Starting phenix.real_space_refine on Wed Aug 5 14:50:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.map" model { file = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8se9_40407/08_2026/8se9_40407.cif" } resolution = 3.2 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= 0.023 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 C 6480 2.51 5 N 1790 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10195 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 633 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.29, per 1000 atoms: 0.22 Number of scatterers: 10195 At special positions: 0 Unit cell: (91.652, 105.816, 117.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 1 15.00 O 1886 8.00 N 1790 7.00 C 6480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 413.1 milliseconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 44.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.533A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.909A pdb=" N ASP A 71 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.919A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.837A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.268A pdb=" N HIS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.528A pdb=" N CYS A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.921A pdb=" N ARG A 479 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 480' Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.557A pdb=" N ASP A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.835A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.359A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.602A pdb=" N THR A 600 " --> pdb=" O PRO A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 Processing helix chain 'A' and resid 624 through 631 removed outlier: 4.043A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.302A pdb=" N THR A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 removed outlier: 4.771A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 722 through 740 removed outlier: 3.638A pdb=" N TYR A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.512A pdb=" N GLN A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.611A pdb=" N ILE A 768 " --> pdb=" O GLN A 764 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 798 Processing helix chain 'A' and resid 816 through 832 removed outlier: 3.553A pdb=" N PHE A 820 " --> pdb=" O PHE A 816 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.678A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 874 " --> pdb=" O LYS A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 927 through 939 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.589A pdb=" N LEU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.605A pdb=" N GLY B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.616A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.610A pdb=" N LEU C 48 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.642A pdb=" N VAL C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'D' and resid 103 through 116 removed outlier: 4.677A pdb=" N GLN D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 3.991A pdb=" N GLU D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.869A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU A 36 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.630A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.404A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 254 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 183 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.853A pdb=" N LEU A 464 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 512 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.354A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ARG A 944 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA A 955 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.689A pdb=" N LEU B 85 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N MET B 150 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B 87 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B 152 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.025A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 85 through 86 removed outlier: 7.757A pdb=" N LEU D 85 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N MET D 150 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 151 " --> pdb=" O TRP D 123 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP D 123 " --> pdb=" O ASN D 151 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1146 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: 1.72 Time building geometry restraints manager: 1.44 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: 3379 1.34 - 1.46: 1342 1.46 - 1.57: 5665 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 10447 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.415 1.624 -0.209 1.50e-02 4.44e+03 1.94e+02 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.526 1.363 0.163 1.50e-02 4.44e+03 