Starting phenix.real_space_refine on Thu Nov 14 17:41:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3g_29695/11_2024/8g3g_29695.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3g_29695/11_2024/8g3g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3g_29695/11_2024/8g3g_29695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3g_29695/11_2024/8g3g_29695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3g_29695/11_2024/8g3g_29695.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3g_29695/11_2024/8g3g_29695.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 5.01, per 1000 atoms: 0.71 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: 1.58 Conformation dependent library (CDL) restraints added in 994.5 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 35.3% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'J' and resid 1 through 8 Processing helix chain 'J' and resid 73 through 86 Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 65 through 86 removed outlier: 4.418A pdb=" N ALA A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 65 through 86 removed outlier: 3.893A pdb=" N ARG B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 65 through 86 removed outlier: 3.585A pdb=" N ARG C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS C 72 " --> pdb=" O PHE C 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 65 through 86 removed outlier: 3.810A pdb=" N ALA D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 66 through 86 removed outlier: 4.069A pdb=" N ARG E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS E 72 " --> pdb=" O PHE E 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 27 through 31 Processing helix chain 'F' and resid 65 through 86 removed outlier: 3.633A pdb=" N ARG F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS F 72 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 68 through 86 removed outlier: 4.269A pdb=" N LYS G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 65 through 86 removed outlier: 3.766A pdb=" N ARG H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS H 72 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 8 Processing helix chain 'I' and resid 27 through 31 Processing helix chain 'I' and resid 65 through 71 removed outlier: 3.718A pdb=" N ARG I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 86 Processing sheet with id=AA1, first strand: chain 'J' and resid 15 through 22 removed outlier: 5.911A pdb=" N THR J 15 " --> pdb=" O THR J 43 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR J 43 " --> pdb=" O THR J 15 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL J 17 " --> pdb=" O ARG J 41 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG J 41 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 15 through 22 removed outlier: 5.911A pdb=" N THR J 15 " --> pdb=" O THR J 43 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR J 43 " --> pdb=" O THR J 15 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL J 17 " --> pdb=" O ARG J 41 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG J 41 " --> pdb=" O VAL J 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 24 removed outlier: 6.752A pdb=" N ILE A 39 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 20 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 22 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY A 35 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 22 removed outlier: 6.644A pdb=" N ILE B 39 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 20 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR B 37 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE B 22 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLY B 35 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 40 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 22 removed outlier: 6.324A pdb=" N VAL D 17 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG D 41 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 42 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 22 removed outlier: 6.324A pdb=" N VAL D 17 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG D 41 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 17 through 25 removed outlier: 5.957A pdb=" N VAL E 17 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ARG E 41 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER E 19 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP E 23 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY E 35 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL E 40 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 14 through 22 removed outlier: 5.515A pdb=" N THR F 15 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR F 43 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL F 17 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 41 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 40 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP F 52 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL F 42 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 16 through 22 removed outlier: 5.383A pdb=" N VAL G 17 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG G 41 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL G 42 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 22 removed outlier: 5.383A pdb=" N VAL G 17 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG G 41 " --> pdb=" O VAL G 17 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 14 through 24 removed outlier: 5.632A pdb=" N THR H 15 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR H 43 " --> pdb=" O THR H 15 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL H 17 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG H 41 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY H 35 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL H 42 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 14 through 24 removed outlier: 5.632A pdb=" N THR H 15 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR H 43 " --> pdb=" O THR H 15 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL H 17 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG H 41 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY H 35 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 16 through 22 removed outlier: 5.276A pdb=" N VAL I 17 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG I 41 " --> pdb=" O VAL I 17 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.85 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.140 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.960 ------------------------------------------------------------------------------- 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= 0.448 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 : 12.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.002 TRP B 13 PHE 0.024 0.002 PHE J 68 TYR 0.016 0.002 TYR H 49 ARG 0.009 0.001 ARG F 62 *********************** 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 : 0.840 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: 0.7707 (p-90) REVERT: C 13 TRP cc_start: 0.8305 (p-90) cc_final: 0.7693 (p-90) REVERT: E 23 ASP cc_start: 0.6412 (p0) cc_final: 0.6178 (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: 0.6777 (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: 0.3170 time to fit residues: 111.1594 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 : 0.870 ------------------------------------------------------------------------------- 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 75 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2024 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= 0.236 Angle : 0.717 6.423 9570 Z= 0.385 Chirality : 0.047 0.208 1060 Planarity : 0.004 0.032 1240 Dihedral : 7.040 54.335 1027 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 9.04 % Allowed : 27.12 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.27), residues: 880 helix: 0.10 (0.32), residues: 210 sheet: -1.88 (0.29), residues: 300 loop : -2.16 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 13 PHE 0.016 0.001 PHE G 24 TYR 0.012 0.001 TYR B 49 ARG 0.011 0.001 ARG B 41 *********************** 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 : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 6 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7929 (tm-30) REVERT: J 41 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7998 (ttt90) REVERT: J 68 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.6206 (t80) REVERT: E 68 PHE cc_start: 0.7416 (t80) cc_final: 0.7207 (t80) REVERT: G 31 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8232 (mmmt) REVERT: G 41 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7721 (ttt90) REVERT: I 19 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7956 (p) outliers start: 66 outliers final: 44 residues processed: 270 average time/residue: 0.2982 time to fit residues: 96.9079 Evaluate side-chains 268 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 40 VAL 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 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 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 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 36 CYS Chi-restraints excluded: chain G residue 41 ARG 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 45 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 0.0570 chunk 27 optimal weight: 0.0170 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7120 Z= 0.179 Angle : 0.657 6.252 9570 Z= 0.350 Chirality : 0.044 0.154 1060 Planarity : 0.003 0.028 1240 Dihedral : 5.957 59.952 1014 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 6.30 % Allowed : 29.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.27), residues: 880 helix: 0.28 (0.32), residues: 210 sheet: -1.85 (0.30), residues: 300 loop : -2.17 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 13 PHE 0.010 0.001 PHE J 68 TYR 0.015 0.001 TYR D 49 ARG 0.007 0.001 ARG A 28 *********************** 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 289 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 0.806 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: J 41 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8062 (ttt90) REVERT: J 68 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6201 (t80) REVERT: A 29 GLN cc_start: 0.8197 (pm20) cc_final: 0.7939 (mp10) REVERT: A 63 ARG cc_start: 0.8099 (ttt-90) cc_final: 0.7885 (ttt-90) REVERT: A 68 PHE cc_start: 0.7473 (t80) cc_final: 0.7109 (t80) REVERT: D 49 TYR cc_start: 0.8569 (p90) cc_final: 0.8335 (p90) REVERT: E 13 TRP cc_start: 0.8055 (p-90) cc_final: 0.7717 (p-90) REVERT: E 68 PHE cc_start: 0.7521 (t80) cc_final: 0.7258 (t80) REVERT: F 41 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.7895 (ttt90) REVERT: G 23 ASP cc_start: 0.7315 (p0) cc_final: 0.7010 (p0) REVERT: I 19 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8143 (p) REVERT: I 55 TYR cc_start: 0.7689 (t80) cc_final: 0.7471 (t80) outliers start: 46 outliers final: 34 residues processed: 258 average time/residue: 0.3072 time to fit residues: 94.5178 Evaluate side-chains 261 