Starting phenix.real_space_refine on Tue Mar 3 17:44:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xou_22280/03_2026/6xou_22280.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xou_22280/03_2026/6xou_22280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2026/6xou_22280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2026/6xou_22280.map" model { file = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2026/6xou_22280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2026/6xou_22280.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 39 5.16 5 C 4897 2.51 5 N 1304 2.21 5 O 1457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 7697 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7697 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 965, 7691 Classifications: {'peptide': 965} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 965, 7691 Classifications: {'peptide': 965} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902} Chain breaks: 1 bond proxies already assigned to first conformer: 7875 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 Time building chain proxies: 2.88, per 1000 atoms: 0.37 Number of scatterers: 7697 At special positions: 0 Unit cell: (84.744, 98.44, 103.576, 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 39 16.00 O 1457 8.00 N 1304 7.00 C 4897 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: 0.55 Conformation dependent library (CDL) restraints added in 511.3 milliseconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 53.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.096A pdb=" N ARG A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.927A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.532A pdb=" N MET A 126 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.725A pdb=" N VAL A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.866A pdb=" N GLU A 244 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.916A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.566A pdb=" N ILE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 4.750A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 527 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.639A pdb=" N ARG A 612 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Proline residue: A 613 - end of helix Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 631 through 642 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 695 through 713 removed outlier: 3.703A pdb=" N PHE A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.550A pdb=" N VAL A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.294A pdb=" N ARG A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.323A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 Processing helix chain 'A' and resid 928 through 945 removed outlier: 3.505A pdb=" N LEU A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 964 Processing helix chain 'A' and resid 968 through 972 removed outlier: 3.566A pdb=" N LYS A 972 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.947A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 997 through 1008 Processing helix chain 'A' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.798A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET A 135 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 149 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.798A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.721A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 373 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.721A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579 removed outlier: 3.554A pdb=" N ASP A 575 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 598 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 645 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 673 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 643 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912 removed outlier: 6.325A pdb=" N THR A 855 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY A1022 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N PHE A 857 " --> pdb=" O GLY A1022 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS A 854 " --> pdb=" O ILE A1035 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1360 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: 1.41 Time building geometry restraints manager: 0.78 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: 2447 1.34 - 1.46: 1495 1.46 - 1.58: 3885 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 7889 Sorted by residual: bond pdb=" C ILE A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.46e+00 bond pdb=" C ILE A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.76e+00 bond pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.71e+00 bond pdb=" CB ASN A 712 " pdb=" CG ASN A 712 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.40e+00 bond pdb=" CG1 ILE A 885 " pdb=" CD1 ILE A 885 