Starting phenix.real_space_refine on Fri Aug 22 18:40:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3g_29695/08_2025/8g3g_29695.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3g_29695/08_2025/8g3g_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3g_29695/08_2025/8g3g_29695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3g_29695/08_2025/8g3g_29695.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3g_29695/08_2025/8g3g_29695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3g_29695/08_2025/8g3g_29695.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 1.71, per 1000 atoms: 0.24 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: 0.59 Conformation dependent library (CDL) restraints added in 332.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.79 Time building geometry restraints manager: 0.73 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.890 Find NCS groups from input model: 0.090 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.250 ------------------------------------------------------------------------------- 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 aren 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 : 0.282 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: 0.6176 (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: 0.8247 (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: 0.1215 time to fit residues: 42.7188 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 : 0.282 ------------------------------------------------------------------------------- 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 aren 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 : 0.182 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: 0.8451 (OUTLIER) cc_final: 0.8008 (ttt90) REVERT: J 68 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6178 (t80) REVERT: A 73 LYS cc_start: 0.8056 (pptt) cc_final: 0.7851 (pttp) REVERT: E 68 PHE cc_start: 0.7410 (t80) cc_final: 0.7192 (t80) REVERT: F 41 ARG cc_start: 0.8556 (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: 0.8358 (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: 0.8744 (p90) cc_final: 0.8503 (p90) REVERT: I 19 SER cc_start: 0.8340 (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: 0.1153 time to fit residues: 37.8012 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 : 0.182 ------------------------------------------------------------------------------- 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 aren 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 : 0.166 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: 0.6803 (OUTLIER) cc_final: 0.6214 (t80) REVERT: A 29 GLN cc_start: 0.8291 (pm20) cc_final: 0.7961 (mp10) REVERT: B 73 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7630 (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: 0.6998 (p0) REVERT: G 34 ILE cc_start: 0.8277 (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: 0.1180 time to fit residues: 37.8706 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 : 0.350 ------------------------------------------------------------------------------- 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 aren 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 : 0.230 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: 0.8503 (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: 0.8256 (m-10) cc_final: 0.8026 (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: 0.8266 (p) outliers start: 89 outliers final: 72 residues processed: 278 average time/residue: 0.1179 time to fit residues: 39.5585 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 : 0.292 ------------------------------------------------------------------------------- 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 aren 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 : 0.182 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: 0.8545 (p90) cc_final: 0.8302 (p90) REVERT: A 52 ASP cc_start: 0.6212 (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) outliers start: 79 outliers final: 66 residues processed: 276 average time/residue: 0.1229 time to fit residues: 40.9786 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 : 0.177 ------------------------------------------------------------------------------- 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 = 0.4070 r_free = 0.4070 target = 0.148703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.126556 restraints weight = 11728.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.129876 restraints weight = 7477.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132011 restraints weight = 5493.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133265 restraints weight = 4447.