 not shown) Planarity restraints: 1693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 744 " -0.017 2.00e-02 2.50e+03 1.81e-02 5.75e+00 pdb=" CG PHE A 744 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 744 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 744 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 744 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 744 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 744 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 297 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 298 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 710 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C GLU A 710 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU A 710 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A 711 " -0.010 2.00e-02 2.50e+03 ... (remaining 1690 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 660 2.74 - 3.28: 9908 3.28 - 3.82: 15885 3.82 - 4.36: 18308 4.36 - 4.90: 31056 Nonbonded interactions: 75817 Sorted by model distance: nonbonded pdb=" O MET A1005 " pdb=" OG SER A1008 " model vdw 2.195 3.040 nonbonded pdb=" O CYS A 971 " pdb=" OG1 THR A 974 " model vdw 2.255 3.040 nonbonded pdb=" O LEU A 568 " pdb=" OG SER A 571 " model vdw 2.256 3.040 nonbonded pdb=" O HIS A 450 " pdb=" NE2 GLN A1014 " model vdw 2.259 3.120 nonbonded pdb=" O LEU A 367 " pdb=" ND2 ASN A 575 " model vdw 2.259 3.120 ... (remaining 75812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 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 0.097 9828 Z= 0.141 Angle : 0.584 8.095 13247 Z= 0.309 Chirality : 0.042 0.278 1436 Planarity : 0.004 0.062 1693 Dihedral : 14.710 89.989 3763 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1140 helix: 0.73 (0.24), residues: 513 sheet: -0.33 (0.50), residues: 123 loop : -0.66 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 832 TYR 0.013 0.001 TYR B 556 PHE 0.042 0.002 PHE A 744 TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9828) covalent geometry : angle 0.58431 (13247) hydrogen bonds : bond 0.12923 ( 441) hydrogen bonds : angle 5.35593 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 355 TYR cc_start: 0.7073 (p90) cc_final: 0.6803 (p90) REVERT: A 405 SER cc_start: 0.8209 (p) cc_final: 0.7997 (p) REVERT: A 545 GLU cc_start: 0.7084 (pm20) cc_final: 0.6808 (pm20) REVERT: A 546 GLN cc_start: 0.7425 (mp10) cc_final: 0.6894 (tm130) REVERT: A 549 ASP cc_start: 0.8054 (m-30) cc_final: 0.7700 (m-30) REVERT: A 849 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6487 (mm-30) REVERT: B 359 ASP cc_start: 0.7680 (m-30) cc_final: 0.7380 (m-30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5161 time to fit residues: 94.0912 Evaluate side-chains 149 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.263756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.202244 restraints weight = 11551.239| |-----------------------------------------------------------------------------| r_work (start): 0.4502 rms_B_bonded: 4.14 r_work: 0.4312 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9828 Z= 0.129 Angle : 0.576 7.326 13247 Z= 0.297 Chirality : 0.041 0.155 1436 Planarity : 0.004 0.065 1693 Dihedral : 4.058 17.020 1275 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 1.12 % Allowed : 10.44 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1140 helix: 1.01 (0.23), residues: 524 sheet: -0.30 (0.52), residues: 112 loop : -0.59 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.017 0.001 TYR B 556 PHE 0.034 0.002 PHE A 744 TRP 0.021 0.001 TRP A 479 HIS 0.005 0.001 HIS A 931 