1.17e+02 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.454 1.294 0.160 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.499 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 10442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 14118 2.72 - 5.45: 93 5.45 - 8.17: 7 8.17 - 10.89: 2 10.89 - 13.62: 4 Bond angle restraints: 14224 Sorted by residual: angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 108.20 94.58 13.62 1.50e+00 4.44e-01 8.24e+01 angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 114.00 126.43 -12.43 1.50e+00 4.44e-01 6.87e+01 angle pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C3' AMP B1101 " ideal model delta sigma weight residual 101.50 106.56 -5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.91 12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" O1P AMP B1101 " pdb=" P AMP B1101 " pdb=" O2P AMP B1101 " ideal model delta sigma weight residual 119.90 106.93 12.97 3.00e+00 1.11e-01 1.87e+01 ... (remaining 14219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5885 17.67 - 35.35: 323 35.35 - 53.02: 65 53.02 - 70.70: 14 70.70 - 88.37: 8 Dihedral angle restraints: 6295 sinusoidal: 2548 harmonic: 3747 Sorted by residual: dihedral pdb=" CA SER A 188 " pdb=" C SER A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C1' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C5' AMP B1101 " ideal model delta sinusoidal sigma weight residual -123.00 -145.10 22.10 1 8.00e+00 1.56e-02 1.10e+01 ... (remaining 6292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 987 0.029 - 0.058: 416 0.058 - 0.087: 106 0.087 - 0.116: 69 0.116 - 0.145: 10 Chirality restraints: 1588 Sorted by residual: chirality pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" C3' AMP B1101 " pdb=" O2' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.52 -2.37 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 945 " pdb=" N ILE A 945 " pdb=" C ILE A 945 " pdb=" CB ILE A 945 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1585 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 518 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 188 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 189 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 923 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 924 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 924 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 924 " -0.015 5.00e-02 4.00e+02 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 941 2.74 - 3.28: 10079 3.28 - 3.82: 16340 3.82 - 4.36: 18988 4.36 - 4.90: 33477 Nonbonded interactions: 79825 Sorted by model distance: nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A 972 " model vdw 2.204 3.040 nonbonded pdb=" O TYR A 514 " pdb=" OH TYR A 524 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR C 46 " pdb=" O TYR C 75 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP A 468 " pdb=" O2' AMP B1101 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN C 15 " pdb=" O LEU C 25 " model vdw 2.289 3.120 ... (remaining 79820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 82 through 157) selection = chain 'D' } 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: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.110 Find NCS groups from input model: 0.070 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 0.209 10450 Z= 0.304 Angle : 0.584 13.618 14226 Z= 0.292 Chirality : 0.038 0.145 1588 Planarity : 0.004 0.048 1865 Dihedral : 11.987 88.369 3868 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 7.45 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.48 (0.24), residues: 1289 helix: 1.53 (0.24), residues: 457 sheet: -0.62 (0.40), residues: 171 loop : -0.21 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 118 TYR 0.008 0.001 TYR C 61 PHE 0.008 0.001 PHE A 146 TRP 0.006 0.001 TRP C 95 HIS 0.002 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.28 (10447) covalent geometry : angle 0.58378 / 0.29 (14224) SS BOND : bond 0.00140 / 0.07 ( 1) SS BOND : angle 0.71986 / 0.41 ( 2) hydrogen bonds : bond 0.16395 / 10.86 ( 411) hydrogen bonds : angle 6.83715 / 4.94 ( 1146) Misc. bond : bond 0.08991 / 4.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 225 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 373 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 508 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7171 (mt0) REVERT: A 531 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7513 (ptp-110) REVERT: A 638 THR cc_start: 0.3736 (OUTLIER) cc_final: 0.3269 (m) REVERT: A 738 MET cc_start: 0.3515 (ppp) cc_final: 0.0512 (mmm) REVERT: C 5 MET cc_start: 0.8894 (tpt) cc_final: 0.8506 (tpt) REVERT: C 43 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 70 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: D 99 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7529 (mmm160) outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.1097 time to fit residues: 23.3680 Evaluate side-chains 120 