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.134672 restraints weight = 3883.644| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3073 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= 0.163 Angle : 0.701 7.800 9570 Z= 0.372 Chirality : 0.044 0.145 1060 Planarity : 0.004 0.036 1240 Dihedral : 6.009 55.227 1010 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 11.78 % Allowed : 28.63 % Favored : 59.59 % 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 aren not related in a simple way. whole: -2.21 (0.27), residues: 880 helix: 0.43 (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 0.010 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 0.00361 ( 7120) covalent geometry : angle 0.70142 ( 9570) hydrogen bonds : bond 0.03947 ( 298) hydrogen bonds : angle 5.00921 ( 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 319 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 233 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8454 (ttt180) cc_final: 0.8138 (ttt90) REVERT: C 73 LYS cc_start: 0.7271 (pttp) cc_final: 0.6897 (pttp) REVERT: D 68 PHE cc_start: 0.8086 (t80) cc_final: 0.7814 (t80) REVERT: E 68 PHE cc_start: 0.7733 (t80) cc_final: 0.7333 (t80) REVERT: E 70 ARG cc_start: 0.5799 (ppt170) cc_final: 0.5588 (ppt170) REVERT: F 41 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8190 (ttm-80) REVERT: G 34 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8072 (pt) outliers start: 86 outliers final: 80 residues processed: 280 average time/residue: 0.1234 time to fit residues: 41.9040 Evaluate side-chains 304 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 222 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.145644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.123323 restraints weight = 11593.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126570 restraints weight = 7491.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.128610 restraints weight = 5571.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.130029 restraints weight = 4545.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.131221 restraints weight = 3924.961| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7120 Z= 0.210 Angle : 0.757 7.485 9570 Z= 0.402 Chirality : 0.046 0.152 1060 Planarity : 0.004 0.040 1240 Dihedral : 6.214 59.260 1010 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 11.78 % Allowed : 28.77 % 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 aren not related in a simple way. whole: -2.36 (0.27), residues: 880 helix: 0.10 (0.33), residues: 200 sheet: -2.00 (0.29), residues: 300 loop : -1.99 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 62 TYR 0.012 0.001 TYR A 49 PHE 0.019 0.002 PHE A 68 TRP 0.021 0.002 TRP I 13 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 7120) covalent geometry : angle 0.75744 ( 9570) hydrogen bonds : bond 0.04368 ( 298) hydrogen bonds : angle 5.21952 ( 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 319 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 233 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8286 (mmm160) REVERT: B 70 ARG cc_start: 0.5845 (ppt170) cc_final: 0.5519 (ppt170) REVERT: C 19 SER cc_start: 0.7991 (t) cc_final: 0.7770 (t) REVERT: D 27 GLU cc_start: 0.8194 (tp30) cc_final: 0.7943 (tp30) REVERT: D 51 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7377 (mt-10) REVERT: D 68 PHE cc_start: 0.8098 (t80) cc_final: 0.7863 (t80) REVERT: E 68 PHE cc_start: 0.7740 (t80) cc_final: 0.7356 (t80) REVERT: G 27 GLU cc_start: 0.8089 (tp30) cc_final: 0.7643 (tp30) REVERT: G 34 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8205 (pt) REVERT: H 73 LYS cc_start: 0.7258 (pttm) cc_final: 0.7055 (pttp) outliers start: 86 outliers final: 81 residues processed: 280 average time/residue: 0.1183 time to fit residues: 40.3405 Evaluate side-chains 308 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 226 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 42 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 77 THR 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 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 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 42 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 87 PHE 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 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: 1.9990 chunk 84 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.147112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124375 restraints weight = 11635.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127980 restraints weight = 7277.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.130076 restraints weight = 5268.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.131986 restraints weight = 4257.