Starting phenix.real_space_refine on Wed Mar 4 06:37:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6see_10153/03_2026/6see_10153.cif Found real_map, /net/cci-nas-00/data/ceres_data/6see_10153/03_2026/6see_10153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6see_10153/03_2026/6see_10153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6see_10153/03_2026/6see_10153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6see_10153/03_2026/6see_10153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6see_10153/03_2026/6see_10153.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6628 2.51 5 N 2240 2.21 5 O 2783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11949 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 637 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 731 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 618 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "V" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 2.74, per 1000 atoms: 0.23 Number of scatterers: 11949 At special positions: 0 Unit cell: (78, 120.9, 115.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2783 8.00 N 2240 7.00 C 6628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 340.2 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 71.4% alpha, 1.6% beta 144 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.515A pdb=" N GLU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.161A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.507A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.592A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.379A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.531A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 removed outlier: 4.715A pdb=" N ALA C 21 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.750A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.351A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.858A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.919A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.509A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 80 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.943A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 4.543A pdb=" N LYS E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.881A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 removed outlier: 3.667A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.782A pdb=" N ARG E 131 " --> pdb=" O GLN E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 4.116A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.958A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.345A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.585A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.916A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.648A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 122 removed outlier: 3.748A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.114A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.681A pdb=" N LEU E 121 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.842A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 77 through 78 373 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.26 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: 2239 1.33 - 1.45: 4367 1.45 - 1.57: 5561 1.57 - 1.69: 576 1.69 - 1.81: 18 Bond restraints: 12761 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.71e+00 bond pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.25e+00 ... (remaining 12756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 18145 2.69 - 5.38: 304 5.38 - 8.07: 24 8.07 - 10.75: 1 10.75 - 13.44: 2 Bond angle restraints: 18476 Sorted by residual: angle pdb=" CA LEU G 116 " pdb=" CB LEU G 116 " pdb=" CG LEU G 116 " ideal model delta sigma weight residual 116.30 129.74 -13.44 3.50e+00 8.16e-02 1.48e+01 angle pdb=" C3' DG I -30 " pdb=" O3' DG I -30 " pdb=" P DC I -29 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sigma weight residual 120.20 125.45 -5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " pdb=" P DT J 22 " ideal model delta sigma weight residual 120.20 125.41 -5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " pdb=" P DT I -28 " ideal model delta sigma weight residual 120.20 125.36 -5.16 1.50e+00 4.44e-01 1.18e+01 ... (remaining 18471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 5514 35.82 - 71.64: 1344 71.64 - 107.46: 15 107.46 - 143.29: 6 143.29 - 179.11: 2 Dihedral angle restraints: 6881 sinusoidal: 4708 harmonic: 2173 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.11 -179.11 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.64 144.36 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 93.35 126.65 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 6878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1652 0.065 - 0.130: 389 0.130 - 0.195: 43 0.195 - 0.260: 6 0.260 - 0.325: 1 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CB ILE V 523 " pdb=" CA ILE V 523 " pdb=" CG1 ILE V 523 " pdb=" CG2 ILE V 523 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' DT I 68 " pdb=" O4' DT I 68 " pdb=" C2' DT I 68 " pdb=" N1 DT I 68 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2088 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.052 2.00e-02 2.50e+03 2.39e-02 1.72e+01 pdb=" N9 DG I 26 " 0.061 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.016 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.040 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" N9 DG I 28 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.018 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 95 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C VAL