Starting phenix.real_space_refine on Tue Mar 3 16:10:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3g_29695/03_2026/8g3g_29695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3g_29695/03_2026/8g3g_29695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2026/8g3g_29695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2026/8g3g_29695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2026/8g3g_29695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2026/8g3g_29695.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 4400 2.51 5 N 1280 2.21 5 O 1330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.00s 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: 7020 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "A" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "B" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "C" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "D" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "E" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "F" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "G" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "H" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "I" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 1.83, per 1000 atoms: 0.26 Number of scatterers: 7020 At special positions: 0 Unit cell: (89.3, 91.18, 62.98, 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 10 16.00 O 1330 8.00 N 1280 7.00 C 4400 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: 0.57 Conformation dependent library (CDL) restraints added in 236.0 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 35.3% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'J' and resid 1 through 8 Processing helix chain 'J' and resid 73 through 86 Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 65 through 86 removed outlier: 4.418A pdb=" N ALA A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 65 through 86 removed outlier: 3.893A pdb=" N ARG B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 65 through 86 removed outlier: 3.585A pdb=" N ARG C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS C 72 " --> pdb=" O PHE C 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 65 through 86 removed outlier: 3.810A pdb=" N ALA D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 66 through 86 removed outlier: 4.069A pdb=" N ARG E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS E 72 " --> pdb=" O PHE E 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 27 through 31 Processing helix chain 'F' and resid 65 through 86 removed outlier: 3.633A pdb=" N ARG F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS F 72 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 68 through 86 removed outlier: 4.269A pdb=" N LYS G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 65 through 86 removed outlier: 3.766A pdb=" N ARG H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS H 72 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 8 Processing helix chain 'I' and resid 27 through 31 Processing helix chain 'I' and resid 65 through 71 removed outlier: 3.718A pdb=" N ARG I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 86 Processing sheet with id=AA1, first strand: chain 'J' and resid 15 through 22 removed outlier: 5.911A pdb=" N THR J 15 " --> pdb=" O THR J 43 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR J 43 " --> pdb=" O THR J 15 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL J 17 " --> pdb=" O ARG J 41 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG J 41 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 15 through 22 removed outlier: 5.911A pdb=" N THR J 15 " --> pdb=" O THR J 43 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR J 43 " --> pdb=" O THR J 15 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL J 17 " --> pdb=" O ARG J 41 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG J 41 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 24 removed outlier: 6.752A pdb=" N ILE A 39 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 20 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 22 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY A 35 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 22 removed outlier: 6.644A pdb=" N ILE B 39 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 20 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR B 37 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE B 22 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY B 35 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 40 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 22 removed outlier: 6.324A pdb=" N VAL D 17 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG D 41 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 42 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 22 removed outlier: 6.324A pdb=" N VAL D 17 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG D 41 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 17 through 25 removed outlier: 5.957A pdb=" N VAL E 17 