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.10e+00 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10166 2.10 - 4.20: 422 4.20 - 6.30: 66 6.30 - 8.40: 28 8.40 - 10.50: 16 Bond angle restraints: 10698 Sorted by residual: angle pdb=" N ASP A 458 " pdb=" CA ASP A 458 " pdb=" C ASP A 458 " ideal model delta sigma weight residual 111.54 117.53 -5.99 1.36e+00 5.41e-01 1.94e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 111.30 106.10 5.20 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C ALA A 580 " pdb=" N GLY A 581 " pdb=" CA GLY A 581 " ideal model delta sigma weight residual 121.70 128.18 -6.48 1.80e+00 3.09e-01 1.30e+01 angle pdb=" C LYS A 893 " pdb=" N PHE A 894 " pdb=" CA PHE A 894 " ideal model delta sigma weight residual 121.54 114.71 6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CA VAL A 615 " pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 118.88 124.27 -5.39 1.54e+00 4.22e-01 1.23e+01 ... (remaining 10693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4386 17.76 - 35.52: 295 35.52 - 53.27: 65 53.27 - 71.03: 15 71.03 - 88.79: 10 Dihedral angle restraints: 4771 sinusoidal: 1952 harmonic: 2819 Sorted by residual: dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N THR A 211 " pdb=" CA THR A 211 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PRO A 170 " pdb=" C PRO A 170 " pdb=" N CYS A 171 " pdb=" CA CYS A 171 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C VAL A 102 " pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" CB VAL A 102 " ideal model delta harmonic sigma weight residual -122.00 -131.21 9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 921 0.070 - 0.140: 213 0.140 - 0.209: 32 0.209 - 0.279: 5 0.279 - 0.349: 1 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CG LEU A 467 " pdb=" CB LEU A 467 " pdb=" CD1 LEU A 467 " pdb=" CD2 LEU A 467 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.18 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR A 94 " pdb=" CA THR A 94 " pdb=" OG1 THR A 94 " pdb=" CG2 THR A 94 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1169 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 301 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C THR A 301 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 301 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 302 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 334 " -0.036 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 335 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 793 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C GLU A 793 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU A 793 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 794 " -0.012 2.00e-02 2.50e+03 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1748 2.79 - 3.32: 6901 3.32 - 3.84: 12652 3.84 - 4.37: 14147 4.37 - 4.90: 24954 Nonbonded interactions: 60402 Sorted by model distance: nonbonded pdb=" ND2 ASN A 783 " pdb=" O PRO A 969 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR A 146 " pdb=" OH TYR A 258 " model vdw 2.270 3.040 nonbonded pdb=" O SER A 351 " pdb=" OG SER A 355 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP A 98 " pdb=" OG1 THR A 100 " model vdw 2.302 3.040 nonbonded pdb=" O HIS A 457 " pdb=" OD1 ASP A 458 " model vdw 2.310 3.040 ... (remaining 60397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.005 0.075 7889 Z= 0.241 Angle : 1.064 10.498 10698 Z= 0.563 Chirality : 0.061 0.349 1172 Planarity : 0.007 0.056 1397 Dihedral : 13.628 88.791 2947 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.23 % Allowed : 2.10 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.51 (0.24), residues: 964 helix: -1.05 (0.21), residues: 447 sheet: 0.29 (0.36), residues: 178 loop : -1.42 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 81 TYR 0.016 0.002 TYR A 662 PHE 0.021 0.002 PHE A 848 TRP 0.016 0.003 TRP A 684 HIS 0.008 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 7889) covalent geometry : angle 1.06367 (10698) hydrogen bonds : bond 0.17832 ( 425) hydrogen bonds : angle 7.64618 ( 1360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8860 (m) cc_final: 0.8624 (p) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0862 time to fit residues: 18.0087 Evaluate side-chains 94 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 151 GLN A 204 ASN A 325 GLN A 430 HIS A 637 GLN A 638 GLN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.044523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035104 restraints weight = 46805.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.036525 restraints weight = 27035.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.037531 restraints weight = 18236.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.038285 restraints weight = 13467.