D 95 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL D 95 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG D 96 " 0.017 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2368 2.78 - 3.31: 10294 3.31 - 3.84: 24661 3.84 - 4.37: 27163 4.37 - 4.90: 38345 Nonbonded interactions: 102831 Sorted by model distance: nonbonded pdb=" N2 DG I -58 " pdb=" O2 DC J 58 " model vdw 2.252 2.496 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.258 3.040 nonbonded pdb=" O2 DC I -4 " pdb=" N2 DG J 4 " model vdw 2.271 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.274 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.279 2.496 ... (remaining 102826 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 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 110) } ncs_group { reference = (chain 'D' and resid 32 through 121) selection = chain 'H' } 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.620 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.008 0.062 12761 Z= 0.345 Angle : 0.935 13.444 18476 Z= 0.540 Chirality : 0.055 0.325 2091 Planarity : 0.006 0.035 1328 Dihedral : 27.452 179.107 5481 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.26), residues: 738 helix: -0.62 (0.19), residues: 512 sheet: None (None), residues: 0 loop : -2.17 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 11 TYR 0.018 0.003 TYR F 72 PHE 0.020 0.003 PHE E 84 TRP 0.033 0.003 TRP V 531 HIS 0.010 0.002 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00764 (12761) covalent geometry : angle 0.93549 (18476) hydrogen bonds : bond 0.12847 ( 732) hydrogen bonds : angle 4.13660 ( 1787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.199 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9341 (mmtm) cc_final: 0.8984 (pttp) REVERT: A 67 PHE cc_start: 0.9233 (t80) cc_final: 0.9029 (t80) REVERT: A 83 ASP cc_start: 0.6939 (t70) cc_final: 0.6472 (t0) REVERT: A 86 TRP cc_start: 0.8802 (m100) cc_final: 0.8502 (m-10) REVERT: A 95 GLN cc_start: 0.9341 (tt0) cc_final: 0.8568 (tt0) REVERT: A 96 GLU cc_start: 0.8607 (tp30) cc_final: 0.8373 (tp30) REVERT: A 99 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8060 (mt-10) REVERT: A 104 HIS cc_start: 0.8917 (m-70) cc_final: 0.8611 (t-170) REVERT: A 107 GLU cc_start: 0.8469 (pp20) cc_final: 0.8133 (pp20) REVERT: A 111 LEU cc_start: 0.9375 (mm) cc_final: 0.9020 (mm) REVERT: A 130 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8450 (ttt-90) REVERT: B 31 LYS cc_start: 0.9316 (mttp) cc_final: 0.9116 (ttpt) REVERT: B 63 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8685 (tm-30) REVERT: B 79 LYS cc_start: 0.9403 (mttp) cc_final: 0.9030 (mtmt) REVERT: C 38 ASN cc_start: 0.8818 (m-40) cc_final: 0.7985 (p0) REVERT: C 73 ASN cc_start: 0.9059 (t0) cc_final: 0.8587 (t0) REVERT: C 82 HIS cc_start: 0.8710 (m170) cc_final: 0.8425 (m-70) REVERT: C 95 LYS cc_start: 0.9487 (tttm) cc_final: 0.9124 (mttm) REVERT: D 39 TYR cc_start: 0.8793 (t80) cc_final: 0.8184 (t80) REVERT: D 43 LYS cc_start: 0.9079 (tttt) cc_final: 0.8682 (tppt) REVERT: D 56 MET cc_start: 0.9128 (tpp) cc_final: 0.8924 (tpp) REVERT: D 65 ASP cc_start: 0.9180 (t0) cc_final: 0.8912 (t0) REVERT: D 68 GLU cc_start: 0.9034 (tt0) cc_final: 0.8172 (tm-30) REVERT: D 69 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8130 (mtm180) REVERT: E 55 GLN cc_start: 0.9177 (mt0) cc_final: 0.8524 (mm-40) REVERT: E 87 GLN cc_start: 0.8693 (mt0) cc_final: 0.7995 (mt0) REVERT: E 89 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8373 (pm20) REVERT: E 95 GLN cc_start: 0.9159 (tt0) cc_final: 0.8929 (tt0) REVERT: E 104 HIS cc_start: 0.9414 (m-70) cc_final: 0.9120 (m90) REVERT: E 127 GLN cc_start: 0.9386 (tp-100) cc_final: 0.8845 (tm-30) REVERT: F 64 ASN cc_start: 0.9248 (t0) cc_final: 0.8333 (m-40) REVERT: F 67 ARG cc_start: 0.9361 (ttm170) cc_final: 0.9122 (tmm-80) REVERT: F 68 ASP cc_start: 0.8965 (m-30) cc_final: 0.7265 (m-30) REVERT: F 70 VAL cc_start: 0.8761 (p) cc_final: 0.8006 (p) REVERT: F 71 THR cc_start: 0.8773 (p) cc_final: 0.8119 (p) REVERT: F 81 VAL cc_start: 0.9554 (t) cc_final: 0.9171 (t) REVERT: F 88 TYR cc_start: 0.9087 (m-10) cc_final: 0.8525 (m-80) REVERT: F 90 LEU cc_start: 0.9782 (mt) cc_final: 0.9579 (mp) REVERT: F 97 LEU cc_start: 0.9178 (mm) cc_final: 0.8968 (mm) REVERT: G 25 PHE cc_start: 0.8320 (m-80) cc_final: 0.7975 (m-80) REVERT: G 36 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8667 (mmmt) REVERT: G 56 GLU cc_start: 0.9539 (tm-30) cc_final: 0.9251 (tm-30) REVERT: G 68 ASN cc_start: 0.8930 (m-40) cc_final: 0.8624 (m-40) REVERT: G 87 ILE cc_start: 0.9037 (mm) cc_final: 0.8680 (mm) REVERT: G 89 ASN cc_start: 0.8546 (m-40) cc_final: 0.8333 (m110) REVERT: G 94 ASN cc_start: 0.9313 (t0) cc_final: 0.9067 (m-40) REVERT: H 62 MET cc_start: 0.9312 (mmm) cc_final: 0.9037 (mmm) REVERT: H 68 ASP cc_start: 0.8998 (t70) cc_final: 0.8786 (t0) REVERT: H 71 GLU cc_start: 0.8888 (tp30) cc_final: 0.8624 (tm-30) REVERT: H 106 LEU cc_start: 0.9371 (mt) cc_final: 0.8870 (mt) REVERT: H 120 LYS cc_start: 0.9518 (tttt) cc_final: 0.9124 (tttm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1561 time to fit residues: 61.3942 Evaluate side-chains 212 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 59 HIS B 64 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN G 31 HIS G 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.051273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038503 restraints weight = 86397.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.039603 restraints weight = 47156.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040467 restraints weight = 31249.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041059 restraints weight = 23444.