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.132924 restraints weight = 3598.269| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7120 Z= 0.171 Angle : 0.755 8.021 9570 Z= 0.397 Chirality : 0.045 0.149 1060 Planarity : 0.004 0.035 1240 Dihedral : 5.953 56.206 1006 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 11.78 % Allowed : 27.95 % 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 aren not related in a simple way. whole: -2.29 (0.27), residues: 880 helix: 0.27 (0.34), residues: 200 sheet: -2.03 (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 J 62 TYR 0.009 0.001 TYR H 49 PHE 0.014 0.001 PHE J 68 TRP 0.020 0.002 TRP B 13 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7120) covalent geometry : angle 0.75528 ( 9570) hydrogen bonds : bond 0.04074 ( 298) hydrogen bonds : angle 5.13716 ( 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 323 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 237 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 41 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8048 (ttt90) REVERT: J 73 LYS cc_start: 0.5564 (mmtt) cc_final: 0.5163 (mmtm) REVERT: A 41 ARG cc_start: 0.8579 (ttt90) cc_final: 0.8270 (ttt90) REVERT: B 28 ARG cc_start: 0.8431 (mmm160) cc_final: 0.8150 (mmm-85) REVERT: B 70 ARG cc_start: 0.6018 (ppt170) cc_final: 0.5604 (ppt170) REVERT: C 19 SER cc_start: 0.8011 (t) cc_final: 0.7774 (t) REVERT: C 85 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.4227 (mmt180) REVERT: D 27 GLU cc_start: 0.8240 (tp30) cc_final: 0.7970 (tp30) REVERT: D 51 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7391 (mt-10) REVERT: D 68 PHE cc_start: 0.8117 (t80) cc_final: 0.7899 (t80) REVERT: E 68 PHE cc_start: 0.7737 (t80) cc_final: 0.7343 (t80) REVERT: E 70 ARG cc_start: 0.5850 (ppt170) cc_final: 0.5421 (ppt170) REVERT: G 27 GLU cc_start: 0.8178 (tp30) cc_final: 0.7708 (tp30) REVERT: G 34 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8121 (pt) REVERT: I 73 LYS cc_start: 0.6996 (pttm) cc_final: 0.6782 (pttm) outliers start: 86 outliers final: 80 residues processed: 284 average time/residue: 0.1226 time to fit residues: 42.3131 Evaluate side-chains 309 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 227 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 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 21 VAL 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.147975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.125729 restraints weight = 11667.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.128988 restraints weight = 7433.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131386 restraints weight = 5493.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.132863 restraints weight = 4410.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.133767 restraints weight = 3790.904| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3453 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= 0.169 Angle : 0.769 7.985 9570 Z= 0.405 Chirality : 0.046 0.193 1060 Planarity : 0.004 0.035 1240 Dihedral : 5.801 53.110 1006 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 11.64 % Allowed : 28.22 % Favored : 60.14 % 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 aren not related in a simple way. whole: -2.31 (0.28), residues: 880 helix: 0.29 (0.34), residues: 200 sheet: -2.07 (0.29), residues: 300 loop : -1.95 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 28 TYR 0.011 0.001 TYR B 49 PHE 0.013 0.001 PHE J 68 TRP 0.023 0.002 TRP H 13 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7120) covalent geometry : angle 0.76897 ( 9570) hydrogen bonds : bond 0.04039 ( 298) hydrogen bonds : angle 5.14942 ( 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 316 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 231 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 73 LYS cc_start: 0.5760 (mmtt) cc_final: 0.5286 (mmtm) REVERT: A 28 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8135 (mmm160) REVERT: A 41 ARG cc_start: 0.8546 (ttt90) cc_final: 0.8249 (ttt90) REVERT: B 28 ARG cc_start: 0.8387 (mmm160) cc_final: 0.8164 (mmm-85) REVERT: B 70 ARG cc_start: 0.5952 (ppt170) cc_final: 0.5535 (ppt170) REVERT: C 19 SER cc_start: 0.7976 (t) cc_final: 0.7772 (t) REVERT: C 73 LYS cc_start: 0.7358 (pttm) cc_final: 0.7038 (pttm) REVERT: C 84 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5313 (pp) REVERT: C 85 ARG cc_start: 0.4598 (OUTLIER) cc_final: 0.4294 (mmt180) REVERT: D 27 GLU cc_start: 0.8095 (tp30) cc_final: 0.7836 (tp30) REVERT: D 51 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7286 (mt-10) REVERT: D 68 PHE cc_start: 0.8056 (t80) cc_final: 0.7829 (t80) REVERT: E 68 PHE cc_start: 0.7661 (t80) cc_final: 0.7283 (t80) REVERT: E 70 ARG cc_start: 0.5778 (ppt170) cc_final: 0.5520 (ppt170) REVERT: G 27 GLU cc_start: 0.8104 (tp30) cc_final: 0.7648 (tp30) REVERT: G 34 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8148 (pt) REVERT: I 73 LYS cc_start: 0.6921 (pttm) cc_final: 0.6689 (pttm) outliers start: 85 outliers final: 80 residues processed: 276 average time/residue: 0.1228 time to fit residues: 41.1340 Evaluate side-chains 309 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 226 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 21 VAL 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 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 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 19 SER 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 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 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 80 LEU 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: 3.