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 35 optimal weight: 0.7980 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 140 HIS A 199 ASN A 634 GLN A 637 HIS A 786 GLN A 817 HIS A 939 HIS A1009 HIS B 106 HIS B 110 GLN C 103 GLN D 106 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.201242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152936 restraints weight = 12390.962| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.59 r_work: 0.3207 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10450 Z= 0.118 Angle : 0.562 10.416 14226 Z= 0.273 Chirality : 0.039 0.157 1588 Planarity : 0.004 0.053 1865 Dihedral : 5.938 59.440 1432 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.00 % Allowed : 10.55 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.49 (0.24), residues: 1289 helix: 1.59 (0.24), residues: 470 sheet: -0.61 (0.40), residues: 170 loop : -0.29 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 258 TYR 0.012 0.001 TYR B 140 PHE 0.016 0.001 PHE A 481 TRP 0.016 0.001 TRP A 677 HIS 0.007 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10447) covalent geometry : angle 0.56234 / 0.27 (14224) SS BOND : bond 0.00261 / 0.14 ( 1) SS BOND : angle 0.42637 / 0.24 ( 2) hydrogen bonds : bond 0.03945 / 2.68 ( 411) hydrogen bonds : angle 5.24209 / 3.72 ( 1146) Misc. bond : bond 0.00123 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8644 (mp) REVERT: A 225 PRO cc_start: 0.8414 (Cg_exo) cc_final: 0.8187 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 373 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8717 (mm) REVERT: A 508 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7340 (mt0) REVERT: A 531 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7682 (ptp-110) REVERT: A 568 TRP cc_start: 0.8708 (m100) cc_final: 0.8437 (m100) REVERT: A 638 THR cc_start: 0.3781 (OUTLIER) cc_final: 0.3491 (m) REVERT: A 738 MET cc_start: 0.3707 (ppp) cc_final: 0.0765 (mmm) REVERT: C 5 MET cc_start: 0.8792 (tpt) cc_final: 0.8420 (tpt) REVERT: C 70 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: D 99 ARG cc_start: 0.8161 (mmp-170) cc_final: 0.7654 (mmm160) REVERT: D 110 GLN cc_start: 0.1917 (OUTLIER) cc_final: 0.1440 (mp10) outliers start: 22 outliers final: 10 residues processed: 130 average time/residue: 0.1037 time to fit residues: 18.6760 Evaluate side-chains 123 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 610 HIS ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.197133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122606 restraints weight = 12503.814| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.28 r_work: 0.3257 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10450 Z= 0.246 Angle : 0.632 10.286 14226 Z= 0.304 Chirality : 0.042 0.152 1588 Planarity : 0.005 0.058 1865 Dihedral : 6.367 57.182 1430 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 3.09 % Allowed : 10.73 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.11 (0.23), residues: 1289 helix: 1.27 (0.24), residues: 469 sheet: -0.77 (0.40), residues: 172 loop : -0.52 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 137 TYR 0.010 0.002 TYR C 61 PHE 0.012 0.002 PHE A 389 TRP 0.019 0.001 TRP A 677 HIS 0.005 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.25 (10447) covalent geometry : angle 0.63236 / 0.30 (14224) SS BOND : bond 0.00317 / 0.17 ( 1) SS BOND : angle 0.75576 / 0.41 ( 2) hydrogen bonds : bond 0.04164 / 2.88 ( 411) hydrogen bonds : angle 5.18503 / 3.66 ( 1146) Misc. bond : bond 0.00081 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8844 (mp) REVERT: A 225 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6740 (ttm170) cc_final: 0.6482 (ttm170) REVERT: A 273 GLN cc_start: 0.7567 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 508 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7335 (mt0) REVERT: A 638 THR cc_start: 0.4309 (OUTLIER) cc_final: 0.4060 (m) REVERT: A 713 GLN cc_start: 0.9078 (tt0) cc_final: 0.8694 (pp30) REVERT: A 738 MET cc_start: 0.3996 (ppp) cc_final: 0.1274 (mmm) REVERT: B 140 TYR cc_start: 0.8175 (m-80) cc_final: 0.7603 (m-10) REVERT: C 5 MET cc_start: 0.8850 (tpt) cc_final: 0.8523 (tpt) REVERT: C 70 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: C 128 LEU cc_start: 0.8368 (mp) cc_final: 0.8012 (tt) REVERT: D 99 ARG cc_start: 0.8274 (mmp-170) cc_final: 0.7756 (mmm160) REVERT: D 110 GLN cc_start: 0.2002 (OUTLIER) cc_final: 0.1700 (mp10) outliers start: 34 outliers final: 20 residues processed: 134 average time/residue: 0.0916 time to fit residues: 17.5620 Evaluate side-chains 128 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 55 optimal weight: 0.0980 chunk 117 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.199394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127158 restraints weight = 12567.597| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.38 r_work: 0.3248 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10450 Z= 0.132 Angle : 0.562 10.307 14226 Z= 0.268 Chirality : 