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.041450 restraints weight = 19262.073| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12761 Z= 0.240 Angle : 0.675 9.414 18476 Z= 0.391 Chirality : 0.037 0.243 2091 Planarity : 0.004 0.029 1328 Dihedral : 31.118 176.491 4002 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.32 % Allowed : 4.64 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 738 helix: 0.83 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.87 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 92 TYR 0.020 0.002 TYR E 110 PHE 0.012 0.002 PHE B 100 TRP 0.006 0.001 TRP A 47 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00520 (12761) covalent geometry : angle 0.67541 (18476) hydrogen bonds : bond 0.07128 ( 732) hydrogen bonds : angle 3.35065 ( 1787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.297 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9346 (mmtm) cc_final: 0.9124 (pttp) REVERT: A 50 GLU cc_start: 0.9322 (mp0) cc_final: 0.9104 (pp20) REVERT: A 64 LYS cc_start: 0.9124 (mppt) cc_final: 0.8881 (mmtm) REVERT: A 67 PHE cc_start: 0.9372 (t80) cc_final: 0.9127 (t80) REVERT: A 83 ASP cc_start: 0.6883 (t70) cc_final: 0.6572 (t0) REVERT: A 86 TRP cc_start: 0.9069 (m100) cc_final: 0.8734 (m100) REVERT: A 104 HIS cc_start: 0.8865 (m-70) cc_final: 0.8557 (t-170) REVERT: A 107 GLU cc_start: 0.8504 (pp20) cc_final: 0.8115 (pp20) REVERT: A 110 TYR cc_start: 0.8643 (t80) cc_final: 0.8164 (t80) REVERT: A 130 ARG cc_start: 0.8994 (mtp180) cc_final: 0.8526 (ttt-90) REVERT: B 27 GLN cc_start: 0.8740 (pt0) cc_final: 0.8409 (pp30) REVERT: B 63 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8837 (tm-30) REVERT: B 74 GLU cc_start: 0.9365 (tt0) cc_final: 0.8876 (pt0) REVERT: B 79 LYS cc_start: 0.9374 (mttp) cc_final: 0.8930 (mtmt) REVERT: B 98 TYR cc_start: 0.8372 (m-10) cc_final: 0.8090 (m-80) REVERT: C 36 LYS cc_start: 0.9276 (mmmm) cc_final: 0.8872 (mmmm) REVERT: C 38 ASN cc_start: 0.8871 (m-40) cc_final: 0.8625 (m-40) REVERT: C 81 ARG cc_start: 0.8778 (tpp80) cc_final: 0.8257 (tpp80) REVERT: C 89 ASN cc_start: 0.8443 (m-40) cc_final: 0.7968 (m110) REVERT: C 95 LYS cc_start: 0.9456 (tttm) cc_final: 0.9093 (mttm) REVERT: D 39 TYR cc_start: 0.8896 (t80) cc_final: 0.8342 (t80) REVERT: D 43 LYS cc_start: 0.9083 (tttt) cc_final: 0.8687 (tppt) REVERT: D 65 ASP cc_start: 0.9382 (t0) cc_final: 0.9115 (t0) REVERT: D 68 GLU cc_start: 0.9131 (tt0) cc_final: 0.8396 (tm-30) REVERT: D 77 LEU cc_start: 0.9603 (tt) cc_final: 0.9284 (tt) REVERT: D 110 GLU cc_start: 0.8835 (tt0) cc_final: 0.8334 (tt0) REVERT: E 50 GLU cc_start: 0.9093 (tt0) cc_final: 0.8813 (tt0) REVERT: E 87 GLN cc_start: 0.8838 (mt0) cc_final: 0.8485 (mt0) REVERT: E 95 GLN cc_start: 0.9270 (tt0) cc_final: 0.8994 (tt0) REVERT: E 104 HIS cc_start: 0.9399 (m-70) cc_final: 0.9125 (m90) REVERT: E 108 ASP cc_start: 0.8985 (m-30) cc_final: 0.8708 (m-30) REVERT: E 127 GLN cc_start: 0.9465 (tp40) cc_final: 0.9160 (tm-30) REVERT: F 44 LYS cc_start: 0.8641 (tptp) cc_final: 0.7837 (tptt) REVERT: F 64 ASN cc_start: 0.9059 (t0) cc_final: 0.7951 (m-40) REVERT: F 67 ARG cc_start: 0.9340 (ttm170) cc_final: 0.9130 (tmm-80) REVERT: F 68 ASP cc_start: 0.8881 (m-30) cc_final: 0.8064 (m-30) REVERT: F 70 VAL cc_start: 0.8710 (p) cc_final: 0.8053 (p) REVERT: F 71 THR cc_start: 0.8670 (p) cc_final: 0.8141 (p) REVERT: F 74 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8692 (mt-10) REVERT: F 81 VAL cc_start: 0.9472 (t) cc_final: 0.9087 (t) REVERT: G 25 PHE cc_start: 0.8679 (m-80) cc_final: 0.8182 (m-80) REVERT: G 36 LYS cc_start: 0.9194 (mtpt) cc_final: 0.8738 (mmmt) REVERT: G 56 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9324 (tm-30) REVERT: G 89 ASN cc_start: 0.8498 (m-40) cc_final: 0.8249 (m110) REVERT: G 94 ASN cc_start: 0.9365 (t0) cc_final: 0.9030 (m110) REVERT: H 47 GLN cc_start: 0.9284 (tm-30) cc_final: 0.9072 (tm-30) REVERT: H 62 MET cc_start: 0.9347 (mmm) cc_final: 0.9016 (mmm) REVERT: H 116 LYS cc_start: 0.9411 (ptmt) cc_final: 0.9177 (pttm) REVERT: H 120 LYS cc_start: 0.9549 (tttt) cc_final: 0.9231 (tttm) outliers start: 2 outliers final: 1 residues processed: 268 average time/residue: 0.1456 time to fit residues: 51.3043 Evaluate side-chains 210 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 overall best weight: 6.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 95 GLN C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037083 restraints weight = 89041.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038207 restraints weight = 48325.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039071 restraints weight = 32291.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.039660 restraints weight = 24399.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.040051 restraints weight = 20041.284| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12761 Z= 0.283 Angle : 0.682 9.802 18476 Z= 0.396 Chirality : 0.038 0.163 2091 Planarity : 0.005 0.038 1328 Dihedral : 31.185 175.912 4002 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.30), residues: 738 helix: 1.16 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.76 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 130 TYR 0.028 0.002 TYR H 83 PHE 0.012 0.002 PHE B 100 TRP 0.007 0.001 TRP V 531 HIS 0.006 0.002 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00606 (12761) covalent geometry : angle 0.68222 (18476) hydrogen bonds : bond 0.07628 ( 732) hydrogen bonds : angle 3.49583 ( 1787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.190 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9240 (mmtm) cc_final: 0.8939 (pttp) REVERT: A 64 LYS cc_start: 0.9312 (mppt) cc_final: 0.9096 (mmtm) REVERT: A 83 ASP cc_start: 0.7287 (t70) cc_final: 0.6909 (t0) REVERT: A 86 TRP cc_start: 0.8974 (m100) cc_final: 0.8667 (m100) REVERT: A 92 LEU cc_start: 0.9199 (mm) cc_final: 0.8739 (pp) REVERT: A 104 HIS cc_start: 0.8813 (m-70) cc_final: 0.8528 (t-170) REVERT: A 107 GLU cc_start: 0.8509 (pp20) cc_final: 0.8177 (pp20) REVERT: A 111 LEU cc_start: 0.9291 (mm) cc_final: 0.8962 (mm) REVERT: A 130 ARG cc_start: 0.9154 (mtp180) cc_final: 0.8717 (ttt-90) REVERT: B 27 GLN cc_start: 0.8782 (pt0) cc_final: 0.8501 (pp30) REVERT: B 63 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8824 (tm-30) REVERT: B 74 GLU cc_start: 0.9386 (tt0) cc_final: 0.8947 (pt0) REVERT: B 79 LYS cc_start: 0.9343 (mttp) cc_final: 0.8836 (mtmt) REVERT: B 98 TYR cc_start: 0.8526 (m-10) cc_final: 0.8148 (m-80) REVERT: C 32 ARG cc_start: 0.8749 (ttp-110) cc_final: 0.8369 (ttp-110) REVERT: C 36 LYS cc_start: 0.9269 (mmmm) cc_final: 0.8951 (mmmm) REVERT: C 38 ASN cc_start: 0.8915 (m-40) cc_final: 0.8712 (m-40) REVERT: C 81 ARG cc_start: 0.8731 (tpp80) cc_final: 0.8080 (tpp80) REVERT: C 82 HIS cc_start: 0.8751 (m90) cc_final: 0.8531 (m-70) REVERT: C 89 ASN cc_start: 0.8437 (m110) cc_final: 0.8075 (m110) REVERT: C 95 LYS cc_start: 0.9565 (tttm) cc_final: 0.9104 (mttm) REVERT: D 39 TYR cc_start: 0.8888 (t80) cc_final: 0.8503 (t80) REVERT: D 43 LYS cc_start: 0.9108 (tttt) cc_final: 0.8732 (tppt) REVERT: D 65 ASP cc_start: 0.9457 (t0) cc_final: 0.9165 (t0) REVERT: D 68 GLU cc_start: 0.9118 (tt0) cc_final: 0.8383 (tm-30) REVERT: D 69 ARG cc_start: 0.9051 (ptp-170) cc_final: 0.8750 (ptm160) REVERT: D 77 LEU cc_start: 0.9514 (tt) cc_final: 0.9168 (tt) REVERT: E 50 GLU cc_start: 0.8962 (tt0) cc_final: 0.8718 (tt0) REVERT: E 87 GLN cc_start: 0.8651 (mt0) cc_final: 0.7932 (mt0) REVERT: E 104 HIS cc_start: 0.9364 (m-70) cc_final: 0.9131 (m90) REVERT: E 115 HIS cc_start: 0.8279 (t-90) cc_final: 0.7977 (t70) REVERT: E 124 LYS cc_start: 0.9250 (mppt) cc_final: 0.8980 (tmmt) REVERT: E 125 ASP cc_start: 0.8895 (m-30) cc_final: 0.8639 (m-30) REVERT: E 127 GLN cc_start: 0.9503 (tp40) cc_final: 0.9180 (tm-30) REVERT: F 64 ASN cc_start: 0.9130 (t0) cc_final: 0.8374 (m-40) REVERT: F 68 ASP cc_start: 0.9061 (m-30) cc_final: 0.8849 (p0) REVERT: F 70 VAL cc_start: 0.8774 (p) cc_final: 0.8209 (p) REVERT: F 71 THR cc_start: 0.8625 (p) cc_final: 0.8171 (p) REVERT: F 81 VAL cc_start: 0.9554 (t) cc_final: 0.8927 (t) REVERT: G 23 LEU cc_start: 0.9219 (mt) cc_final: 0.8912 (tp) REVERT: G 25 PHE cc_start: 0.8664 (m-10) cc_final: 0.8364 (m-80) REVERT: G 36 LYS cc_start: 0.9246 (mtpt) cc_final: 0.8811 (mmmt) REVERT: G 56 GLU cc_start: 0.9574 (tm-30) cc_final: 0.9136 (tm-30) REVERT: G 68 ASN cc_start: 0.8953 (m-40) cc_final: 0.8748 (m-40) REVERT: G 89 ASN cc_start: 0.8489 (m-40) cc_final: 0.8194 (m110) REVERT: G 94 ASN cc_start: 0.9445 (t0) cc_final: 0.9075 (m-40) REVERT: H 62 MET cc_start: 0.9340 (mmm) cc_final: 0.9066 (mmm) REVERT: H 116 LYS cc_start: 0.9391 (ptmt) cc_final: 0.9144 (pttm) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1359 time to fit residues: 45.4882 Evaluate side-chains 202 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037589 restraints weight = 88823.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.038732 restraints weight = 48339.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039609 restraints weight = 32207.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040146 restraints weight = 24216.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.040555 restraints weight = 20091.544| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12761 Z= 0.235 Angle : 0.649 9.883 18476 Z= 0.377 Chirality : 0.037 0.156 2091 Planarity : 0.004 0.031 1328 Dihedral : 31.136 174.386 4002 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.30), residues: 738 helix: 1.41 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.033 0.002 TYR H 83 PHE 0.007 0.001 PHE B 100 TRP 0.007 0.001 TRP V 531 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00507 (12761) covalent geometry : angle 0.64868 (18476) hydrogen bonds : bond 0.06990 ( 732) hydrogen bonds : angle 3.32484 ( 1787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.211 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9235 (mmtm) cc_final: 0.8910 (pttp) REVERT: A 64 LYS cc_start: 0.9427 (mppt) cc_final: 0.9176 (mmtm) REVERT: A 83 ASP cc_start: 0.7207 (t70) cc_final: 0.6841 (t0) REVERT: A 86 TRP cc_start: 0.8981 (m100) cc_final: 0.8697 (m100) REVERT: A 92 LEU cc_start: 0.9239 (mm) cc_final: 0.8801 (pp) REVERT: A 95 GLN cc_start: 0.9317 (tt0) cc_final: 0.8961 (tt0) REVERT: A 96 GLU cc_start: 0.8705 (tp30) cc_final: 0.8409 (tt0) REVERT: A 99 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 104 HIS cc_start: 0.8849 (m-70) cc_final: 0.8493 (t-90) REVERT: A 107 GLU cc_start: 0.8463 (pp20) cc_final: 0.8081 (pp20) REVERT: A 130 ARG cc_start: 0.9094 (mtp180) cc_final: 0.8667 (ttt-90) REVERT: B 27 GLN cc_start: 0.8760 (pt0) cc_final: 0.7968 (pm20) REVERT: B 63 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8856 (tm-30) REVERT: B 74 GLU cc_start: 0.9396 (tt0) cc_final: 0.8971 (pt0) REVERT: B 79 LYS cc_start: 0.9367 (mttp) cc_final: 0.8873 (mtmt) REVERT: C 32 ARG cc_start: 0.8787 (ttp-110) cc_final: 0.8471 (ttp80) REVERT: C 36 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8933 (mmmm) REVERT: C 38 ASN cc_start: 0.8859 (m-40) cc_final: 0.8600 (m-40) REVERT: C 89 ASN cc_start: 0.8394 (m110) cc_final: 0.8041 (m110) REVERT: C 95 LYS cc_start: 0.9567 (tttm) cc_final: 0.9058 (mttm) REVERT: C 104 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8016 (tp-100) REVERT: C 107 VAL cc_start: 0.8688 (t) cc_final: 0.8481 (t) REVERT: D 39 TYR cc_start: 0.8872 (t80) cc_final: 0.8525 (t80) REVERT: D 43 LYS cc_start: 0.9085 (tttt) cc_final: 0.8669 (tppt) REVERT: D 65 ASP cc_start: 0.9437 (t0) cc_final: 0.9001 (t0) REVERT: D 68 GLU cc_start: 0.9082 (tt0) cc_final: 0.8348 (tm-30) REVERT: D 69 ARG cc_start: 0.9040 (ptp-170) cc_final: 0.8519 (ptm160) REVERT: E 50 GLU cc_start: 0.8998 (tt0) cc_final: 0.8750 (tt0) REVERT: E 87 GLN cc_start: 0.8639 (mt0) cc_final: 0.7988 (mt0) REVERT: E 104 HIS cc_start: 0.9414 (m-70) cc_final: 0.9142 (m90) REVERT: E 108 ASP cc_start: 0.9145 (m-30) cc_final: 0.8661 (m-30) REVERT: E 115 HIS cc_start: 0.8323 (t-90) cc_final: 0.8041 (t70) REVERT: E 125 ASP cc_start: 0.8908 (m-30) cc_final: 0.8707 (m-30) REVERT: E 127 GLN cc_start: 0.9499 (tp40) cc_final: 0.9180 (tm-30) REVERT: E 133 ARG cc_start: 0.8878 (ttt180) cc_final: 0.8561 (ttm170) REVERT: F 29 ILE cc_start: 0.9467 (mm) cc_final: 0.9080 (tp) REVERT: F 46 ILE cc_start: 0.9441 (mp) cc_final: 0.9117 (pt) REVERT: F 68 ASP cc_start: 0.9252 (m-30) cc_final: 0.8821 (m-30) REVERT: F 70 VAL cc_start: 0.8778 (p) cc_final: 0.8091 (p) REVERT: F 71 THR cc_start: 0.8667 (p) cc_final: 0.8138 (p) REVERT: F 81 VAL cc_start: 0.9528 (t) cc_final: 0.8946 (t) REVERT: G 23 LEU cc_start: 0.9219 (mt) cc_final: 0.8895 (tp) REVERT: G 25 PHE cc_start: 0.8785 (m-10) cc_final: 0.8319 (m-80) REVERT: G 36 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8803 (mmmt) REVERT: G 56 GLU cc_start: 0.9558 (tm-30) cc_final: 0.9189 (tm-30) REVERT: G 68 ASN cc_start: 0.8949 (m-40) cc_final: 0.8742 (m-40) REVERT: G 73 ASN cc_start: 0.9152 (m110) cc_final: 0.8942 (m110) REVERT: G 89 ASN cc_start: 0.8526 (m-40) cc_final: 0.8287 (m110) REVERT: G 94 ASN cc_start: 0.9418 (t0) cc_final: 0.9040 (m-40) REVERT: G 104 GLN cc_start: 0.8393 (mp10) cc_final: 0.8122 (mp10) REVERT: H 59 MET cc_start: 0.8830 (tpp) cc_final: 0.8473 (tpp) REVERT: H 62 MET cc_start: 0.9319 (mmm) cc_final: 0.9031 (mmm) REVERT: H 83 TYR cc_start: 0.8813 (m-80) cc_final: 0.8535 (m-80) REVERT: H 120 LYS cc_start: 0.9561 (tttt) cc_final: 0.9326 (ttpp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1444 time to fit residues: 47.4674 Evaluate side-chains 203 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 0.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.038094 restraints weight = 88538.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039355 restraints weight = 48469.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.040264 restraints weight = 32096.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040856 restraints weight = 24039.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041266 restraints weight = 19704.360| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12761 Z= 0.204 Angle : 0.628 10.051 18476 Z= 0.365 Chirality : 0.036 0.154 2091 Planarity : 0.004 0.031 1328 Dihedral : 31.059 172.202 4002 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.30), residues: 738 helix: 1.54 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.66 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 81 TYR 0.031 0.002 TYR D 80 PHE 0.013 0.001 PHE A 67 TRP 0.007 0.001 TRP V 531 HIS 0.004 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00440 (12761) covalent geometry : angle 0.62811 (18476) hydrogen bonds : bond 0.06471 ( 732) hydrogen bonds : angle 3.23001 ( 1787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.316 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9473 (mppt) cc_final: 0.9143 (mmtm) REVERT: A 83 ASP cc_start: 0.6970 (t70) cc_final: 0.6704 (t0) REVERT: A 86 TRP cc_start: 0.8991 (m100) cc_final: 0.8683 (m100) REVERT: A 95 GLN cc_start: 0.9285 (tt0) cc_final: 0.9038 (tt0) REVERT: A 96 GLU cc_start: 0.8762 (tp30) cc_final: 0.8501 (tt0) REVERT: A 99 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 104 HIS cc_start: 0.8855 (m-70) cc_final: 0.8446 (t-90) REVERT: A 107 GLU cc_start: 0.8436 (pp20) cc_final: 0.8134 (pp20) REVERT: A 111 LEU cc_start: 0.9182 (mm) cc_final: 0.8898 (mm) REVERT: A 130 ARG cc_start: 0.9118 (mtp180) cc_final: 0.8724 (ttt-90) REVERT: B 27 GLN cc_start: 0.8813 (pt0) cc_final: 0.8121 (pm20) REVERT: B 63 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8817 (tm-30) REVERT: B 74 GLU cc_start: 0.9397 (tt0) cc_final: 0.8959 (pt0) REVERT: B 79 LYS cc_start: 0.9380 (mttp) cc_final: 0.8884 (mtmt) REVERT: B 98 TYR cc_start: 0.8652 (m-80) cc_final: 0.7507 (m-80) REVERT: C 32 ARG cc_start: 0.8856 (ttp-110) cc_final: 0.8415 (ttp80) REVERT: C 38 ASN cc_start: 0.8814 (m-40) cc_final: 0.8451 (m110) REVERT: C 64 GLU cc_start: 0.8940 (tp30) cc_final: 0.8631 (tp30) REVERT: C 84 GLN cc_start: 0.9314 (tp40) cc_final: 0.8983 (tp40) REVERT: C 89 ASN cc_start: 0.8342 (m110) cc_final: 0.7927 (m110) REVERT: C 95 LYS cc_start: 0.9553 (tttm) cc_final: 0.9046 (mttm) REVERT: C 104 GLN cc_start: 0.8399 (tp-100) cc_final: 0.7747 (tp-100) REVERT: D 39 TYR cc_start: 0.8882 (t80) cc_final: 0.8533 (t80) REVERT: D 43 LYS cc_start: 0.9098 (tttt) cc_final: 0.8683 (tppt) REVERT: D 65 ASP cc_start: 0.9448 (t0) cc_final: 0.9125 (t0) REVERT: D 68 GLU cc_start: 0.8958 (tt0) cc_final: 0.8356 (tm-30) REVERT: D 69 ARG cc_start: 0.9031 (ptp-170) cc_final: 0.8448 (ptm160) REVERT: D 110 GLU cc_start: 0.9031 (tt0) cc_final: 0.8450 (tm-30) REVERT: E 50 GLU cc_start: 0.9033 (tt0) cc_final: 0.8769 (tt0) REVERT: E 55 GLN cc_start: 0.9400 (mt0) cc_final: 0.8653 (mm-40) REVERT: E 87 GLN cc_start: 0.8667 (mt0) cc_final: 0.7995 (mt0) REVERT: E 104 HIS cc_start: 0.9400 (m-70) cc_final: 0.9183 (m90) REVERT: E 108 ASP cc_start: 0.9098 (m-30) cc_final: 0.8590 (m-30) REVERT: E 110 TYR cc_start: 0.8627 (t80) cc_final: 0.8172 (t80) REVERT: E 115 HIS cc_start: 0.8315 (t-90) cc_final: 0.7978 (t70) REVERT: E 133 