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9828) covalent geometry : angle 0.57594 (13247) hydrogen bonds : bond 0.04068 ( 441) hydrogen bonds : angle 4.21550 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.364 Fit side-chains REVERT: A 30 MET cc_start: 0.4552 (mmp) cc_final: 0.4038 (mmm) REVERT: A 123 MET cc_start: 0.6384 (ppp) cc_final: 0.6077 (ppp) REVERT: A 286 MET cc_start: 0.5654 (tmt) cc_final: 0.4432 (ptm) REVERT: A 355 TYR cc_start: 0.7117 (p90) cc_final: 0.6533 (p90) REVERT: A 405 SER cc_start: 0.8575 (p) cc_final: 0.8370 (p) REVERT: A 479 TRP cc_start: 0.7015 (t-100) cc_final: 0.6806 (t-100) REVERT: A 546 GLN cc_start: 0.7794 (mp10) cc_final: 0.7173 (tm130) REVERT: A 549 ASP cc_start: 0.8550 (m-30) cc_final: 0.8238 (m-30) REVERT: A 579 GLU cc_start: 0.5037 (tt0) cc_final: 0.4655 (tt0) REVERT: A 608 ASP cc_start: 0.8305 (t70) cc_final: 0.8015 (t70) REVERT: A 745 MET cc_start: 0.7058 (mpp) cc_final: 0.6786 (mmt) REVERT: A 811 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6611 (mpp) REVERT: A 825 GLN cc_start: 0.6602 (tm-30) cc_final: 0.6188 (tp-100) REVERT: A 849 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6727 (mm-30) REVERT: A 899 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7566 (mmm-85) REVERT: A 1055 MET cc_start: 0.2299 (mpp) cc_final: 0.2018 (mpp) REVERT: B 355 PHE cc_start: 0.6550 (p90) cc_final: 0.6258 (p90) REVERT: B 359 ASP cc_start: 0.8058 (m-30) cc_final: 0.7613 (m-30) outliers start: 12 outliers final: 3 residues processed: 174 average time/residue: 0.4900 time to fit residues: 92.2135 Evaluate side-chains 156 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 845 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.261323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.200728 restraints weight = 11461.638| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 4.05 r_work: 0.4257 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9828 Z= 0.167 Angle : 0.590 6.554 13247 Z= 0.304 Chirality : 0.042 0.159 1436 Planarity : 0.004 0.065 1693 Dihedral : 4.121 16.009 1275 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 2.61 % Allowed : 13.89 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1140 helix: 1.06 (0.23), residues: 523 sheet: -0.44 (0.50), residues: 113 loop : -0.67 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.017 0.001 TYR B 556 PHE 0.034 0.002 PHE A 744 TRP 0.010 0.001 TRP A 574 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9828) covalent geometry : angle 0.58985 (13247) hydrogen bonds : bond 0.04027 ( 441) hydrogen bonds : angle 4.18933 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.4476 (mmp) cc_final: 0.4113 (mmm) REVERT: A 123 MET cc_start: 0.6365 (ppp) cc_final: 0.6068 (ppp) REVERT: A 259 GLU cc_start: 0.7362 (mp0) cc_final: 0.7101 (mp0) REVERT: A 355 TYR cc_start: 0.7066 (p90) cc_final: 0.6525 (p90) REVERT: A 479 TRP cc_start: 0.7042 (t-100) cc_final: 0.6702 (t-100) REVERT: A 546 GLN cc_start: 0.7859 (mp10) cc_final: 0.7334 (tm130) REVERT: A 549 ASP cc_start: 0.8590 (m-30) cc_final: 0.8307 (m-30) REVERT: A 579 GLU cc_start: 0.5195 (tt0) cc_final: 0.4624 (tt0) REVERT: A 608 ASP cc_start: 0.8318 (t70) cc_final: 0.7964 (t70) REVERT: A 610 MET cc_start: 0.6987 (mpp) cc_final: 0.6694 (mpp) REVERT: A 811 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6819 (mpp) REVERT: A 825 GLN cc_start: 0.6609 (tm-30) cc_final: 0.6107 (tp-100) REVERT: A 849 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6717 (mm-30) REVERT: A 886 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7407 (mmpt) REVERT: A 899 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7718 (mmm-85) REVERT: A 925 ASP cc_start: 0.7665 (t70) cc_final: 0.6626 (p0) REVERT: A 1037 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6506 (mm-30) REVERT: A 1055 MET cc_start: 0.2122 (mpp) cc_final: 0.1449 (mpp) REVERT: B 359 ASP cc_start: 0.8114 (m-30) cc_final: 0.7681 (m-30) REVERT: B 398 PHE cc_start: 0.6922 (m-80) cc_final: 0.6510 (t80) outliers start: 28 outliers final: 9 residues processed: 171 average time/residue: 0.5321 time to fit residues: 97.7780 Evaluate side-chains 165 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 82 optimal weight: 0.0570 chunk 39 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.261993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.201791 restraints weight = 11492.158| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 4.03 r_work: 0.4272 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9828 Z= 0.149 Angle : 0.582 7.497 13247 Z= 0.299 Chirality : 0.041 0.157 1436 Planarity : 0.004 0.068 1693 Dihedral : 4.091 16.500 1275 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 2.33 % Allowed : 16.59 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1140 helix: 1.14 (0.24), residues: 523 sheet: -0.70 (0.46), residues: 123 loop : -0.69 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 916 TYR 0.016 0.001 TYR B 556 PHE 0.032 0.002 PHE A 744 TRP 0.011 0.001 TRP A 574 HIS 0.021 0.001 HIS A1047 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9828) covalent geometry : angle 0.58196 (13247) hydrogen bonds : bond 0.03853 ( 441) hydrogen bonds : angle 4.09401 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.4321 (mmp) cc_final: 0.3687 (mmm) REVERT: A 123 MET cc_start: 0.6378 (ppp) cc_final: 0.6039 (ppp) REVERT: A 259 GLU cc_start: 0.7453 (mp0) cc_final: 0.7206 (mp0) REVERT: A 355 TYR cc_start: 0.7004 (p90) cc_final: 0.6490 (p90) REVERT: A 479 TRP cc_start: 0.7069 (t-100) cc_final: 0.6772 (t-100) REVERT: A 486 PHE cc_start: 0.7339 (t80) cc_final: 0.7114 (t80) REVERT: A 489 MET cc_start: 0.8588 (mmp) cc_final: 0.7746 (mpp) REVERT: A 546 GLN cc_start: 0.8004 (mp10) cc_final: 0.7435 (tm130) REVERT: A 549 ASP cc_start: 0.8567 (m-30) cc_final: 0.8299 (m-30) REVERT: A 579 GLU cc_start: 0.5157 (tt0) cc_final: 0.4561 (tt0) REVERT: A 608 ASP cc_start: 0.8221 (t70) cc_final: 0.7876 (t70) REVERT: A 610 MET cc_start: 0.7014 (mpp) cc_final: 0.6610 (mpp) REVERT: A 811 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6780 (mpp) REVERT: A 825 GLN cc_start: 0.6617 (tm-30) cc_final: 0.6085 (tp-100) REVERT: A 849 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6632 (mm-30) REVERT: A 886 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7432 (mmpt) REVERT: A 899 ARG cc_start: 0.7975 (mmt90) cc_final: 0.7731 (mmm-85) REVERT: A 925 ASP cc_start: 0.7643 (t70) cc_final: 0.6607 (p0) REVERT: A 1037 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6550 (mm-30) REVERT: A 1055 MET cc_start: 0.2048 (mpp) cc_final: 0.1287 (mpp) REVERT: B 355 PHE cc_start: 0.6335 (p90) cc_final: 0.6070 (p90) REVERT: B 359 ASP cc_start: 0.8148 (m-30) cc_final: 0.7758 (m-30) outliers start: 25 outliers final: 9 residues processed: 169 average time/residue: 0.5005 time to fit residues: 91.3268 Evaluate side-chains 161 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 917 HIS ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.261705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.201969 restraints weight = 11481.889| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 4.03 r_work: 0.4264 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9828 Z= 0.150 Angle : 0.593 7.263 