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.038836 restraints weight = 10580.397| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7889 Z= 0.179 Angle : 0.773 10.911 10698 Z= 0.386 Chirality : 0.045 0.191 1172 Planarity : 0.005 0.045 1397 Dihedral : 4.428 22.787 1036 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.40 % Allowed : 11.32 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.33 (0.26), residues: 964 helix: 0.75 (0.24), residues: 453 sheet: 0.97 (0.37), residues: 179 loop : -0.86 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 751 TYR 0.014 0.002 TYR A 587 PHE 0.023 0.002 PHE A 918 TRP 0.032 0.002 TRP A 455 HIS 0.005 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7889) covalent geometry : angle 0.77274 (10698) hydrogen bonds : bond 0.04008 ( 425) hydrogen bonds : angle 5.32434 ( 1360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9536 (tp) cc_final: 0.9317 (tp) REVERT: A 388 TYR cc_start: 0.9302 (p90) cc_final: 0.8791 (p90) REVERT: A 400 ASP cc_start: 0.8975 (t0) cc_final: 0.8644 (t0) REVERT: A 595 MET cc_start: 0.8277 (mmm) cc_final: 0.8053 (mmm) REVERT: A 752 ILE cc_start: 0.9426 (mm) cc_final: 0.9216 (mm) REVERT: A 918 PHE cc_start: 0.9338 (t80) cc_final: 0.9126 (t80) outliers start: 10 outliers final: 5 residues processed: 98 average time/residue: 0.0714 time to fit residues: 10.1855 Evaluate side-chains 84 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN A 771 HIS A 787 GLN A 856 HIS ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.034193 restraints weight = 48236.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.035605 restraints weight = 27435.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.036596 restraints weight = 18322.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.037328 restraints weight = 13494.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.037756 restraints weight = 10532.282| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7889 Z= 0.178 Angle : 0.734 11.438 10698 Z= 0.366 Chirality : 0.044 0.170 1172 Planarity : 0.005 0.043 1397 Dihedral : 4.300 19.920 1036 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.17 % Allowed : 13.19 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.72 (0.26), residues: 964 helix: 1.09 (0.24), residues: 460 sheet: 1.20 (0.37), residues: 170 loop : -0.71 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 599 TYR 0.012 0.002 TYR A 632 PHE 0.018 0.002 PHE A 918 TRP 0.022 0.002 TRP A 455 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7889) covalent geometry : angle 0.73373 (10698) hydrogen bonds : bond 0.03671 ( 425) hydrogen bonds : angle 5.04554 ( 1360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9600 (tp) cc_final: 0.9392 (tp) REVERT: A 126 MET cc_start: 0.8983 (tpt) cc_final: 0.8689 (tpt) REVERT: A 135 MET cc_start: 0.7646 (ttt) cc_final: 0.7404 (ttt) REVERT: A 225 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9326 (mt) REVERT: A 321 ASP cc_start: 0.8952 (p0) cc_final: 0.8743 (t70) REVERT: A 388 TYR cc_start: 0.9255 (p90) cc_final: 0.8838 (p90) REVERT: A 400 ASP cc_start: 0.9038 (t0) cc_final: 0.8717 (t0) REVERT: A 595 MET cc_start: 0.8285 (mmm) cc_final: 0.7887 (mmm) REVERT: A 853 MET cc_start: 0.8534 (mmm) cc_final: 0.8326 (mmm) REVERT: A 911 LYS cc_start: 0.9107 (mttt) cc_final: 0.8887 (mttp) REVERT: A 974 MET cc_start: 0.8651 (tpp) cc_final: 0.8447 (tpp) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.0635 time to fit residues: 7.8134 Evaluate side-chains 77 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 895 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.044587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.035217 restraints weight = 47170.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.036681 restraints weight = 26517.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.037724 restraints weight = 17630.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038480 restraints weight = 12880.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039048 restraints weight = 10053.302| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.119 Angle : 0.701 10.518 10698 Z= 0.337 Chirality : 0.043 0.152 1172 Planarity : 0.004 0.044 1397 Dihedral : 4.084 20.090 1036 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.47 % Allowed : 13.30 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.07 (0.27), residues: 964 helix: 1.38 (0.25), residues: 460 sheet: 1.07 (0.37), residues: 178 loop : -0.38 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 779 TYR 0.011 0.001 TYR A 268 PHE 0.014 0.001 PHE A 935 TRP 0.013 0.001 TRP A 455 HIS 0.002 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7889) covalent geometry : angle 0.70078 (10698) hydrogen bonds : bond 0.03185 ( 425) hydrogen bonds : angle 4.73610 ( 1360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9554 (tp) cc_final: 0.9342 (tp) REVERT: A 123 PHE cc_start: 0.8476 (t80) cc_final: 0.7539 (t80) REVERT: A 225 LEU cc_start: 0.9528 (mt) cc_final: 0.9266 (mt) REVERT: A 388 TYR cc_start: 0.9246 (p90) cc_final: 0.8839 (p90) REVERT: A 400 ASP cc_start: 0.8932 (t0) cc_final: 0.8465 (t0) REVERT: A 431 LYS cc_start: 