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG E 41 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER E 19 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP E 23 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY E 35 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL E 40 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 14 through 22 removed outlier: 5.515A pdb=" N THR F 15 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR F 43 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 17 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 41 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 40 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP F 52 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL F 42 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 16 through 22 removed outlier: 5.383A pdb=" N VAL G 17 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG G 41 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL G 42 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 22 removed outlier: 5.383A pdb=" N VAL G 17 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG G 41 " --> pdb=" O VAL G 17 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 14 through 24 removed outlier: 5.632A pdb=" N THR H 15 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR H 43 " --> pdb=" O THR H 15 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL H 17 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG H 41 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY H 35 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL H 42 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 14 through 24 removed outlier: 5.632A pdb=" N THR H 15 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR H 43 " --> pdb=" O THR H 15 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL H 17 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG H 41 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY H 35 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 16 through 22 removed outlier: 5.276A pdb=" N VAL I 17 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG I 41 " --> pdb=" O VAL I 17 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 849 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: 1.00 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1895 1.33 - 1.45: 1307 1.45 - 1.57: 3908 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 7120 Sorted by residual: bond pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta sigma weight residual 1.456 1.499 -0.042 1.14e-02 7.69e+03 1.38e+01 bond pdb=" N VAL D 40 " pdb=" CA VAL D 40 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" N ILE H 22 " pdb=" CA ILE H 22 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.26e-02 6.30e+03 1.10e+01 bond pdb=" N ILE A 34 " pdb=" CA ILE A 34 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.15e-02 7.56e+03 1.08e+01 bond pdb=" N VAL H 40 " pdb=" CA VAL H 40 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 ... (remaining 7115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 8953 2.36 - 4.71: 548 4.71 - 7.07: 63 7.07 - 9.43: 3 9.43 - 11.79: 3 Bond angle restraints: 9570 Sorted by residual: angle pdb=" CA PHE J 68 " pdb=" CB PHE J 68 " pdb=" CG PHE J 68 " ideal model delta sigma weight residual 113.80 120.25 -6.45 1.00e+00 1.00e+00 4.17e+01 angle pdb=" N ARG E 63 " pdb=" CA ARG E 63 " pdb=" C ARG E 63 " ideal model delta sigma weight residual 109.96 100.39 9.57 1.50e+00 4.44e-01 4.07e+01 angle pdb=" N ALA E 66 " pdb=" CA ALA E 66 " pdb=" C ALA E 66 " ideal model delta sigma weight residual 113.01 106.17 6.84 1.20e+00 6.94e-01 3.25e+01 angle pdb=" C GLN D 29 " pdb=" CA GLN D 29 " pdb=" CB GLN D 29 " ideal model delta sigma weight residual 111.73 119.71 -7.98 1.42e+00 4.96e-01 3.16e+01 angle pdb=" N GLY D 9 " pdb=" CA GLY D 9 " pdb=" C GLY D 9 " ideal model delta sigma weight residual 112.89 104.14 8.75 1.58e+00 4.01e-01 3.07e+01 ... (remaining 9565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 3456 16.70 - 33.40: 564 33.40 - 50.10: 154 50.10 - 66.80: 45 66.80 - 83.50: 21 Dihedral angle restraints: 4240 sinusoidal: 1700 harmonic: 2540 Sorted by residual: dihedral pdb=" C GLN D 29 " pdb=" N GLN D 29 " pdb=" CA GLN D 29 " pdb=" CB GLN D 29 " ideal model delta harmonic sigma weight residual -122.60 -136.76 14.16 0 2.50e+00 1.60e-01 3.21e+01 dihedral pdb=" CA LYS G 64 " pdb=" C LYS G 64 " pdb=" N PRO G 65 " pdb=" CA PRO G 65 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA LYS B 64 " pdb=" C LYS B 64 " pdb=" N PRO B 65 " pdb=" CA PRO B 65 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 4237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 834 0.082 - 0.165: 166 0.165 - 0.247: 46 0.247 - 0.329: 11 0.329 - 0.412: 3 Chirality restraints: 1060 Sorted by residual: chirality pdb=" CA GLN D 29 " pdb=" N GLN D 29 " pdb=" C GLN D 29 " pdb=" CB GLN D 29 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA ILE H 39 " pdb=" N ILE H 39 " pdb=" C ILE H 39 " pdb=" CB ILE H 39 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ARG