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8416 (ttm170) REVERT: F 29 ILE cc_start: 0.9463 (mm) cc_final: 0.9085 (tp) REVERT: F 58 LEU cc_start: 0.9433 (tp) cc_final: 0.9177 (pp) REVERT: F 64 ASN cc_start: 0.9157 (m-40) cc_final: 0.8833 (m-40) REVERT: F 68 ASP cc_start: 0.9002 (m-30) cc_final: 0.7887 (m-30) REVERT: F 70 VAL cc_start: 0.8751 (p) cc_final: 0.8004 (p) REVERT: F 71 THR cc_start: 0.8652 (p) cc_final: 0.8106 (p) REVERT: F 81 VAL cc_start: 0.9507 (t) cc_final: 0.8798 (t) REVERT: G 23 LEU cc_start: 0.9179 (mt) cc_final: 0.8894 (tp) REVERT: G 25 PHE cc_start: 0.8780 (m-10) cc_final: 0.8272 (m-80) REVERT: G 36 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8805 (mmmt) REVERT: G 56 GLU cc_start: 0.9535 (tm-30) cc_final: 0.9197 (tm-30) REVERT: G 68 ASN cc_start: 0.8940 (m-40) cc_final: 0.8735 (m-40) REVERT: G 73 ASN cc_start: 0.9150 (m110) cc_final: 0.8907 (m110) REVERT: G 87 ILE cc_start: 0.9026 (mm) cc_final: 0.8570 (pt) REVERT: G 89 ASN cc_start: 0.8578 (m-40) cc_final: 0.8350 (m110) REVERT: G 94 ASN cc_start: 0.9388 (t0) cc_final: 0.9082 (m-40) REVERT: H 62 MET cc_start: 0.9356 (mmm) cc_final: 0.9053 (mmm) REVERT: H 120 LYS cc_start: 0.9541 (tttt) cc_final: 0.9239 (ttpp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1449 time to fit residues: 48.0729 Evaluate side-chains 199 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.050336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037555 restraints weight = 89412.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038733 restraints weight = 48155.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.039627 restraints weight = 31813.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040202 restraints weight = 23770.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.040601 restraints weight = 19484.819| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12761 Z= 0.225 Angle : 0.640 9.972 18476 Z= 0.372 Chirality : 0.036 0.152 2091 Planarity : 0.004 0.040 1328 Dihedral : 31.056 170.394 4002 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.16 % Allowed : 1.60 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.30), residues: 738 helix: 1.47 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 99 TYR 0.027 0.002 TYR E 110 PHE 0.024 0.002 PHE A 67 TRP 0.005 0.001 TRP V 531 HIS 0.004 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00490 (12761) covalent geometry : angle 0.64047 (18476) hydrogen bonds : bond 0.06855 ( 732) hydrogen bonds : angle 3.25173 ( 1787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.335 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9494 (mppt) cc_final: 0.9194 (mmtm) REVERT: A 83 ASP cc_start: 0.7037 (t70) cc_final: 0.6751 (t0) REVERT: A 86 TRP cc_start: 0.8983 (m100) cc_final: 0.8658 (m100) REVERT: A 95 GLN cc_start: 0.9251 (tt0) cc_final: 0.8969 (tt0) REVERT: A 96 GLU cc_start: 0.8808 (tp30) cc_final: 0.8523 (tt0) REVERT: A 99 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 104 HIS cc_start: 0.8615 (m-70) cc_final: 0.8225 (t-170) REVERT: A 107 GLU cc_start: 0.8452 (pp20) cc_final: 0.8100 (pp20) REVERT: A 130 ARG cc_start: 0.9128 (mtp180) cc_final: 0.8744 (ttt-90) REVERT: B 27 GLN cc_start: 0.8749 (pt0) cc_final: 0.8292 (pm20) REVERT: B 63 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8836 (tm-30) REVERT: B 74 GLU cc_start: 0.9402 (tt0) cc_final: 0.8964 (pt0) REVERT: B 79 LYS cc_start: 0.9376 (mttp) cc_final: 0.8851 (mtmt) REVERT: B 98 TYR cc_start: 0.8702 (m-80) cc_final: 0.8495 (m-80) REVERT: C 38 ASN cc_start: 0.8884 (m-40) cc_final: 0.8185 (p0) REVERT: C 89 ASN cc_start: 0.8473 (m110) cc_final: 0.7960 (m110) REVERT: C 93 LEU cc_start: 0.9585 (mt) cc_final: 0.9202 (mt) REVERT: C 95 LYS cc_start: 0.9563 (tttm) cc_final: 0.9068 (mttm) REVERT: C 104 GLN cc_start: 0.8521 (tp-100) cc_final: 0.7869 (tp-100) REVERT: D 39 TYR cc_start: 0.8877 (t80) cc_final: 0.8449 (t80) REVERT: D 43 LYS cc_start: 0.9095 (tttt) cc_final: 0.8740 (tppt) REVERT: D 65 ASP cc_start: 0.9468 (t0) cc_final: 0.9048 (t0) REVERT: D 68 GLU cc_start: 0.9022 (tt0) cc_final: 0.8388 (tm-30) REVERT: D 69 ARG cc_start: 0.9026 (ptp-170) cc_final: 0.8335 (ptm160) REVERT: D 110 GLU cc_start: 0.9123 (tt0) cc_final: 0.8634 (tm-30) REVERT: E 50 GLU cc_start: 0.9047 (tt0) cc_final: 0.8765 (tt0) REVERT: E 55 GLN cc_start: 0.9380 (mt0) cc_final: 0.8693 (mm-40) REVERT: E 62 ILE cc_start: 0.9251 (mm) cc_final: 0.9034 (mm) REVERT: E 87 GLN cc_start: 0.8769 (mt0) cc_final: 0.8221 (mt0) REVERT: E 95 GLN cc_start: 0.9199 (tt0) cc_final: 0.8859 (tt0) REVERT: E 104 HIS cc_start: 0.9422 (m-70) cc_final: 0.8906 (m90) REVERT: E 108 ASP cc_start: 0.9053 (m-30) cc_final: 0.8156 (m-30) REVERT: E 110 TYR cc_start: 0.8671 (t80) cc_final: 0.8467 (t80) REVERT: E 115 HIS cc_start: 0.8336 (t-90) cc_final: 0.8039 (t70) REVERT: E 124 LYS cc_start: 0.9181 (mppt) cc_final: 0.8952 (tmmt) REVERT: E 125 ASP cc_start: 0.9067 (m-30) cc_final: 0.8807 (m-30) REVERT: E 133 ARG cc_start: 0.8928 (ttt180) cc_final: 0.8658 (ttm170) REVERT: F 29 ILE cc_start: 0.9460 (mm) cc_final: 0.9108 (tp) REVERT: F 44 LYS cc_start: 0.8798 (tptp) cc_final: 0.8176 (tptt) REVERT: F 46 ILE cc_start: 0.9445 (mp) cc_final: 0.9122 (pt) REVERT: F 58 LEU cc_start: 0.9464 (tp) cc_final: 0.9189 (pp) REVERT: F 68 ASP cc_start: 0.9047 (m-30) cc_final: 0.8748 (m-30) REVERT: F 71 THR cc_start: 0.8700 (p) cc_final: 0.8192 (p) REVERT: F 79 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7439 (mtmm) REVERT: F 81 VAL cc_start: 0.9407 (t) cc_final: 0.8853 (t) REVERT: G 25 PHE cc_start: 0.8821 (m-10) cc_final: 0.8337 (m-80) REVERT: G 36 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8829 (mmmt) REVERT: G 56 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9277 (tm-30) REVERT: G 68 ASN cc_start: 0.8944 (m-40) cc_final: 0.8739 (m-40) REVERT: G 87 ILE cc_start: 0.8975 (mm) cc_final: 0.8522 (pt) REVERT: G 89 ASN cc_start: 0.8542 (m-40) cc_final: 0.8308 (m110) REVERT: G 94 ASN cc_start: 0.9416 (t0) cc_final: 0.9078 (m-40) REVERT: H 59 MET cc_start: 0.8700 (tpp) cc_final: 0.8410 (tpp) REVERT: H 62 MET cc_start: 0.9301 (mmm) cc_final: 0.8952 (mmm) REVERT: H 85 LYS cc_start: 0.9646 (mttt) cc_final: 0.9367 (mmmm) REVERT: H 86 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.8394 (mmt-90) REVERT: H 120 LYS cc_start: 0.9550 (tttt) cc_final: 0.9243 (ttpp) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1470 time to fit residues: 47.3477 Evaluate side-chains 194 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.050391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037594 restraints weight = 87778.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038752 restraints weight = 47424.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039645 restraints weight = 31378.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.040215 restraints weight = 23478.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.040607 restraints weight = 19247.320| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12761 Z= 0.217 Angle : 0.646 10.080 18476 Z= 0.372 Chirality : 0.036 0.153 2091 Planarity : 0.004 0.038 1328 Dihedral : 31.028 168.737 4002 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.30), residues: 738 helix: 1.50 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 32 TYR 0.027 0.003 TYR H 83 PHE 0.027 0.002 PHE A 67 TRP 0.005 0.001 TRP V 531 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00472 (12761) covalent geometry : angle 0.64570 (18476) hydrogen bonds : bond 0.06712 ( 732) hydrogen bonds : angle 3.24854 ( 1787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.298 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9208 (mmtm) cc_final: 0.8901 (pttp) REVERT: A 64 LYS cc_start: 0.9414 (mppt) cc_final: 0.9148 (mmtm) REVERT: A 83 ASP cc_start: 0.7063 (t70) cc_final: 0.6774 (t0) REVERT: A 86 TRP cc_start: 0.8954 (m100) cc_final: 0.8648 (m100) REVERT: A 95 GLN cc_start: 0.9260 (tt0) cc_final: 0.8944 (tt0) REVERT: A 96 GLU cc_start: 0.8741 (tp30) cc_final: 0.8529 (tt0) REVERT: A 99 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 104 HIS cc_start: 0.8672 (m-70) cc_final: 0.8264 (t-170) REVERT: A 107 GLU cc_start: 0.8437 (pp20) cc_final: 0.8060 (pp20) REVERT: A 130 ARG cc_start: 0.9125 (mtp180) cc_final: 0.8749 (ttt-90) REVERT: B 63 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8996 (tm-30) REVERT: B 74 GLU cc_start: 0.9408 (tt0) cc_final: 0.8946 (pt0) REVERT: B 79 LYS cc_start: 0.9410 (mttp) cc_final: 0.8882 (mtmt) REVERT: B 98 TYR cc_start: 0.8794 (m-80) cc_final: 0.8282 (m-80) REVERT: C 38 ASN cc_start: 0.8846 (m-40) cc_final: 0.8161 (p0) REVERT: C 84 GLN cc_start: 0.9317 (tp40) cc_final: 0.8680 (mt0) REVERT: C 89 ASN cc_start: 0.8210 (m110) cc_final: 0.7920 (m110) REVERT: C 90 ASP cc_start: 0.7487 (t70) cc_final: 0.7283 (t70) REVERT: C 93 LEU cc_start: 0.9565 (mt) cc_final: 0.9281 (mt) REVERT: C 95 LYS cc_start: 0.9537 (tttm) cc_final: 0.9064 (mttm) REVERT: C 104 GLN cc_start: 0.8548 (tp-100) cc_final: 0.7839 (tp-100) REVERT: D 39 TYR cc_start: 0.8861 (t80) cc_final: 0.8473 (t80) REVERT: D 43 LYS cc_start: 0.9088 (tttt) cc_final: 0.8734 (tppt) REVERT: D 65 ASP cc_start: 0.9447 (t0) cc_final: 0.9082 (t0) REVERT: D 68 GLU cc_start: 0.9041 (tt0) cc_final: 0.8389 (tm-30) REVERT: D 69 ARG cc_start: 0.9007 (ptp-170) cc_final: 0.8281 (ptm160) REVERT: D 90 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8047 (tp30) REVERT: E 50 GLU cc_start: 0.9110 (tt0) cc_final: 0.8863 (tt0) REVERT: E 55 GLN cc_start: 0.9307 (mt0) cc_final: 0.8745 (mm-40) REVERT: E 62 ILE cc_start: 0.9273 (mm) cc_final: 0.9036 (mm) REVERT: E 87 GLN cc_start: 0.8714 (mt0) cc_final: 0.8350 (mt0) REVERT: E 95 GLN cc_start: 0.9198 (tt0) cc_final: 0.8871 (tt0) REVERT: E 104 HIS cc_start: 0.9431 (m-70) cc_final: 0.8942 (m90) REVERT: E 108 ASP cc_start: 0.8682 (m-30) cc_final: 0.8161 (m-30) REVERT: E 115 HIS cc_start: 0.8335 (t-90) cc_final: 0.7998 (t70) REVERT: E 124 LYS cc_start: 0.9147 (mppt) cc_final: 0.8924 (ptmm) REVERT: E 125 ASP cc_start: 0.9050 (m-30) cc_final: 0.8817 (m-30) REVERT: E 133 ARG cc_start: 0.9054 (ttt180) cc_final: 0.8705 (ttm170) REVERT: F 29 ILE cc_start: 0.9437 (mm) cc_final: 0.9154 (tp) REVERT: F 46 ILE cc_start: 0.9491 (mp) cc_final: 0.9169 (pt) REVERT: F 58 LEU cc_start: 0.9483 (tp) cc_final: 0.9169 (pp) REVERT: F 68 ASP cc_start: 0.9015 (m-30) cc_final: 0.7905 (m-30) REVERT: F 71 THR cc_start: 0.8699 (p) cc_final: 0.8229 (p) REVERT: F 79 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7569 (mtmm) REVERT: F 81 VAL cc_start: 0.9385 (t) cc_final: 0.8928 (t) REVERT: G 25 PHE cc_start: 0.8826 (m-10) cc_final: 0.8319 (m-80) REVERT: G 36 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8825 (mmmt) REVERT: G 56 GLU cc_start: 0.9577 (tm-30) cc_final: 0.9272 (tm-30) REVERT: G 68 ASN cc_start: 0.8951 (m-40) cc_final: 0.8744 (m-40) REVERT: G 87 ILE cc_start: 0.9089 (mm) cc_final: 0.8552 (pt) REVERT: G 89 ASN cc_start: 0.8570 (m-40) cc_final: 0.8328 (m110) REVERT: G 94 ASN cc_start: 0.9410 (t0) cc_final: 0.9101 (m-40) REVERT: H 85 LYS cc_start: 0.9645 (mttt) cc_final: 0.9411 (mmmm) REVERT: H 120 LYS cc_start: 0.9500 (tttt) cc_final: 0.9159 (ttpp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1419 time to fit residues: 44.9393 Evaluate side-chains 194 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.037991 restraints weight = 87819.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039122 restraints weight = 47687.