0.9508 (tppp) cc_final: 0.9236 (tppt) REVERT: A 455 TRP cc_start: 0.8985 (t60) cc_final: 0.8682 (t60) REVERT: A 527 GLU cc_start: 0.9189 (pp20) cc_final: 0.8982 (pp20) REVERT: A 582 ASP cc_start: 0.9335 (p0) cc_final: 0.9091 (t0) REVERT: A 595 MET cc_start: 0.8284 (mmm) cc_final: 0.7905 (mmm) REVERT: A 681 MET cc_start: 0.9370 (mmm) cc_final: 0.9064 (mmm) REVERT: A 755 MET cc_start: 0.8800 (mpp) cc_final: 0.8515 (mpp) outliers start: 2 outliers final: 2 residues processed: 84 average time/residue: 0.0708 time to fit residues: 8.6199 Evaluate side-chains 80 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 617 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.042700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.033762 restraints weight = 49699.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.035158 restraints weight = 28018.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036140 restraints weight = 18617.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.036852 restraints weight = 13645.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.037357 restraints weight = 10674.010| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7889 Z= 0.195 Angle : 0.741 13.260 10698 Z= 0.358 Chirality : 0.043 0.141 1172 Planarity : 0.004 0.040 1397 Dihedral : 4.219 20.797 1036 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.17 % Allowed : 14.70 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.03 (0.26), residues: 964 helix: 1.42 (0.24), residues: 453 sheet: 1.11 (0.36), residues: 174 loop : -0.49 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.012 0.001 TYR A 632 PHE 0.016 0.002 PHE A 598 TRP 0.013 0.002 TRP A 455 HIS 0.005 0.001 HIS A 511 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7889) covalent geometry : angle 0.74085 (10698) hydrogen bonds : bond 0.03356 ( 425) hydrogen bonds : angle 4.85002 ( 1360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9640 (tp) cc_final: 0.9314 (tp) REVERT: A 388 TYR cc_start: 0.9221 (p90) cc_final: 0.8827 (p90) REVERT: A 400 ASP cc_start: 0.9043 (t0) cc_final: 0.8598 (t0) REVERT: A 431 LYS cc_start: 0.9482 (tppp) cc_final: 0.9202 (tppt) REVERT: A 455 TRP cc_start: 0.9108 (t60) cc_final: 0.8719 (t60) REVERT: A 586 GLN cc_start: 0.9339 (tt0) cc_final: 0.8751 (tm-30) REVERT: A 595 MET cc_start: 0.8286 (mmm) cc_final: 0.7878 (mmm) REVERT: A 681 MET cc_start: 0.9398 (mmm) cc_final: 0.9091 (mmm) outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.0689 time to fit residues: 7.9383 Evaluate side-chains 78 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 62 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.042708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.033507 restraints weight = 49214.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.034922 restraints weight = 27750.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.035912 restraints weight = 18453.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.036640 restraints weight = 13550.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.037091 restraints weight = 10647.711| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.157 Angle : 0.738 12.150 10698 Z= 0.354 Chirality : 0.043 0.180 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.196 20.734 1036 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.17 % Allowed : 15.99 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.05 (0.27), residues: 964 helix: 1.42 (0.24), residues: 452 sheet: 1.02 (0.36), residues: 176 loop : -0.39 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 801 TYR 0.011 0.001 TYR A 632 PHE 0.020 0.001 PHE A 123 TRP 0.012 0.001 TRP A 455 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7889) covalent geometry : angle 0.73844 (10698) hydrogen bonds : bond 0.03302 ( 425) hydrogen bonds : angle 4.80918 ( 1360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9640 (tp) cc_final: 0.9331 (tp) REVERT: A 388 TYR cc_start: 0.9226 (p90) cc_final: 0.8788 (p90) REVERT: A 400 ASP cc_start: 0.9022 (t0) cc_final: 0.8794 (t0) REVERT: A 431 LYS cc_start: 0.9489 (tppp) cc_final: 0.9239 (tppt) REVERT: A 582 ASP cc_start: 0.9382 (p0) cc_final: 0.8997 (t0) REVERT: A 586 GLN cc_start: 0.9317 (tt0) cc_final: 0.8741 (tm-30) REVERT: A 595 MET cc_start: 0.8234 (mmm) cc_final: 0.7829 (mmm) REVERT: A 681 MET cc_start: 0.9368 (mmm) cc_final: 0.9042 (mmm) REVERT: A 911 LYS cc_start: 0.9150 (ptpp) cc_final: 0.8950 (mptt) REVERT: A 985 MET cc_start: 0.9133 (ptp) cc_final: 0.8916 (ptp) outliers start: 8 outliers final: 8 residues processed: 76 average time/residue: 0.0645 time to fit residues: 7.3033 Evaluate side-chains 78 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 918 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 275 GLN A 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.041564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.032638 restraints weight = 50667.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.034038 restraints weight = 28475.