E 63 " pdb=" N ARG E 63 " pdb=" C ARG E 63 " pdb=" CB ARG E 63 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1057 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 33 " 0.014 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C SER E 33 " -0.051 2.00e-02 2.50e+03 pdb=" O SER E 33 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE E 34 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 33 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C SER H 33 " 0.043 2.00e-02 2.50e+03 pdb=" O SER H 33 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE H 34 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 60 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ASN E 60 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN E 60 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU E 61 " -0.014 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 950 2.75 - 3.29: 7082 3.29 - 3.83: 11790 3.83 - 4.36: 14493 4.36 - 4.90: 23163 Nonbonded interactions: 57478 Sorted by model distance: nonbonded pdb=" NH1 ARG I 28 " pdb=" OE1 GLN I 29 " model vdw 2.216 3.120 nonbonded pdb=" OD2 ASP C 23 " pdb=" OH TYR C 55 " model vdw 2.403 3.040 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.405 3.120 nonbonded pdb=" N ASP H 52 " pdb=" OD1 ASP H 52 " model vdw 2.408 3.120 nonbonded pdb=" N ASP C 23 " pdb=" OD1 ASP C 23 " model vdw 2.432 3.120 ... (remaining 57473 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 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: 2.280 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 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 : 0.007 0.042 7120 Z= 0.505 Angle : 1.147 11.787 9570 Z= 0.763 Chirality : 0.076 0.412 1060 Planarity : 0.005 0.037 1240 Dihedral : 19.088 83.499 2620 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 9.45 % Allowed : 29.59 % Favored : 60.96 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % 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: -2.51 (0.27), residues: 880 helix: 0.24 (0.33), residues: 210 sheet: -2.10 (0.29), residues: 300 loop : -2.31 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 62 TYR 0.016 0.002 TYR H 49 PHE 0.024 0.002 PHE J 68 TRP 0.026 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 7120) covalent geometry : angle 1.14717 ( 9570) hydrogen bonds : bond 0.17836 ( 298) hydrogen bonds : angle 7.20703 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 260 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 TRP cc_start: 0.8083 (p-90) cc_final: 0.7708 (p-90) REVERT: C 13 TRP cc_start: 0.8305 (p-90) cc_final: 0.7692 (p-90) REVERT: E 23 ASP cc_start: 0.6412 (p0) cc_final: 0.6177 (p0) REVERT: E 55 TYR cc_start: 0.7529 (t80) cc_final: 0.7267 (t80) REVERT: E 68 PHE cc_start: 0.7012 (t80) cc_final: 0.6766 (t80) REVERT: F 19 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8262 (p) REVERT: G 49 TYR cc_start: 0.8248 (p90) cc_final: 0.7811 (p90) REVERT: H 49 TYR cc_start: 0.8209 (p90) cc_final: 0.7904 (p90) REVERT: I 19 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7784 (p) outliers start: 69 outliers final: 16 residues processed: 292 average time/residue: 0.1247 time to fit residues: 43.7345 Evaluate side-chains 255 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 48 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.150449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.128548 restraints weight = 11658.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.131984 restraints weight = 7429.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.134111 restraints weight = 5437.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.135862 restraints weight = 4394.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.137198 restraints weight = 3709.110| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7120 Z= 0.188 Angle : 0.734 6.459 9570 Z= 0.395 Chirality : 0.047 0.205 1060 Planarity : 0.004 0.033 1240 Dihedral : 7.156 55.569 1027 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 9.04 % Allowed : 26.85 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.32 (0.27), residues: 880 helix: 0.19 (0.32), residues: 200 sheet: -1.87 (0.29), residues: 300 loop : -2.10 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 50 TYR 0.012 0.001 TYR G 49 PHE 0.016 0.002 PHE J 68 TRP 0.015 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7120) covalent geometry : angle 0.73399 ( 9570) hydrogen bonds : bond 0.04507 ( 298) hydrogen bonds : angle 5.38044 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 6 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7892 (tm-30) REVERT: J 41 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8007 (ttt90) REVERT: J 68 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6178 (t80) REVERT: A 73 LYS cc_start: 0.8056 (pptt) cc_final: 0.7852 (pttp) REVERT: E 68 PHE cc_start: 0.7410 (t80) cc_final: 0.7192 (t80) REVERT: F 41 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8241 (ttm-80) REVERT: F 70 ARG cc_start: 0.5959 (ppt170) cc_final: 0.5697 (ppt170) REVERT: G 34 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8155 (pt) REVERT: G 41 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7862 (ttt90) REVERT: H 49 TYR cc_start: 0.8743 (p90) cc_final: 0.8503 (p90) REVERT: I 19 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7973 (p) REVERT: I 28 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8446 (mmm160) outliers start: 66 outliers final: 47 residues processed: 271 average time/residue: 0.1215 time to fit residues: 39.8643 Evaluate side-chains 275 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 27 optimal weight: 0.0270 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6216 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.152245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130217 restraints weight = 11531.