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.146330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.124076 restraints weight = 11667.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127398 restraints weight = 7474.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129596 restraints weight = 5511.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.130950 restraints weight = 4455.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.132333 restraints weight = 3867.200| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7120 Z= 0.199 Angle : 0.807 11.027 9570 Z= 0.425 Chirality : 0.047 0.154 1060 Planarity : 0.005 0.034 1240 Dihedral : 5.620 49.841 1006 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 11.78 % Allowed : 28.49 % 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 aren not related in a simple way. whole: -2.35 (0.28), residues: 880 helix: 0.21 (0.34), residues: 200 sheet: -2.09 (0.29), residues: 300 loop : -1.96 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 28 TYR 0.011 0.001 TYR B 55 PHE 0.010 0.002 PHE B 68 TRP 0.022 0.002 TRP I 13 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7120) covalent geometry : angle 0.80658 ( 9570) hydrogen bonds : bond 0.04183 ( 298) hydrogen bonds : angle 5.21559 ( 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 316 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 230 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 73 LYS cc_start: 0.5872 (mmtt) cc_final: 0.5414 (mmtm) REVERT: A 28 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.8217 (mmm160) REVERT: B 70 ARG cc_start: 0.5974 (ppt170) cc_final: 0.5472 (ppt170) REVERT: C 19 SER cc_start: 0.8021 (t) cc_final: 0.7816 (t) REVERT: C 84 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5289 (pp) REVERT: D 27 GLU cc_start: 0.7968 (tp30) cc_final: 0.7768 (tp30) REVERT: D 51 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7302 (mt-10) REVERT: D 68 PHE cc_start: 0.8068 (t80) cc_final: 0.7839 (t80) REVERT: E 36 CYS cc_start: 0.7571 (t) cc_final: 0.6468 (t) REVERT: E 68 PHE cc_start: 0.7619 (t80) cc_final: 0.7310 (t80) REVERT: E 70 ARG cc_start: 0.5959 (ppt170) cc_final: 0.5361 (ppt170) REVERT: G 27 GLU cc_start: 0.8021 (tp30) cc_final: 0.7692 (tp30) REVERT: G 34 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8184 (pt) REVERT: H 73 LYS cc_start: 0.7286 (pptt) cc_final: 0.6671 (mmtp) REVERT: I 28 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8413 (mmm-85) outliers start: 86 outliers final: 82 residues processed: 277 average time/residue: 0.1261 time to fit residues: 42.3246 Evaluate side-chains 312 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 228 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 21 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 42 VAL 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 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 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 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 80 LEU 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: 10.0000 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.146593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.123693 restraints weight = 11582.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127278 restraints weight = 7163.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129237 restraints weight = 5161.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.130909 restraints weight = 4200.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.132581 restraints weight = 3575.723| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7120 Z= 0.182 Angle : 0.808 10.208 9570 Z= 0.424 Chirality : 0.047 0.163 1060 Planarity : 0.005 0.041 1240 Dihedral : 5.589 47.532 1005 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 11.10 % Allowed : 29.18 % 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 aren not related in a simple way. whole: -2.37 (0.28), residues: 880 helix: 0.15 (0.34), residues: 200 sheet: -2.11 (0.29), residues: 300 loop : -1.93 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 62 TYR 0.019 0.001 TYR A 49 PHE 0.014 0.001 PHE A 68 TRP 0.022 0.002 TRP I 13 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7120) covalent geometry : angle 0.80771 ( 9570) hydrogen bonds : bond 0.04049 ( 298) hydrogen bonds : angle 5.19527 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1296.93 seconds wall clock time: 23 minutes 4.24 seconds (1384.24 seconds total)