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035001 restraints weight = 18898.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035714 restraints weight = 13845.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.036198 restraints weight = 10846.993| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7889 Z= 0.222 Angle : 0.774 11.419 10698 Z= 0.377 Chirality : 0.044 0.156 1172 Planarity : 0.004 0.040 1397 Dihedral : 4.401 23.510 1036 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.40 % Allowed : 15.99 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.84 (0.27), residues: 964 helix: 1.28 (0.24), residues: 453 sheet: 0.73 (0.36), residues: 176 loop : -0.44 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.012 0.002 TYR A 632 PHE 0.019 0.002 PHE A 123 TRP 0.011 0.002 TRP A 941 HIS 0.006 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 7889) covalent geometry : angle 0.77410 (10698) hydrogen bonds : bond 0.03574 ( 425) hydrogen bonds : angle 4.93025 ( 1360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9681 (tp) cc_final: 0.9395 (tp) REVERT: A 87 LEU cc_start: 0.8787 (tt) cc_final: 0.8421 (tt) REVERT: A 135 MET cc_start: 0.7550 (tmt) cc_final: 0.6941 (tmt) REVERT: A 142 ASP cc_start: 0.8820 (t0) cc_final: 0.8519 (t0) REVERT: A 318 PHE cc_start: 0.9315 (m-80) cc_final: 0.9043 (m-80) REVERT: A 388 TYR cc_start: 0.9205 (p90) cc_final: 0.8781 (p90) REVERT: A 400 ASP cc_start: 0.9070 (t0) cc_final: 0.8849 (t0) REVERT: A 431 LYS cc_start: 0.9488 (tppp) cc_final: 0.9234 (tppt) REVERT: A 582 ASP cc_start: 0.9400 (p0) cc_final: 0.9053 (t0) REVERT: A 586 GLN cc_start: 0.9324 (tt0) cc_final: 0.8719 (tm-30) REVERT: A 681 MET cc_start: 0.9419 (mmm) cc_final: 0.9107 (mmm) REVERT: A 975 ASP cc_start: 0.9226 (p0) cc_final: 0.9012 (p0) outliers start: 10 outliers final: 10 residues processed: 75 average time/residue: 0.0653 time to fit residues: 7.2977 Evaluate side-chains 78 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 918 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 84 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.043497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034190 restraints weight = 48410.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035651 restraints weight = 27426.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.036660 restraints weight = 18256.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037407 restraints weight = 13391.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037970 restraints weight = 10505.132| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7889 Z= 0.122 Angle : 0.746 11.643 10698 Z= 0.353 Chirality : 0.043 0.194 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.156 20.865 1036 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.93 % Allowed : 16.45 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.11 (0.27), residues: 964 helix: 1.53 (0.25), residues: 452 sheet: 0.76 (0.36), residues: 174 loop : -0.27 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 924 TYR 0.009 0.001 TYR A 268 PHE 0.023 0.001 PHE A 123 TRP 0.011 0.001 TRP A 851 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7889) covalent geometry : angle 0.74554 (10698) hydrogen bonds : bond 0.03235 ( 425) hydrogen bonds : angle 4.72823 ( 1360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9529 (tp) cc_final: 0.9310 (tp) REVERT: A 87 LEU cc_start: 0.8787 (tt) cc_final: 0.8517 (tt) REVERT: A 318 PHE cc_start: 0.9331 (m-80) cc_final: 0.9066 (m-80) REVERT: A 388 TYR cc_start: 0.9198 (p90) cc_final: 0.8737 (p90) REVERT: A 400 ASP cc_start: 0.8910 (t0) cc_final: 0.8638 (t0) REVERT: A 431 LYS cc_start: 0.9473 (tppp) cc_final: 0.9218 (tppt) REVERT: A 582 ASP cc_start: 0.9416 (p0) cc_final: 0.9136 (t0) REVERT: A 586 GLN cc_start: 0.9312 (tt0) cc_final: 0.8687 (tm-30) REVERT: A 595 MET cc_start: 0.8318 (mmm) cc_final: 0.7967 (mmm) REVERT: A 681 MET cc_start: 0.9332 (mmm) cc_final: 0.8934 (mmp) REVERT: A 859 MET cc_start: 0.8651 (mmm) cc_final: 0.8374 (mmm) REVERT: A 975 ASP cc_start: 0.9201 (p0) cc_final: 0.8997 (p0) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 0.0579 time to fit residues: 6.9256 Evaluate side-chains 78 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.042475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.033463 restraints weight = 49164.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.034872 restraints weight = 27889.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.035869 restraints weight = 18574.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.036590 restraints weight = 13601.