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.133940 restraints weight = 7148.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.136235 restraints weight = 5102.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.138160 restraints weight = 4047.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.138852 restraints weight = 3379.707| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7120 Z= 0.143 Angle : 0.668 6.278 9570 Z= 0.357 Chirality : 0.044 0.158 1060 Planarity : 0.003 0.032 1240 Dihedral : 6.492 58.346 1020 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 9.04 % Allowed : 27.67 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.21 (0.27), residues: 880 helix: 0.38 (0.33), residues: 200 sheet: -1.83 (0.29), residues: 300 loop : -2.07 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 28 TYR 0.019 0.001 TYR D 49 PHE 0.012 0.001 PHE J 68 TRP 0.016 0.001 TRP I 13 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7120) covalent geometry : angle 0.66818 ( 9570) hydrogen bonds : bond 0.03968 ( 298) hydrogen bonds : angle 5.12886 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 243 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8098 (ttt90) REVERT: J 68 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6213 (t80) REVERT: A 29 GLN cc_start: 0.8292 (pm20) cc_final: 0.7961 (mp10) REVERT: B 73 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7631 (mmtt) REVERT: D 49 TYR cc_start: 0.8609 (p90) cc_final: 0.8404 (p90) REVERT: E 68 PHE cc_start: 0.7544 (t80) cc_final: 0.7237 (t80) REVERT: F 41 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: G 23 ASP cc_start: 0.7331 (p0) cc_final: 0.6997 (p0) REVERT: G 34 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8053 (pt) REVERT: I 19 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8159 (p) REVERT: I 29 GLN cc_start: 0.8146 (pm20) cc_final: 0.7888 (pm20) outliers start: 66 outliers final: 45 residues processed: 269 average time/residue: 0.1291 time to fit residues: 41.6049 Evaluate side-chains 276 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.148437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.126309 restraints weight = 11730.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129310 restraints weight = 7490.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.131631 restraints weight = 5584.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133146 restraints weight = 4535.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.133735 restraints weight = 3866.426| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7120 Z= 0.189 Angle : 0.696 8.528 9570 Z= 0.373 Chirality : 0.045 0.151 1060 Planarity : 0.004 0.036 1240 Dihedral : 6.445 58.698 1017 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 12.19 % Allowed : 25.75 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.19 (0.27), residues: 880 helix: 0.35 (0.33), residues: 200 sheet: -1.83 (0.30), residues: 300 loop : -2.02 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 63 TYR 0.011 0.001 TYR E 49 PHE 0.012 0.002 PHE J 68 TRP 0.018 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7120) covalent geometry : angle 0.69623 ( 9570) hydrogen bonds : bond 0.04164 ( 298) hydrogen bonds : angle 5.09360 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 232 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8027 (ttt90) REVERT: J 68 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.6125 (t80) REVERT: D 49 TYR cc_start: 0.8723 (p90) cc_final: 0.8441 (p90) REVERT: D 68 PHE cc_start: 0.8065 (t80) cc_final: 0.7790 (t80) REVERT: E 68 PHE cc_start: 0.7694 (t80) cc_final: 0.7329 (t80) REVERT: F 8 PHE cc_start: 0.8257 (m-10) cc_final: 0.8027 (m-10) REVERT: F 29 GLN cc_start: 0.8682 (pm20) cc_final: 0.8474 (pm20) REVERT: G 34 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8074 (pt) REVERT: I 19 SER cc_start: 0.8486 (p) cc_final: 0.8267 (p) outliers start: 89 outliers final: 72 residues processed: 278 average time/residue: 0.1243 time to fit residues: 41.7561 Evaluate side-chains 301 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 226 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 1 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 76 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.149173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.126890 restraints weight = 11635.