13247 Z= 0.303 Chirality : 0.041 0.161 1436 Planarity : 0.004 0.066 1693 Dihedral : 4.093 16.172 1275 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 2.61 % Allowed : 17.24 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1140 helix: 1.14 (0.24), residues: 524 sheet: -0.80 (0.46), residues: 123 loop : -0.71 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 832 TYR 0.016 0.001 TYR A 343 PHE 0.030 0.002 PHE A 744 TRP 0.016 0.002 TRP A 574 HIS 0.007 0.001 HIS A 917 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9828) covalent geometry : angle 0.59317 (13247) hydrogen bonds : bond 0.03830 ( 441) hydrogen bonds : angle 4.06209 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.4139 (mmp) cc_final: 0.3485 (mmm) REVERT: A 123 MET cc_start: 0.6268 (ppp) cc_final: 0.5909 (ppp) REVERT: A 259 GLU cc_start: 0.7539 (mp0) cc_final: 0.7307 (mp0) REVERT: A 355 TYR cc_start: 0.6978 (p90) cc_final: 0.6476 (p90) REVERT: A 479 TRP cc_start: 0.7057 (t-100) cc_final: 0.6785 (t-100) REVERT: A 545 GLU cc_start: 0.8127 (pm20) cc_final: 0.7490 (pm20) REVERT: A 546 GLN cc_start: 0.8008 (mp10) cc_final: 0.7409 (tm130) REVERT: A 549 ASP cc_start: 0.8568 (m-30) cc_final: 0.8281 (m-30) REVERT: A 579 GLU cc_start: 0.5078 (tt0) cc_final: 0.4463 (tt0) REVERT: A 608 ASP cc_start: 0.8241 (t70) cc_final: 0.7876 (t70) REVERT: A 610 MET cc_start: 0.7125 (mpp) cc_final: 0.6692 (mpp) REVERT: A 795 GLN cc_start: 0.7999 (tp40) cc_final: 0.7781 (mm110) REVERT: A 811 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6795 (mpp) REVERT: A 825 GLN cc_start: 0.6572 (tm-30) cc_final: 0.6020 (tp-100) REVERT: A 886 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7446 (mmpt) REVERT: A 899 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7756 (mmm-85) REVERT: A 925 ASP cc_start: 0.7684 (t70) cc_final: 0.6665 (p0) REVERT: A 1037 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: A 1055 MET cc_start: 0.2174 (mpp) cc_final: 0.1254 (mpp) REVERT: B 355 PHE cc_start: 0.6327 (p90) cc_final: 0.6083 (p90) REVERT: B 359 ASP cc_start: 0.8167 (m-30) cc_final: 0.7785 (m-30) outliers start: 28 outliers final: 15 residues processed: 168 average time/residue: 0.5080 time to fit residues: 92.0984 Evaluate side-chains 168 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.257454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.197459 restraints weight = 11513.386| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 4.00 r_work: 0.4239 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9828 Z= 0.243 Angle : 0.702 9.062 13247 Z= 0.357 Chirality : 0.044 0.161 1436 Planarity : 0.005 0.067 1693 Dihedral : 4.455 16.857 1275 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 2.89 % Allowed : 19.85 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 1140 helix: 0.83 (0.23), residues: 525 sheet: -0.75 (0.47), residues: 116 loop : -0.85 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 503 TYR 0.021 0.002 TYR A 165 PHE 0.027 0.002 PHE A 744 TRP 0.015 0.002 TRP A 574 HIS 0.012 0.001 HIS A1047 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 9828) covalent geometry : angle 0.70246 (13247) hydrogen bonds : bond 0.04506 ( 441) hydrogen bonds : angle 4.38109 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.4463 (mmp) cc_final: 0.3867 (mmm) REVERT: A 123 MET cc_start: 0.6389 (ppp) cc_final: 0.5990 (ppp) REVERT: A 259 GLU cc_start: 0.7645 (mp0) cc_final: 0.7377 (mp0) REVERT: A 304 MET cc_start: 0.5543 (mpt) cc_final: 0.5215 (mmm) REVERT: A 355 TYR cc_start: 0.7025 (p90) cc_final: 0.6556 (p90) REVERT: A 428 ASN cc_start: 0.7654 (m-40) cc_final: 0.7201 (m-40) REVERT: A 479 TRP cc_start: 0.7137 (t-100) cc_final: 0.6832 (t-100) REVERT: A 545 GLU cc_start: 0.8133 (pm20) cc_final: 0.7564 (pm20) REVERT: A 546 GLN cc_start: 0.8059 (mp10) cc_final: 0.7518 (tm130) REVERT: A 549 ASP cc_start: 0.8640 (m-30) cc_final: 0.8352 (m-30) REVERT: A 579 GLU cc_start: 0.5269 (tt0) cc_final: 0.4582 (tt0) REVERT: A 587 VAL cc_start: 0.4384 (OUTLIER) cc_final: 0.3057 (m) REVERT: A 596 GLU cc_start: 0.7216 (tp30) cc_final: 0.6513 (tp30) REVERT: A 608 ASP cc_start: 0.8383 (t70) cc_final: 0.8159 (t70) REVERT: A 683 ARG cc_start: 0.6208 (ttm110) cc_final: 0.5929 (ttm-80) REVERT: A 760 GLN cc_start: 0.6851 (mp10) cc_final: 0.6483 (mm-40) REVERT: A 795 GLN cc_start: 0.7984 (tp40) cc_final: 0.7537 (mm110) REVERT: A 811 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6820 (mpp) REVERT: A 825 GLN cc_start: 0.6613 (tm-30) cc_final: 0.6062 (tp-100) REVERT: A 849 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6575 (mm-30) REVERT: A 886 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7434 (mmpt) REVERT: A 925 ASP cc_start: 0.7895 (t70) cc_final: 0.6776 (p0) REVERT: A 1037 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: A 1055 MET cc_start: 0.2100 (mpp) cc_final: 0.1164 (mpp) REVERT: B 359 ASP cc_start: 0.8165 (m-30) cc_final: 0.7841 (m-30) outliers start: 31 outliers final: 15 residues processed: 176 average time/residue: 0.5071 time to fit residues: 96.2817 Evaluate side-chains 171 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.258267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.197463 restraints weight = 11479.327| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 4.00 r_work: 0.4196 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9828 Z= 0.207 Angle : 0.685 9.336 13247 Z= 0.345 Chirality : 0.043 0.181 1436 Planarity : 0.005 0.067 1693 Dihedral : 4.477 16.521 1275 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.74 % Rotamer: Outliers : 2.61 % Allowed : 21.25 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1140 helix: 0.79 (0.23), residues: 524 sheet: -1.16 (0.46), residues: 123 loop : -0.82 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 832 TYR 0.018 0.001 TYR A 343 PHE 0.026 0.002 PHE A 744 TRP 0.013 0.002 TRP A 195 HIS 0.006 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 9828) covalent geometry : angle 0.68459 (13247) hydrogen bonds : bond 0.04306 ( 441) hydrogen bonds : angle 4.37615 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.6392 (ppp) cc_final: 0.5948 (ppp) REVERT: A 259 GLU cc_start: 0.7706 (mp0) cc_final: 0.7393 (mp0) REVERT: A 355 TYR cc_start: 0.7097 (p90) cc_final: 0.6613 (p90) REVERT: A 428 ASN cc_start: 0.7498 (m-40) cc_final: 0.6999 (m-40) REVERT: A 479 TRP cc_start: 0.7184 (t-100) cc_final: 0.6813 (t-100) REVERT: A 545 GLU cc_start: 0.8126 (pm20) cc_final: 0.7516 (pm20) REVERT: A 546 GLN cc_start: 0.8100 (mp10) cc_final: 0.7498 (tm130) REVERT: A 549 ASP cc_start: 0.8570 (m-30) cc_final: 0.8276 (m-30) REVERT: A 579 GLU cc_start: 0.5222 (tt0) cc_final: 0.4540 (tt0) REVERT: A 596 GLU cc_start: 0.7203 (tp30) cc_final: 0.6481 (tp30) REVERT: A 605 ASN cc_start: 0.7549 (m-40) cc_final: 0.7315 (m-40) REVERT: A 608 ASP cc_start: 0.8351 (t70) cc_final: 0.8112 (t70) REVERT: A 760 GLN cc_start: 0.6836 (mp10) cc_final: 0.6433 (mm-40) REVERT: A 795 GLN cc_start: 0.7958 (tp40) cc_final: 0.7696 (mm110) REVERT: A 811 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6868 (mpp) REVERT: A 825 GLN cc_start: 0.6591 (tm-30) cc_final: 0.6024 (tp-100) REVERT: A 849 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6549 (mm-30) REVERT: A 886 