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.037140 restraints weight = 10656.880| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7889 Z= 0.164 Angle : 0.756 12.052 10698 Z= 0.358 Chirality : 0.043 0.186 1172 Planarity : 0.004 0.039 1397 Dihedral : 4.209 22.655 1036 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.17 % Allowed : 16.80 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.06 (0.27), residues: 964 helix: 1.47 (0.25), residues: 452 sheet: 0.68 (0.36), residues: 175 loop : -0.24 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.011 0.001 TYR A 632 PHE 0.020 0.001 PHE A 123 TRP 0.010 0.001 TRP A 851 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7889) covalent geometry : angle 0.75603 (10698) hydrogen bonds : bond 0.03371 ( 425) hydrogen bonds : angle 4.79313 ( 1360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.279 Fit side-chains REVERT: A 87 LEU cc_start: 0.8793 (tt) cc_final: 0.8474 (tt) REVERT: A 268 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8143 (t80) REVERT: A 318 PHE cc_start: 0.9310 (m-80) cc_final: 0.9051 (m-80) REVERT: A 388 TYR cc_start: 0.9192 (p90) cc_final: 0.8759 (p90) REVERT: A 400 ASP cc_start: 0.9040 (t0) cc_final: 0.8797 (t0) REVERT: A 431 LYS cc_start: 0.9472 (tppp) cc_final: 0.9214 (tppt) REVERT: A 582 ASP cc_start: 0.9440 (p0) cc_final: 0.9117 (t0) REVERT: A 586 GLN cc_start: 0.9301 (tt0) cc_final: 0.8690 (tm-30) REVERT: A 595 MET cc_start: 0.8282 (mmm) cc_final: 0.7966 (mmm) REVERT: A 681 MET cc_start: 0.9401 (mmm) cc_final: 0.9019 (mmp) REVERT: A 911 LYS cc_start: 0.9218 (ptpp) cc_final: 0.8950 (mptt) REVERT: A 975 ASP cc_start: 0.9229 (p0) cc_final: 0.9026 (p0) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.0629 time to fit residues: 7.2718 Evaluate side-chains 78 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.034600 restraints weight = 48171.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.036063 restraints weight = 27105.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.037097 restraints weight = 17976.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.037854 restraints weight = 13128.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.038436 restraints weight = 10225.092| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7889 Z= 0.118 Angle : 0.762 11.734 10698 Z= 0.353 Chirality : 0.043 0.191 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.080 20.850 1036 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.05 % Allowed : 17.27 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.17 (0.27), residues: 964 helix: 1.55 (0.25), residues: 452 sheet: 0.66 (0.36), residues: 177 loop : -0.12 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.009 0.001 TYR A 268 PHE 0.024 0.001 PHE A 123 TRP 0.011 0.001 TRP A 851 HIS 0.003 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7889) covalent geometry : angle 0.76200 (10698) hydrogen bonds : bond 0.03200 ( 425) hydrogen bonds : angle 4.69318 ( 1360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8805 (tt) cc_final: 0.8476 (tt) REVERT: A 318 PHE cc_start: 0.9324 (m-80) cc_final: 0.9076 (m-80) REVERT: A 388 TYR cc_start: 0.9171 (p90) cc_final: 0.8725 (p90) REVERT: A 400 ASP cc_start: 0.8958 (t0) cc_final: 0.8682 (t0) REVERT: A 431 LYS cc_start: 0.9457 (tppp) cc_final: 0.9192 (tppt) REVERT: A 582 ASP cc_start: 0.9453 (p0) cc_final: 0.9181 (t0) REVERT: A 586 GLN cc_start: 0.9278 (tt0) cc_final: 0.8663 (tm-30) REVERT: A 595 MET cc_start: 0.8250 (mmm) cc_final: 0.7909 (mmm) REVERT: A 681 MET cc_start: 0.9363 (mmm) cc_final: 0.8968 (mmp) REVERT: A 743 MET cc_start: 0.8968 (mmm) cc_final: 0.8724 (mmp) REVERT: A 975 ASP cc_start: 0.9203 (p0) cc_final: 0.8970 (p0) REVERT: A 1006 ASP cc_start: 0.8788 (t70) cc_final: 0.8474 (p0) outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.0588 time to fit residues: 7.3396 Evaluate side-chains 79 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 39 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.043754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034430 restraints weight = 48041.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.035890 restraints weight = 27353.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.036925 restraints weight = 18253.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037691 restraints weight = 13365.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.038281 restraints weight = 10454.066| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.122 Angle : 0.753 11.713 10698 Z= 0.351 Chirality : 0.042 0.188 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.058 20.822 1036 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.05 % Allowed : 17.04 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.17 (0.27), residues: 964 helix: 1.55 (0.25), residues: 452 sheet: 0.70 (0.36), residues: 177 loop : -0.14 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 599 TYR 0.009 0.001 TYR A 268 PHE 0.023 0.001 PHE A 123 TRP 0.011 0.001 TRP A 851 HIS 0.002 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7889) covalent geometry : angle 0.75306 (10698) hydrogen bonds : bond 0.03159 ( 425) hydrogen bonds : angle 4.66744 ( 1360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1288.73 seconds wall clock time: 23 minutes 0.75 seconds (1380.75 seconds total)