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.130554 restraints weight = 7165.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.132931 restraints weight = 5116.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.134285 restraints weight = 4050.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.135529 restraints weight = 3504.492| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7120 Z= 0.150 Angle : 0.685 7.766 9570 Z= 0.364 Chirality : 0.044 0.153 1060 Planarity : 0.003 0.034 1240 Dihedral : 6.336 57.439 1014 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 10.82 % Allowed : 27.53 % Favored : 61.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.27), residues: 880 helix: 0.41 (0.33), residues: 200 sheet: -1.86 (0.29), residues: 300 loop : -1.96 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 28 TYR 0.011 0.001 TYR H 49 PHE 0.014 0.001 PHE A 68 TRP 0.019 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 7120) covalent geometry : angle 0.68497 ( 9570) hydrogen bonds : bond 0.03886 ( 298) hydrogen bonds : angle 5.03310 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 235 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8441 (ttt180) cc_final: 0.7978 (ttt90) REVERT: A 28 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.7867 (mmm160) REVERT: A 49 TYR cc_start: 0.8544 (p90) cc_final: 0.8302 (p90) REVERT: A 52 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5934 (p0) REVERT: C 85 ARG cc_start: 0.4359 (OUTLIER) cc_final: 0.4123 (mmt180) REVERT: D 49 TYR cc_start: 0.8706 (p90) cc_final: 0.8458 (p90) REVERT: D 68 PHE cc_start: 0.8049 (t80) cc_final: 0.7784 (t80) REVERT: E 68 PHE cc_start: 0.7660 (t80) cc_final: 0.7355 (t80) REVERT: G 34 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8037 (pt) REVERT: I 19 SER cc_start: 0.8468 (p) cc_final: 0.8268 (p) outliers start: 79 outliers final: 66 residues processed: 276 average time/residue: 0.1231 time to fit residues: 41.0098 Evaluate side-chains 294 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 225 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 1 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.148530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.125796 restraints weight = 11708.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.129380 restraints weight = 7249.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131674 restraints weight = 5216.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.133431 restraints weight = 4166.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.134445 restraints weight = 3512.426| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7120 Z= 0.163 Angle : 0.704 7.777 9570 Z= 0.373 Chirality : 0.045 0.145 1060 Planarity : 0.004 0.036 1240 Dihedral : 6.016 54.946 1010 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 11.37 % Allowed : 29.18 % Favored : 59.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.27), residues: 880 helix: 0.42 (0.34), residues: 200 sheet: -1.95 (0.29), residues: 300 loop : -1.99 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 28 TYR 0.011 0.001 TYR B 49 PHE 0.010 0.001 PHE I 8 TRP 0.020 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 7120) covalent geometry : angle 0.70377 ( 9570) hydrogen bonds : bond 0.03944 ( 298) hydrogen bonds : angle 5.00814 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 237 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8137 (ttt90) REVERT: J 73 LYS cc_start: 0.5147 (mmtt) cc_final: 0.4781 (mmtm) REVERT: C 19 SER cc_start: 0.7867 (t) cc_final: 0.7627 (t) REVERT: C 73 LYS cc_start: 0.7292 (pttp) cc_final: 0.6941 (pttp) REVERT: E 68 PHE cc_start: 0.7748 (t80) cc_final: 0.7351 (t80) REVERT: F 41 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8199 (ttm-80) REVERT: G 27 GLU cc_start: 0.8119 (tp30) cc_final: 0.7824 (tp30) REVERT: G 34 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8077 (pt) REVERT: H 23 ASP cc_start: 0.7824 (m-30) cc_final: 0.7614 (m-30) REVERT: H 37 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8833 (p) outliers start: 83 outliers final: 76 residues processed: 283 average time/residue: 0.1190 time to fit residues: 40.9497 Evaluate side-chains 306 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 227 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain H residue 1 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.148020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.125357 restraints weight = 11565.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.128864 restraints weight = 7238.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130728 restraints weight = 5260.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.132690 restraints weight = 4308.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.133651 restraints weight = 3645.742| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7120 Z= 0.175 Angle : 0.727 7.779 9570 Z= 0.384 Chirality : 0.045 0.146 1060 Planarity : 0.004 0.035 1240 Dihedral : 6.096 58.035 1010 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 11.78 % Allowed : 28.36 % Favored : 59.