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7431 (mmpt) REVERT: A 899 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7469 (mmm-85) REVERT: A 982 GLU cc_start: 0.6391 (pt0) cc_final: 0.5844 (pm20) REVERT: A 1037 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6563 (mm-30) REVERT: A 1055 MET cc_start: 0.2150 (mpp) cc_final: 0.1163 (mpp) REVERT: B 359 ASP cc_start: 0.8232 (m-30) cc_final: 0.7925 (m-30) outliers start: 28 outliers final: 17 residues processed: 175 average time/residue: 0.5064 time to fit residues: 95.6179 Evaluate side-chains 172 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 546 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.260193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.199844 restraints weight = 11482.860| |-----------------------------------------------------------------------------| r_work (start): 0.4485 rms_B_bonded: 4.02 r_work: 0.4303 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9828 Z= 0.151 Angle : 0.657 9.816 13247 Z= 0.330 Chirality : 0.043 0.240 1436 Planarity : 0.004 0.066 1693 Dihedral : 4.335 16.696 1275 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 2.52 % Allowed : 22.37 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1140 helix: 0.88 (0.23), residues: 527 sheet: -1.18 (0.46), residues: 123 loop : -0.79 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 832 TYR 0.015 0.001 TYR B 556 PHE 0.037 0.002 PHE B 355 TRP 0.016 0.002 TRP A 783 HIS 0.005 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9828) covalent geometry : angle 0.65682 (13247) hydrogen bonds : bond 0.03937 ( 441) hydrogen bonds : angle 4.22159 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.6428 (ppp) cc_final: 0.5987 (ppp) REVERT: A 259 GLU cc_start: 0.7659 (mp0) cc_final: 0.7330 (mp0) REVERT: A 355 TYR cc_start: 0.7019 (p90) cc_final: 0.6539 (p90) REVERT: A 428 ASN cc_start: 0.7472 (m-40) cc_final: 0.6979 (m-40) REVERT: A 479 TRP cc_start: 0.7186 (t-100) cc_final: 0.6871 (t-100) REVERT: A 545 GLU cc_start: 0.8091 (pm20) cc_final: 0.7489 (pm20) REVERT: A 546 GLN cc_start: 0.8145 (mp-120) cc_final: 0.7600 (tm130) REVERT: A 549 ASP cc_start: 0.8576 (m-30) cc_final: 0.8274 (m-30) REVERT: A 579 GLU cc_start: 0.4980 (tt0) cc_final: 0.4320 (tt0) REVERT: A 587 VAL cc_start: 0.4429 (OUTLIER) cc_final: 0.3106 (m) REVERT: A 596 GLU cc_start: 0.7135 (tp30) cc_final: 0.6419 (tp30) REVERT: A 605 ASN cc_start: 0.7521 (m-40) cc_final: 0.7303 (m-40) REVERT: A 608 ASP cc_start: 0.8295 (t70) cc_final: 0.8068 (t70) REVERT: A 630 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7769 (tp-100) REVERT: A 795 GLN cc_start: 0.7932 (tp40) cc_final: 0.7673 (mm110) REVERT: A 811 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6858 (mpp) REVERT: A 825 GLN cc_start: 0.6572 (tm-30) cc_final: 0.6012 (tp-100) REVERT: A 886 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7469 (mmpt) REVERT: A 899 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7328 (mmm-85) REVERT: A 982 GLU cc_start: 0.6315 (pt0) cc_final: 0.5797 (pm20) REVERT: A 1037 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6547 (mm-30) REVERT: A 1055 MET cc_start: 0.2317 (mpp) cc_final: 0.1369 (mpp) REVERT: B 355 PHE cc_start: 0.6304 (p90) cc_final: 0.5995 (p90) REVERT: B 359 ASP cc_start: 0.8245 (m-30) cc_final: 0.7939 (m-30) outliers start: 27 outliers final: 16 residues processed: 172 average time/residue: 0.5032 time to fit residues: 93.3780 Evaluate side-chains 172 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 503 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 55 