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 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 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 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 53 ILE Chi-restraints excluded: chain E residue 57 THR 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 36 CYS 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2669 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= 0.217 Angle : 0.670 8.336 9570 Z= 0.356 Chirality : 0.044 0.177 1060 Planarity : 0.003 0.030 1240 Dihedral : 5.869 59.896 1011 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 8.22 % Allowed : 30.00 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.27), residues: 880 helix: 0.47 (0.33), residues: 200 sheet: -1.82 (0.30), residues: 300 loop : -2.00 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 13 PHE 0.013 0.001 PHE A 68 TYR 0.014 0.001 TYR A 49 ARG 0.005 0.001 ARG A 62 *********************** 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 300 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6176 (t80) REVERT: D 49 TYR cc_start: 0.8619 (p90) cc_final: 0.8268 (p90) REVERT: E 68 PHE cc_start: 0.7557 (t80) cc_final: 0.7270 (t80) REVERT: H 31 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7453 (mmtt) REVERT: I 19 SER cc_start: 0.8594 (p) cc_final: 0.8393 (p) outliers start: 60 outliers final: 46 residues processed: 264 average time/residue: 0.3063 time to fit residues: 96.7386 Evaluate side-chains 268 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 36 CYS Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 68 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 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 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 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 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 42 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 21 VAL 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 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 I residue 1 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7120 Z= 0.348 Angle : 0.746 7.258 9570 Z= 0.401 Chirality : 0.047 0.166 1060 Planarity : 0.005 0.040 1240 Dihedral : 6.182 59.545 1008 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.27), residues: 880 helix: 0.07 (0.33), residues: 200 sheet: -1.83 (0.29), residues: 300 loop : -1.99 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 13 PHE 0.022 0.002 PHE A 68 TYR 0.013 0.001 TYR B 55 ARG 0.008 0.001 ARG F 28 *********************** 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 317 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 232 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 68 PHE cc_start: 0.6609 (OUTLIER) cc_final: 0.6391 (t80) REVERT: J 73 LYS cc_start: 0.4969 (mmtt) cc_final: 0.4646 (mmtm) REVERT: A 28 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7843 (mmm160) REVERT: C 73 LYS cc_start: 0.7369 (pttp) cc_final: 0.7139 (pttp) REVERT: D 13 TRP cc_start: 0.8393 (p-90) cc_final: 0.7709 (p-90) REVERT: D 27 GLU cc_start: 0.7819 (tp30) cc_final: 0.7578 (tp30) REVERT: D 49 TYR cc_start: 0.8685 (p90) cc_final: 0.8465 (p90) REVERT: D 68 PHE cc_start: 0.8019 (t80) cc_final: 0.7734 (t80) REVERT: E 68 PHE cc_start: 0.7712 (t80) cc_final: 0.7429 (t80) REVERT: G 27 GLU cc_start: 0.8013 (tp30) cc_final: 0.7574 (tp30) REVERT: G 41 ARG cc_start: 0.8408 (ttt180) cc_final: 0.8032 (ttt90) outliers start: 85 outliers final: 73 residues processed: 279 average time/residue: 0.2998 time to fit residues: 100.6310 Evaluate side-chains 295 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 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 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 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 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 37 THR 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 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 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 34 ILE Chi-restraints excluded: chain I residue 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 chunk 49 optimal weight: 0.9980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7120 Z= 0.198 Angle : 0.693 7.628 9570 Z= 0.367 Chirality : 0.044 0.163 1060 Planarity : 0.003 0.033 1240 Dihedral : 6.010 57.482 1008 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 8.08 % Allowed : 31.92 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.27), residues: 880 helix: 0.52 (0.34), residues: 200 sheet: -1.98 (0.29), residues: 300 loop : -1.96 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 13 PHE 0.012 0.001 PHE F 8 TYR 0.014 0.001 TYR A 49 ARG 0.008 0.001 ARG C 41 *********************** 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 301 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 73 LYS cc_start: 0.5192 (mmtt) cc_final: 0.4845 (mmtm) REVERT: A 41 ARG cc_start: 0.8520 (ttt90) cc_final: 0.8176 (ttt90) REVERT: A 68 PHE cc_start: 0.7452 (t80) cc_final: 0.7241 (t80) REVERT: C 73 LYS cc_start: 0.7193 (pttp) cc_final: 0.6822 (pttp) REVERT: D 13 TRP cc_start: 0.8309 (p-90) cc_final: 0.7848 (p-90) REVERT: E 68 PHE cc_start: 0.7658 (t80) cc_final: 0.7351 (t80) REVERT: F 41 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8091 (ttm-80) REVERT: G 31 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7943 (mmmt) REVERT: G 41 ARG cc_start: 0.8226 (ttt180) cc_final: 0.7898 (ttt90) REVERT: H 29 GLN cc_start: 0.8012 (pm20) cc_final: 0.7587 (pm20) REVERT: I 49 TYR cc_start: 0.8661 (p90) cc_final: 0.8434 (p90) outliers start: 59 outliers final: 48 residues processed: 266 average time/residue: 0.3003 time to fit residues: 95.4725 Evaluate side-chains 275 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 THR 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 B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE 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 57 THR 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 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 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 G residue 21 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 LEU 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 36 CYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3339 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= 0.238 Angle : 0.728 7.682 9570 Z= 0.385 Chirality : 0.044 0.162 1060 Planarity : 0.004 0.033 1240 Dihedral : 5.732 55.840 1006 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 9.04 % Allowed : 31.92 % Favored : 59.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.27), residues: 880 helix: 0.48 (0.34), residues: 200 sheet: -2.07 (0.29), residues: 300 loop : -1.98 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 13 PHE 0.013 0.001 PHE F 8 TYR 0.012 0.001 TYR E 49 ARG 0.010 0.001 ARG H 28 *********************** 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 300 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 73 LYS cc_start: 0.5260 (mmtt) cc_final: 0.4964 (mmtm) REVERT: A 68 PHE cc_start: 0.7496 (t80) cc_final: 0.7291 (t80) REVERT: C 73 LYS cc_start: 0.7312 (pttp) cc_final: 0.7013 (pttm) REVERT: D 13 TRP cc_start: 0.8344 (p-90) cc_final: 0.7820 (p-90) REVERT: E 14 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7696 (m) REVERT: E 68 PHE cc_start: 0.7792 (t80) cc_final: 0.7440 (t80) REVERT: F 28 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8247 (mmm-85) REVERT: F 41 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8179 (ttt90) REVERT: F 73 LYS cc_start: 0.7921 (pttm) cc_final: 0.7390 (pttt) REVERT: G 41 ARG cc_start: 0.8245 (ttt180) cc_final: 0.7953 (ttt90) REVERT: I 49 TYR cc_start: 0.8691 (p90) cc_final: 0.8392 (p90) outliers start: 66 outliers final: 62 residues processed: 266 average time/residue: 0.3248 time to fit residues: 103.4187 Evaluate side-chains 288 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 77 THR Chi-restraints excluded: chain J residue 84 LEU 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 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 84 LEU 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 57 THR 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 14 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain 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 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 36 CYS Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 87 PHE 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 53 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.0010 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7120 Z= 0.225 Angle : 0.725 7.762 9570 Z= 0.382 Chirality : 0.044 0.157 1060 Planarity : 0.003 0.032 1240 Dihedral : 5.774 57.556 1006 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 8.90 % Allowed : 31.92 % Favored : 59.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.28), residues: 880 helix: 0.51 (0.34), residues: 200 sheet: -2.07 (0.29), residues: 300 loop : -1.96 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 13 PHE 0.014 0.001 PHE F 8 TYR 0.011 0.001 TYR B 49 ARG 0.008 0.001 ARG J 62 *********************** 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 298 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 73 LYS cc_start: 0.5344 (mmtt) cc_final: 0.5053 (mmtm) REVERT: A 41 ARG cc_start: 0.8531 (ttt90) cc_final: 0.8233 (ttt90) REVERT: A 68 PHE cc_start: 0.7487 (t80) cc_final: 0.7259 (t80) REVERT: B 70 ARG cc_start: 0.5767 (ppt170) cc_final: 0.5447 (ppt170) REVERT: D 13 TRP cc_start: 0.8301 (p-90) cc_final: 0.7810 (p-90) REVERT: E 68 PHE cc_start: 0.7750 (t80) cc_final: 0.7429 (t80) REVERT: F 41 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: F 73 LYS cc_start: 0.7830 (pttm) cc_final: 0.7238 (pttt) REVERT: G 27 GLU cc_start: 0.8053 (tp30) cc_final: 0.7605 (tp30) REVERT: I 49 TYR cc_start: 0.8673 (p90) cc_final: 0.8455 (p90) outliers start: 65 outliers final: 64 residues processed: 261 average time/residue: 0.3337 time to fit residues: 104.6803 Evaluate side-chains 289 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 77 THR Chi-restraints excluded: chain J residue 84 LEU 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 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 84 LEU 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 57 THR 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 40 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 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 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 53 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7120 Z= 0.236 Angle : 0.756 9.113 9570 Z= 0.398 Chirality : 0.045 0.154 1060 Planarity : 0.004 0.032 1240 Dihedral : 5.784 58.379 1006 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 9.18 % Allowed : 31.78 % Favored : 59.