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.24 (0.27), residues: 880 helix: 0.36 (0.34), residues: 200 sheet: -2.00 (0.29), residues: 300 loop : -1.96 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 62 TYR 0.011 0.001 TYR A 49 PHE 0.014 0.001 PHE A 68 TRP 0.019 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7120) covalent geometry : angle 0.72727 ( 9570) hydrogen bonds : bond 0.04064 ( 298) hydrogen bonds : angle 5.09184 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 236 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8453 (ttt180) cc_final: 0.8125 (ttt90) REVERT: A 28 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8161 (mmm160) REVERT: C 19 SER cc_start: 0.7877 (t) cc_final: 0.7657 (t) REVERT: D 51 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7238 (mt-10) REVERT: E 68 PHE cc_start: 0.7832 (t80) cc_final: 0.7437 (t80) REVERT: F 8 PHE cc_start: 0.8177 (m-10) cc_final: 0.7955 (m-10) REVERT: G 27 GLU cc_start: 0.8067 (tp30) cc_final: 0.7612 (tp30) REVERT: G 34 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8150 (pt) REVERT: I 28 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8248 (mmm-85) outliers start: 86 outliers final: 79 residues processed: 280 average time/residue: 0.1182 time to fit residues: 40.2479 Evaluate side-chains 305 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 225 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain H residue 1 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.149686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.127067 restraints weight = 11637.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130638 restraints weight = 7241.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.132834 restraints weight = 5245.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.134457 restraints weight = 4219.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.135929 restraints weight = 3597.147| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7120 Z= 0.149 Angle : 0.731 7.865 9570 Z= 0.384 Chirality : 0.044 0.144 1060 Planarity : 0.003 0.033 1240 Dihedral : 6.085 59.710 1010 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 10.68 % Allowed : 29.04 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.20 (0.28), residues: 880 helix: 0.48 (0.34), residues: 200 sheet: -2.02 (0.29), residues: 300 loop : -1.93 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 62 TYR 0.010 0.001 TYR B 49 PHE 0.014 0.001 PHE J 68 TRP 0.021 0.001 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 7120) covalent geometry : angle 0.73082 ( 9570) hydrogen bonds : bond 0.03825 ( 298) hydrogen bonds : angle 5.01932 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 235 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8407 (ttt180) cc_final: 0.8104 (ttt90) REVERT: J 73 LYS cc_start: 0.5233 (mmtt) cc_final: 0.4886 (mmtm) REVERT: A 28 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.8143 (mmm160) REVERT: B 28 ARG cc_start: 0.8332 (mmm160) cc_final: 0.8097 (mmm-85) REVERT: B 29 GLN cc_start: 0.7679 (pm20) cc_final: 0.7478 (pm20) REVERT: B 70 ARG cc_start: 0.5790 (ppt170) cc_final: 0.5424 (ppt170) REVERT: C 19 SER cc_start: 0.7881 (t) cc_final: 0.7650 (t) REVERT: E 68 PHE cc_start: 0.7776 (t80) cc_final: 0.7446 (t80) REVERT: F 73 LYS cc_start: 0.7875 (pttm) cc_final: 0.7658 (pttt) REVERT: G 27 GLU cc_start: 0.8096 (tp30) cc_final: 0.7637 (tp30) REVERT: G 34 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8047 (pt) REVERT: H 73 LYS cc_start: 0.6989 (pttm) cc_final: 0.6781 (pttp) outliers start: 78 outliers final: 73 residues processed: 272 average time/residue: 0.1154 time to fit residues: 38.0004 Evaluate side-chains 301 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 1 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.149946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126651 restraints weight = 11699.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.130422 restraints weight = 7084.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132533 restraints weight = 5003.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.134687 restraints weight = 4029.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.135381 restraints weight = 3343.595| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7120 Z= 0.149 Angle : 0.760 8.695 9570 Z= 0.396 Chirality : 0.045 0.181 1060 Planarity : 0.004 0.033 1240 Dihedral : 5.843 59.080 1006 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 10.41 % Allowed : 29.86 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.21 (0.28), residues: 880 helix: 0.51 (0.35), residues: 200 sheet: -2.08 (0.29), residues: 300 loop : -1.91 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 28 TYR 0.014 0.001 TYR A 49 PHE 0.013 0.001 PHE J 68 TRP 0.020 0.001 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7120) covalent geometry : angle 0.76034 ( 9570) hydrogen bonds : bond 0.03759 ( 298) hydrogen bonds : angle 5.03353 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 235 