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.263399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.204758 restraints weight = 11378.892| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 3.97 r_work: 0.4317 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9828 Z= 0.134 Angle : 0.647 10.131 13247 Z= 0.326 Chirality : 0.042 0.163 1436 Planarity : 0.004 0.064 1693 Dihedral : 4.200 16.550 1275 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 1.96 % Allowed : 23.02 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1140 helix: 1.11 (0.24), residues: 520 sheet: -0.92 (0.49), residues: 116 loop : -0.80 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 832 TYR 0.019 0.001 TYR A 343 PHE 0.032 0.002 PHE B 355 TRP 0.027 0.002 TRP A 783 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9828) covalent geometry : angle 0.64660 (13247) hydrogen bonds : bond 0.03748 ( 441) hydrogen bonds : angle 4.13587 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.4371 (mmp) cc_final: 0.3614 (mmm) REVERT: A 123 MET cc_start: 0.6438 (ppp) cc_final: 0.5983 (ppp) REVERT: A 162 ARG cc_start: 0.7001 (pmt170) cc_final: 0.6789 (pmm150) REVERT: A 355 TYR cc_start: 0.7022 (p90) cc_final: 0.6499 (p90) REVERT: A 479 TRP cc_start: 0.7164 (t-100) cc_final: 0.6860 (t-100) REVERT: A 545 GLU cc_start: 0.8067 (pm20) cc_final: 0.7573 (pm20) REVERT: A 546 GLN cc_start: 0.8120 (mp-120) cc_final: 0.7574 (tm130) REVERT: A 549 ASP cc_start: 0.8552 (m-30) cc_final: 0.8240 (m-30) REVERT: A 579 GLU cc_start: 0.4769 (tt0) cc_final: 0.4131 (tt0) REVERT: A 587 VAL cc_start: 0.4480 (OUTLIER) cc_final: 0.3121 (m) REVERT: A 608 ASP cc_start: 0.8222 (t70) cc_final: 0.7982 (t70) REVERT: A 630 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7695 (tp-100) REVERT: A 697 MET cc_start: 0.5944 (ttp) cc_final: 0.5646 (ttm) REVERT: A 700 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6843 (pttm) REVERT: A 772 MET cc_start: -0.0336 (pmt) cc_final: -0.0951 (ptp) REVERT: A 795 GLN cc_start: 0.7889 (tp40) cc_final: 0.7625 (mm110) REVERT: A 806 ASP cc_start: 0.7058 (t70) cc_final: 0.6807 (OUTLIER) REVERT: A 809 GLN cc_start: 0.6982 (pm20) cc_final: 0.6305 (pp30) REVERT: A 811 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6848 (mpp) REVERT: A 825 GLN cc_start: 0.6576 (tm-30) cc_final: 0.6006 (tp-100) REVERT: A 886 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7441 (mmpt) REVERT: A 899 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7536 (mmm-85) REVERT: A 982 GLU cc_start: 0.6254 (pt0) cc_final: 0.5749 (pm20) REVERT: A 1037 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6475 (mm-30) REVERT: A 1055 MET cc_start: 0.2278 (mpp) cc_final: 0.1393 (mpp) REVERT: B 355 PHE cc_start: 0.6393 (p90) cc_final: 0.6087 (p90) REVERT: B 359 ASP cc_start: 0.8229 (m-30) cc_final: 0.7932 (m-30) outliers start: 21 outliers final: 15 residues processed: 160 average time/residue: 0.5071 time to fit residues: 87.3971 Evaluate side-chains 163 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 503 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 79 optimal weight: 0.0070 chunk 105 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.262961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.200210 restraints weight = 11585.609| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 4.22 r_work: 0.4308 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9828 Z= 0.132 Angle : 0.652 10.528 13247 Z= 0.327 Chirality : 0.042 0.206 1436 Planarity : 0.004 0.066 1693 Dihedral : 4.144 16.616 1275 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 1.96 % Allowed : 23.21 