0.039 0.128 1588 Planarity : 0.004 0.057 1865 Dihedral : 6.097 56.957 1428 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.36 % Allowed : 13.18 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.25 (0.24), residues: 1289 helix: 1.42 (0.24), residues: 470 sheet: -0.76 (0.39), residues: 170 loop : -0.45 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.008 0.001 TYR A 547 PHE 0.014 0.001 PHE A 481 TRP 0.020 0.001 TRP A 677 HIS 0.002 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (10447) covalent geometry : angle 0.56180 / 0.27 (14224) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 0.36099 / 0.20 ( 2) hydrogen bonds : bond 0.03506 / 2.43 ( 411) hydrogen bonds : angle 4.89698 / 3.44 ( 1146) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 PRO cc_start: 0.8534 (Cg_exo) cc_final: 0.8260 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6778 (ttm170) cc_final: 0.6512 (ttm170) REVERT: A 273 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 373 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8784 (mm) REVERT: A 508 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7400 (mt0) REVERT: A 638 THR cc_start: 0.4205 (OUTLIER) cc_final: 0.3960 (m) REVERT: A 713 GLN cc_start: 0.9053 (tt0) cc_final: 0.8699 (pp30) REVERT: A 738 MET cc_start: 0.3914 (ppp) cc_final: 0.1174 (mmm) REVERT: A 864 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 140 TYR cc_start: 0.8235 (m-80) cc_final: 0.7979 (m-10) REVERT: C 5 MET cc_start: 0.8790 (tpt) cc_final: 0.8410 (tpt) REVERT: C 70 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: C 128 LEU cc_start: 0.8365 (mp) cc_final: 0.7991 (tt) REVERT: D 110 GLN cc_start: 0.2481 (OUTLIER) cc_final: 0.2257 (mp10) outliers start: 26 outliers final: 14 residues processed: 126 average time/residue: 0.0944 time to fit residues: 17.2193 Evaluate side-chains 122 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120357 restraints weight = 12518.633| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.34 r_work: 0.3264 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10450 Z= 0.175 Angle : 0.580 10.283 14226 Z= 0.278 Chirality : 0.040 0.140 1588 Planarity : 0.004 0.057 1865 Dihedral : 5.971 58.002 1426 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 3.09 % Allowed : 13.36 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.18 (0.23), residues: 1289 helix: 1.36 (0.24), residues: 470 sheet: -0.85 (0.39), residues: 170 loop : -0.48 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.008 0.001 TYR C 61 PHE 0.015 0.001 PHE A 481 TRP 0.023 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (10447) covalent geometry : angle 0.58015 / 0.28 (14224) SS BOND : bond 0.00203 / 0.11 ( 1) SS BOND : angle 0.39676 / 0.21 ( 2) hydrogen bonds : bond 0.03592 / 2.50 ( 411) hydrogen bonds : angle 4.86671 / 3.41 ( 1146) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8211 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6797 (ttm170) cc_final: 0.6536 (ttm170) REVERT: A 273 GLN cc_start: 0.7556 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 373 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8810 (mm) REVERT: A 508 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7293 (pt0) REVERT: A 638 THR cc_start: 0.4182 (OUTLIER) cc_final: 0.3968 (m) REVERT: A 677 TRP cc_start: 0.6096 (t60) cc_final: 0.5846 (t60) REVERT: A 713 GLN cc_start: 0.9095 (tt0) cc_final: 0.8717 (pp30) REVERT: A 738 MET cc_start: 0.3975 (ppp) cc_final: 0.1347 (mmm) REVERT: A 864 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8582 (mt) REVERT: C 5 MET cc_start: 0.8761 (tpt) cc_final: 0.8398 (tpt) REVERT: C 70 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: C 128 LEU cc_start: 0.8336 (mp) cc_final: 0.7933 (tt) REVERT: D 99 ARG cc_start: 0.8346 (mmp-170) cc_final: 0.7745 (mmm160) REVERT: D 110 GLN cc_start: 0.2667 (OUTLIER) cc_final: 0.2463 (mp10) outliers start: 34 outliers final: 20 residues processed: 130 average time/residue: 0.0947 time to fit residues: 17.8626 Evaluate side-chains 127 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 120 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN C 103 GLN ** D 102 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 = 0.4365 r_free = 0.4365 target = 0.200245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126587 restraints weight = 12585.418| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.34 r_work: 0.3317 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10450 Z= 0.104 Angle : 0.542 10.296 14226 Z= 0.257 Chirality : 0.039 0.164 1588 Planarity : 0.004 0.054 1865 Dihedral : 5.775 59.160 1426 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 1.82 % Allowed : 15.45 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.32 (0.24), residues: 1289 helix: 1.51 (0.24), residues: 476 sheet: -0.76 (0.40), residues: 164 loop : -0.45 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 137 TYR 0.014 0.001 TYR B 140 PHE 0.018 0.001 PHE A 481 TRP 0.012 0.001 TRP A 677 HIS 0.003 0.000 