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8400 (ttt180) cc_final: 0.8080 (ttt90) REVERT: J 73 LYS cc_start: 0.5445 (mmtt) cc_final: 0.4953 (mmtm) REVERT: B 28 ARG cc_start: 0.8320 (mmm160) cc_final: 0.8066 (mmm-85) REVERT: B 29 GLN cc_start: 0.7680 (pm20) cc_final: 0.7428 (pm20) REVERT: B 70 ARG cc_start: 0.5886 (ppt170) cc_final: 0.5516 (ppt170) REVERT: C 19 SER cc_start: 0.7900 (t) cc_final: 0.7683 (t) REVERT: E 68 PHE cc_start: 0.7747 (t80) cc_final: 0.7528 (t80) REVERT: E 70 ARG cc_start: 0.5390 (ppt170) cc_final: 0.4641 (ppt170) REVERT: F 73 LYS cc_start: 0.7874 (pttm) cc_final: 0.7651 (pttt) REVERT: G 34 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8059 (pt) REVERT: G 41 ARG cc_start: 0.8388 (ttt90) cc_final: 0.8069 (ttt90) outliers start: 76 outliers final: 73 residues processed: 272 average time/residue: 0.1231 time to fit residues: 40.3301 Evaluate side-chains 300 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 226 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 1 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.145481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121892 restraints weight = 11747.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.125580 restraints weight = 7141.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.127695 restraints weight = 5092.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129819 restraints weight = 4108.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.130582 restraints weight = 3437.903| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7120 Z= 0.226 Angle : 0.815 7.674 9570 Z= 0.431 Chirality : 0.048 0.179 1060 Planarity : 0.005 0.037 1240 Dihedral : 5.815 52.199 1006 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 11.10 % Allowed : 28.90 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.28), residues: 880 helix: 0.16 (0.35), residues: 200 sheet: -2.09 (0.29), residues: 300 loop : -1.88 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 82 TYR 0.016 0.001 TYR A 49 PHE 0.015 0.002 PHE B 68 TRP 0.023 0.002 TRP I 13 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 7120) covalent geometry : angle 0.81478 ( 9570) hydrogen bonds : bond 0.04321 ( 298) hydrogen bonds : angle 5.21740 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8483 (ttt180) cc_final: 0.8260 (ttt180) REVERT: J 73 LYS cc_start: 0.5794 (mmtt) cc_final: 0.5318 (mmtm) REVERT: A 28 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8299 (mmm-85) REVERT: B 68 PHE cc_start: 0.7198 (t80) cc_final: 0.6964 (t80) REVERT: B 70 ARG cc_start: 0.6077 (ppt170) cc_final: 0.5598 (ppt170) REVERT: C 19 SER cc_start: 0.8014 (t) cc_final: 0.7813 (t) REVERT: C 73 LYS cc_start: 0.7382 (pttp) cc_final: 0.7134 (pttp) REVERT: D 51 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7398 (mt-10) REVERT: E 68 PHE cc_start: 0.7729 (t80) cc_final: 0.7450 (t80) REVERT: E 70 ARG cc_start: 0.5731 (ppt170) cc_final: 0.4893 (ppt170) REVERT: G 27 GLU cc_start: 0.8071 (tp30) cc_final: 0.7732 (tp30) REVERT: G 34 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8216 (pt) REVERT: H 31 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7917 (mmtm) outliers start: 81 outliers final: 79 residues processed: 274 average time/residue: 0.1176 time to fit residues: 39.0723 Evaluate side-chains 304 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 224 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 1 ILE Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 36 CYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 1 ILE Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain H residue 1 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain I residue 1 ILE Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 84 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.147328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124775 restraints weight = 11585.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128350 restraints weight = 7176.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130361 restraints weight = 5164.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132038 restraints weight = 4190.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133379 restraints weight = 3570.106| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7120 Z= 0.168 Angle : 0.802 8.248 9570 Z= 0.419 Chirality : 0.047 0.175 1060 Planarity : 0.004 0.038 1240 Dihedral : 5.794 51.206 1006 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 10.27 % Allowed : 30.00 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.29 (0.28), residues: 880 helix: 0.29 (0.35), residues: 200 sheet: -2.13 (0.29), residues: 300 loop : -1.87 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 62 TYR 0.011 0.001 TYR A 49 PHE 0.012 0.001 PHE A 68 TRP 0.022 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7120) covalent geometry : angle 0.80237 ( 9570) hydrogen bonds : bond 0.03913 ( 298) hydrogen bonds : angle 5.12652 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.97 seconds wall clock time: 23 minutes 27.31 seconds (1407.31 seconds total)