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1140 helix: 1.08 (0.24), residues: 526 sheet: -0.88 (0.50), residues: 116 loop : -0.83 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 832 TYR 0.019 0.001 TYR A 343 PHE 0.030 0.002 PHE B 355 TRP 0.038 0.002 TRP A 783 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9828) covalent geometry : angle 0.65212 (13247) hydrogen bonds : bond 0.03718 ( 441) hydrogen bonds : angle 4.10570 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.4334 (mmp) cc_final: 0.3480 (mmm) REVERT: A 123 MET cc_start: 0.6430 (ppp) cc_final: 0.5959 (ppp) REVERT: A 355 TYR cc_start: 0.7008 (p90) cc_final: 0.6459 (p90) REVERT: A 383 TRP cc_start: 0.3456 (m-10) cc_final: 0.1870 (m-10) REVERT: A 479 TRP cc_start: 0.7174 (t-100) cc_final: 0.6861 (t-100) REVERT: A 545 GLU cc_start: 0.8056 (pm20) cc_final: 0.7552 (pm20) REVERT: A 546 GLN cc_start: 0.8127 (mp-120) cc_final: 0.7576 (tm130) REVERT: A 549 ASP cc_start: 0.8555 (m-30) cc_final: 0.8251 (m-30) REVERT: A 579 GLU cc_start: 0.4767 (tt0) cc_final: 0.4131 (tt0) REVERT: A 587 VAL cc_start: 0.4461 (OUTLIER) cc_final: 0.3112 (m) REVERT: A 608 ASP cc_start: 0.8256 (t70) cc_final: 0.8006 (t70) REVERT: A 630 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7701 (tp-100) REVERT: A 697 MET cc_start: 0.5937 (ttp) cc_final: 0.5621 (ttt) REVERT: A 700 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6792 (mptt) REVERT: A 772 MET cc_start: -0.0471 (pmt) cc_final: -0.1075 (ptp) REVERT: A 795 GLN cc_start: 0.7915 (tp40) cc_final: 0.7649 (mm110) REVERT: A 811 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6840 (mpp) REVERT: A 825 GLN cc_start: 0.6579 (tm-30) cc_final: 0.6007 (tp-100) REVERT: A 886 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7410 (mmpt) REVERT: A 982 GLU cc_start: 0.6246 (pt0) cc_final: 0.5741 (pm20) REVERT: A 1037 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6466 (mm-30) REVERT: A 1055 MET cc_start: 0.2314 (mpp) cc_final: 0.1458 (mpp) REVERT: B 355 PHE cc_start: 0.6344 (p90) cc_final: 0.6033 (p90) REVERT: B 359 ASP cc_start: 0.8241 (m-30) cc_final: 0.7942 (m-30) outliers start: 21 outliers final: 15 residues processed: 160 average time/residue: 0.5360 time to fit residues: 92.5366 Evaluate side-chains 162 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LYS Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 503 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 809 GLN ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 GLN B 365 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.260477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.197074 restraints weight = 11623.509| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 4.27 r_work: 0.4287 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9828 Z= 0.163 Angle : 0.682 10.706 13247 Z= 0.343 Chirality : 0.043 0.207 1436 Planarity : 0.004 0.064 1693 Dihedral : 4.213 15.805 1275 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.26 % Rotamer: Outliers : 2.24 % Allowed : 23.11 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 1140 helix: 1.00 (0.24), residues: 526 sheet: -0.97 (0.49), residues: 116 loop : -0.84 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 832 TYR 0.018 0.001 TYR A 343 PHE 0.028 0.002 PHE B 355 TRP 0.032 0.002 TRP A 783 HIS 0.005 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9828) covalent geometry : angle 0.68182 (13247) hydrogen bonds : bond 0.03943 ( 441) hydrogen bonds : angle 4.18936 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4225.97 seconds wall clock time: 72 minutes 27.65 seconds (4347.65 seconds total)