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (10447) covalent geometry : angle 0.54178 / 0.26 (14224) SS BOND : bond 0.00246 / 0.13 ( 1) SS BOND : angle 0.29800 / 0.16 ( 2) hydrogen bonds : bond 0.03106 / 2.14 ( 411) hydrogen bonds : angle 4.63143 / 3.23 ( 1146) Misc. bond : bond 0.00007 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 PRO cc_start: 0.8502 (Cg_exo) cc_final: 0.8223 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6757 (ttm170) cc_final: 0.6497 (ttm170) REVERT: A 273 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 508 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7319 (pt0) REVERT: A 568 TRP cc_start: 0.8687 (m100) cc_final: 0.8390 (m-90) REVERT: A 713 GLN cc_start: 0.9048 (tt0) cc_final: 0.8710 (pp30) REVERT: A 738 MET cc_start: 0.3914 (ppp) cc_final: 0.1310 (mmm) REVERT: A 864 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 70 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: C 128 LEU cc_start: 0.8305 (mp) cc_final: 0.7895 (tt) REVERT: D 110 GLN cc_start: 0.2566 (OUTLIER) cc_final: 0.2347 (mp10) outliers start: 20 outliers final: 11 residues processed: 126 average time/residue: 0.0899 time to fit residues: 16.3223 Evaluate side-chains 119 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.197776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125462 restraints weight = 12517.375| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.38 r_work: 0.3294 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.108 Angle : 0.548 10.326 14226 Z= 0.259 Chirality : 0.040 0.438 1588 Planarity : 0.004 0.052 1865 Dihedral : 5.584 58.398 1425 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.00 % Allowed : 15.64 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.48 (0.24), residues: 1289 helix: 1.63 (0.24), residues: 472 sheet: -0.72 (0.40), residues: 164 loop : -0.32 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 137 TYR 0.028 0.001 TYR B 140 PHE 0.010 0.001 PHE A 481 TRP 0.024 0.001 TRP A 677 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10447) covalent geometry : angle 0.54791 / 0.26 (14224) SS BOND : bond 0.00203 / 0.11 ( 1) SS BOND : angle 0.21391 / 0.12 ( 2) hydrogen bonds : bond 0.03054 / 2.10 ( 411) hydrogen bonds : angle 4.56248 / 3.17 ( 1146) Misc. bond : bond 0.00009 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 PRO cc_start: 0.8496 (Cg_exo) cc_final: 0.8228 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 508 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7384 (pt0) REVERT: A 514 TYR cc_start: 0.8372 (m-80) cc_final: 0.8120 (m-80) REVERT: A 568 TRP cc_start: 0.8764 (m100) cc_final: 0.8439 (m-90) REVERT: A 713 GLN cc_start: 0.9059 (tt0) cc_final: 0.8738 (pp30) REVERT: A 738 MET cc_start: 0.3840 (ppp) cc_final: 0.1316 (mmm) REVERT: A 864 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8555 (mt) REVERT: C 43 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7722 (tm-30) REVERT: C 70 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: C 128 LEU cc_start: 0.8317 (mp) cc_final: 0.7907 (tt) outliers start: 22 outliers final: 15 residues processed: 127 average time/residue: 0.0954 time to fit residues: 17.4282 Evaluate side-chains 124 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 672 TRP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.199300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128144 restraints weight = 12543.055| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.38 r_work: 0.3289 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.115 Angle : 0.554 10.330 14226 Z= 0.263 Chirality : 0.040 0.481 1588 Planarity : 0.004 0.052 1865 Dihedral : 5.343 58.851 1422 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 2.00 % Allowed : 16.18 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1289 helix: 1.62 (0.24), residues: 472 sheet: -0.57 (0.40), residues: 161 loop : -0.30 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.024 0.001 TYR A 603 PHE 0.010 0.001 PHE A 481 TRP 0.021 0.001 TRP A 677 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (10447) covalent geometry : angle 0.55406 / 0.26 (14224) SS BOND : bond 0.00213 / 0.11 ( 1) SS BOND : angle 0.27576 / 0.15 ( 2) hydrogen bonds : bond 0.03055 / 2.11 ( 411) hydrogen bonds : angle 4.52319 / 3.14 ( 1146) Misc. bond : bond 0.00012 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 508 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7457 (pt0) REVERT: A 514 TYR cc_start: 0.8387 (m-80) cc_final: 0.8141 (m-80) REVERT: A 713 GLN cc_start: 0.9100 (tt0) cc_final: 0.8737 (pp30) REVERT: A 738 MET cc_start: 0.3838 (ppp) cc_final: 0.1382 (mmm) REVERT: A 864 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8528 (mt) REVERT: C 70 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: C 128 LEU cc_start: 0.8305 (mp) cc_final: 0.7921 (tt) outliers start: 22 outliers final: 13 residues processed: 122 average time/residue: 0.0866 time to fit residues: 14.9809 Evaluate side-chains 119 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 