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.28), residues: 880 helix: 0.50 (0.34), residues: 200 sheet: -2.10 (0.29), residues: 300 loop : -1.94 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 13 PHE 0.015 0.001 PHE F 8 TYR 0.013 0.001 TYR E 49 ARG 0.007 0.001 ARG F 28 *********************** 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 299 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 PHE cc_start: 0.6044 (t80) cc_final: 0.5770 (t80) REVERT: J 73 LYS cc_start: 0.5575 (mmtt) cc_final: 0.5361 (mmtm) REVERT: A 41 ARG cc_start: 0.8539 (ttt90) cc_final: 0.8213 (ttt90) REVERT: A 68 PHE cc_start: 0.7476 (t80) cc_final: 0.7242 (t80) REVERT: B 70 ARG cc_start: 0.5805 (ppt170) cc_final: 0.5439 (ppt170) REVERT: D 13 TRP cc_start: 0.8339 (p-90) cc_final: 0.7813 (p-90) REVERT: D 51 GLU cc_start: 0.7072 (tt0) cc_final: 0.6857 (mt-10) REVERT: E 68 PHE cc_start: 0.7724 (t80) cc_final: 0.7371 (t80) REVERT: E 70 ARG cc_start: 0.5175 (ppt170) cc_final: 0.4421 (ppt170) REVERT: F 41 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: F 73 LYS cc_start: 0.7837 (pttm) cc_final: 0.7280 (pttt) REVERT: G 27 GLU cc_start: 0.8076 (tp30) cc_final: 0.7627 (tp30) REVERT: I 73 LYS cc_start: 0.6900 (pttm) cc_final: 0.6684 (pttp) outliers start: 67 outliers final: 67 residues processed: 263 average time/residue: 0.3317 time to fit residues: 105.2869 Evaluate side-chains 294 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 41 ARG Chi-restraints excluded: chain J residue 42 VAL 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 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 84 LEU 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 57 THR 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 40 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 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 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 53 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3584 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= 0.225 Angle : 0.773 8.193 9570 Z= 0.406 Chirality : 0.045 0.159 1060 Planarity : 0.003 0.032 1240 Dihedral : 5.697 58.159 1006 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 9.45 % Allowed : 32.19 % Favored : 58.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 880 helix: 0.50 (0.34), residues: 200 sheet: -2.09 (0.29), residues: 300 loop : -1.91 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 13 PHE 0.014 0.001 PHE F 8 TYR 0.012 0.001 TYR B 49 ARG 0.008 0.001 ARG F 62 ********************** 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 305 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 PHE cc_start: 0.6055 (t80) cc_final: 0.5760 (t80) REVERT: J 73 LYS cc_start: 0.5469 (mmtt) cc_final: 0.5257 (mmtm) REVERT: A 41 ARG cc_start: 0.8523 (ttt90) cc_final: 0.8212 (ttt90) REVERT: A 68 PHE cc_start: 0.7441 (t80) cc_final: 0.7225 (t80) REVERT: A 73 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7580 (pttm) REVERT: B 70 ARG cc_start: 0.5901 (ppt170) cc_final: 0.5547 (ppt170) REVERT: D 13 TRP cc_start: 0.8326 (p-90) cc_final: 0.7842 (p-90) REVERT: D 51 GLU cc_start: 0.7016 (tt0) cc_final: 0.6789 (mt-10) REVERT: E 63 ARG cc_start: 0.5647 (ttp-110) cc_final: 0.5256 (ttp80) REVERT: E 68 PHE cc_start: 0.7698 (t80) cc_final: 0.7362 (t80) REVERT: E 70 ARG cc_start: 0.5077 (ppt170) cc_final: 0.4397 (ppt170) REVERT: F 41 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8223 (ttm-80) REVERT: F 73 LYS cc_start: 0.7819 (pttm) cc_final: 0.7249 (pttt) REVERT: G 27 GLU cc_start: 0.8088 (tp30) cc_final: 0.7631 (tp30) REVERT: H 29 GLN cc_start: 0.8252 (pm20) cc_final: 0.7859 (pm20) REVERT: I 73 LYS cc_start: 0.6925 (pttm) cc_final: 0.6704 (pttp) outliers start: 69 outliers final: 65 residues processed: 266 average time/residue: 0.3185 time to fit residues: 101.0842 Evaluate side-chains 296 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 230 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 41 ARG Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 PHE Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 1 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 84 LEU 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 57 THR Chi-restraints excluded: chain D residue 1 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 36 CYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 1 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 36 CYS Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 CYS Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 1 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 36 CYS Chi-restraints excluded: chain G residue 42 VAL 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 13 TRP Chi-restraints excluded: chain H residue 34 ILE 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 53 ILE Chi-restraints excluded: chain I residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.149814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128105 restraints weight = 11603.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.131490 restraints weight = 7378.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.133431 restraints weight = 5404.775| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 0.037 7120 Z= 0.254 Angle : 0.798 10.996 9570 Z= 0.419 Chirality : 0.046 0.179 1060 Planarity : 0.004 0.053 1240 Dihedral : 5.675 59.431 1006 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 9.04 % Allowed : 31.92 % Favored : 59.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.28), residues: 880 helix: 0.43 (0.35), residues: 200 sheet: -2.11 (0.28), residues: 300 loop : -1.91 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 13 PHE 0.018 0.001 PHE E 8 TYR 0.012 0.001 TYR B 49 ARG 0.009 0.001 ARG J 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.29 seconds wall clock time: 41 minutes 58.07 seconds (2518.07 seconds total)