908 HIS C 103 GLN ** D 102 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 = 0.4345 r_free = 0.4345 target = 0.198373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125718 restraints weight = 12517.730| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.37 r_work: 0.3248 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10450 Z= 0.188 Angle : 0.607 10.287 14226 Z= 0.291 Chirality : 0.043 0.569 1588 Planarity : 0.004 0.055 1865 Dihedral : 5.578 57.325 1422 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.91 % Allowed : 16.36 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.33 (0.24), residues: 1289 helix: 1.46 (0.24), residues: 472 sheet: -0.68 (0.39), residues: 167 loop : -0.41 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.035 0.002 TYR B 140 PHE 0.012 0.001 PHE A 481 TRP 0.023 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (10447) covalent geometry : angle 0.60733 / 0.29 (14224) SS BOND : bond 0.00208 / 0.11 ( 1) SS BOND : angle 0.47351 / 0.25 ( 2) hydrogen bonds : bond 0.03546 / 2.47 ( 411) hydrogen bonds : angle 4.69192 / 3.26 ( 1146) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6838 (ttm170) cc_final: 0.6564 (ptp-170) REVERT: A 508 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7436 (pt0) REVERT: A 713 GLN cc_start: 0.9034 (tt0) cc_final: 0.8738 (pp30) REVERT: A 738 MET cc_start: 0.3790 (ppp) cc_final: 0.1305 (mmm) REVERT: A 864 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8604 (mt) REVERT: C 43 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7717 (tm-30) REVERT: C 70 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8111 (m-80) REVERT: C 128 LEU cc_start: 0.8299 (mp) cc_final: 0.7902 (tt) outliers start: 21 outliers final: 14 residues processed: 118 average time/residue: 0.0986 time to fit residues: 16.4462 Evaluate side-chains 116 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.198552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123505 restraints weight = 12478.919| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.41 r_work: 0.3256 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10450 Z= 0.181 Angle : 0.615 12.482 14226 Z= 0.294 Chirality : 0.046 0.904 1588 Planarity : 0.004 0.055 1865 Dihedral : 5.526 57.399 1420 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 1.64 % Allowed : 16.36 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.25 (0.24), residues: 1289 helix: 1.39 (0.24), residues: 472 sheet: -0.74 (0.39), residues: 167 loop : -0.45 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 137 TYR 0.051 0.002 TYR B 140 PHE 0.011 0.001 PHE A 481 TRP 0.029 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (10447) covalent geometry : angle 0.61466 / 0.29 (14224) SS BOND : bond 0.00223 / 0.12 ( 1) SS BOND : angle 0.45830 / 0.24 ( 2) hydrogen bonds : bond 0.03601 / 2.49 ( 411) hydrogen bonds : angle 4.69791 / 3.26 ( 1146) Misc. bond : bond 0.00021 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.6800 (ttm170) cc_final: 0.6471 (ptp-170) REVERT: A 508 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7371 (pt0) REVERT: A 713 GLN cc_start: 0.9103 (tt0) cc_final: 0.8761 (pp30) REVERT: A 738 MET cc_start: 0.3910 (ppp) cc_final: 0.1457 (mmm) REVERT: A 864 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8608 (mt) REVERT: C 43 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7645 (tm-30) REVERT: C 70 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: C 128 LEU cc_start: 0.8289 (mp) cc_final: 0.7939 (tt) REVERT: D 99 ARG cc_start: 0.8035 (mmp-170) cc_final: 0.7479 (mmp80) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.1052 time to fit residues: 17.1189 Evaluate side-chains 115 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 58 optimal weight: 0.0370 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.198653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125437 restraints weight = 12501.192| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.46 r_work: 0.3279 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10450 Z= 0.120 Angle : 0.577 10.261 14226 Z= 0.276 Chirality : 0.041 0.501 1588 Planarity : 0.004 0.053 1865 Dihedral : 5.418 59.446 1420 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 1.36 % Allowed : 16.73 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.38 (0.24), residues: 1289 helix: 1.54 (0.24), residues: 472 sheet: -0.63 (0.40), residues: 161 loop : -0.43 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 137 TYR 0.048 0.002 TYR B 140 PHE 0.011 0.001 PHE B 126 TRP 0.029 0.001 TRP A 677 HIS 0.002 0.000 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10447) covalent geometry : angle 0.57710 / 0.28 (14224) SS BOND : bond 0.00258 / 0.14 ( 1) SS BOND : angle 0.41915 / 0.23 ( 2) hydrogen bonds : bond 0.03244 / 2.24 ( 411) hydrogen bonds : angle 4.55458 / 3.16 ( 1146) Misc. bond : bond 0.00009 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3127.43 seconds wall clock time: 53 minutes 59.01 seconds (3239.01 seconds total)