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040005 restraints weight = 31665.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.040584 restraints weight = 23707.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.040922 restraints weight = 19489.871| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12761 Z= 0.205 Angle : 0.647 10.185 18476 Z= 0.374 Chirality : 0.037 0.217 2091 Planarity : 0.004 0.030 1328 Dihedral : 31.003 167.036 4002 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.30), residues: 738 helix: 1.43 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 81 TYR 0.040 0.002 TYR H 83 PHE 0.032 0.002 PHE A 67 TRP 0.005 0.001 TRP V 531 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00442 (12761) covalent geometry : angle 0.64679 (18476) hydrogen bonds : bond 0.06570 ( 732) hydrogen bonds : angle 3.31524 ( 1787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.317 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: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8885 (pttp) REVERT: A 64 LYS cc_start: 0.9418 (mppt) cc_final: 0.9149 (mmtm) REVERT: A 83 ASP cc_start: 0.7040 (t70) cc_final: 0.6751 (t0) REVERT: A 86 TRP cc_start: 0.8941 (m100) cc_final: 0.8647 (m100) REVERT: A 95 GLN cc_start: 0.9210 (tt0) cc_final: 0.8880 (tt0) REVERT: A 96 GLU cc_start: 0.8725 (tp30) cc_final: 0.8523 (tt0) REVERT: A 99 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 104 HIS cc_start: 0.8626 (m-70) cc_final: 0.8272 (t-170) REVERT: A 107 GLU cc_start: 0.8492 (pp20) cc_final: 0.8117 (pp20) REVERT: A 130 ARG cc_start: 0.9130 (mtp180) cc_final: 0.8751 (ttt-90) REVERT: B 63 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8960 (tm-30) REVERT: B 73 THR cc_start: 0.9294 (p) cc_final: 0.9089 (p) REVERT: B 74 GLU cc_start: 0.9388 (tt0) cc_final: 0.8943 (pt0) REVERT: B 79 LYS cc_start: 0.9392 (mttp) cc_final: 0.8872 (mtmt) REVERT: B 98 TYR cc_start: 0.8721 (m-80) cc_final: 0.8159 (m-80) REVERT: C 38 ASN cc_start: 0.8867 (m-40) cc_final: 0.8186 (p0) REVERT: C 84 GLN cc_start: 0.9253 (tp40) cc_final: 0.8684 (mt0) REVERT: C 89 ASN cc_start: 0.8308 (m-40) cc_final: 0.7903 (m110) REVERT: C 93 LEU cc_start: 0.9548 (mt) cc_final: 0.9251 (mt) REVERT: C 95 LYS cc_start: 0.9540 (tttm) cc_final: 0.9090 (mttm) REVERT: C 104 GLN cc_start: 0.8579 (tp-100) cc_final: 0.7859 (tp-100) REVERT: D 39 TYR cc_start: 0.8867 (t80) cc_final: 0.8523 (t80) REVERT: D 43 LYS cc_start: 0.9077 (tttt) cc_final: 0.8734 (tppt) REVERT: D 44 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9089 (tm-30) REVERT: D 65 ASP cc_start: 0.9473 (t0) cc_final: 0.9075 (t0) REVERT: D 68 GLU cc_start: 0.9038 (tt0) cc_final: 0.8397 (tm-30) REVERT: D 69 ARG cc_start: 0.9004 (ptp-170) cc_final: 0.8255 (ptm160) REVERT: E 50 GLU cc_start: 0.9114 (tt0) cc_final: 0.8841 (tt0) REVERT: E 55 GLN cc_start: 0.9311 (mt0) cc_final: 0.8733 (mm-40) REVERT: E 62 ILE cc_start: 0.9301 (mm) cc_final: 0.9080 (mm) REVERT: E 74 ILE cc_start: 0.9236 (tp) cc_final: 0.8893 (tt) REVERT: E 87 GLN cc_start: 0.8829 (mt0) cc_final: 0.8288 (mt0) REVERT: E 95 GLN cc_start: 0.9186 (tt0) cc_final: 0.8942 (tt0) REVERT: E 104 HIS cc_start: 0.9510 (m-70) cc_final: 0.9114 (m90) REVERT: E 107 GLU cc_start: 0.8983 (pm20) cc_final: 0.8729 (pm20) REVERT: E 108 ASP cc_start: 0.9065 (m-30) cc_final: 0.8424 (m-30) REVERT: E 115 HIS cc_start: 0.8329 (t-90) cc_final: 0.7976 (t70) REVERT: E 124 LYS cc_start: 0.9152 (mppt) cc_final: 0.8932 (ptmm) REVERT: E 133 ARG cc_start: 0.8899 (ttt180) cc_final: 0.8639 (ttt180) REVERT: F 29 ILE cc_start: 0.9449 (mm) cc_final: 0.9113 (tp) REVERT: F 44 LYS cc_start: 0.8845 (tptp) cc_final: 0.8267 (tptt) REVERT: F 46 ILE cc_start: 0.9484 (mp) cc_final: 0.9182 (pt) REVERT: F 63 GLU cc_start: 0.9230 (tp30) cc_final: 0.8893 (tp30) REVERT: F 68 ASP cc_start: 0.8986 (m-30) cc_final: 0.7920 (m-30) REVERT: F 71 THR cc_start: 0.8695 (p) cc_final: 0.8212 (p) REVERT: F 79 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7579 (mtmm) REVERT: F 81 VAL cc_start: 0.9294 (t) cc_final: 0.8752 (t) REVERT: G 25 PHE cc_start: 0.8810 (m-10) cc_final: 0.8296 (m-80) REVERT: G 36 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8794 (mmmt) REVERT: G 56 GLU cc_start: 0.9557 (tm-30) cc_final: 0.9266 (tm-30) REVERT: G 68 ASN cc_start: 0.8942 (m-40) cc_final: 0.8734 (m-40) REVERT: G 87 ILE cc_start: 0.8965 (mm) cc_final: 0.8486 (pt) REVERT: G 89 ASN cc_start: 0.8557 (m-40) cc_final: 0.8315 (m110) REVERT: G 94 ASN cc_start: 0.9388 (t0) cc_final: 0.9076 (m-40) REVERT: H 57 LYS cc_start: 0.9224 (mtpt) cc_final: 0.9023 (mmmm) REVERT: H 59 MET cc_start: 0.8221 (tpt) cc_final: 0.8000 (tpt) REVERT: H 62 MET cc_start: 0.9212 (mmm) cc_final: 0.8827 (mmm) REVERT: H 79 ARG cc_start: 0.9375 (ptp90) cc_final: 0.8576 (ptp-170) REVERT: H 83 TYR cc_start: 0.8915 (m-80) cc_final: 0.8652 (m-10) REVERT: H 85 LYS cc_start: 0.9668 (mttt) cc_final: 0.9415 (mmmm) REVERT: H 120 LYS cc_start: 0.9487 (tttt) cc_final: 0.9176 (ttpp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1350 time to fit residues: 42.7815 Evaluate side-chains 196 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.038012 restraints weight = 88010.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039191 restraints weight = 47439.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040084 restraints weight = 31211.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040658 restraints weight = 23272.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.041005 restraints weight = 19038.374| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12761 Z= 0.209 Angle : 0.657 10.161 18476 Z= 0.377 Chirality : 0.037 0.184 2091 Planarity : 0.004 0.057 1328 Dihedral : 30.993 165.125 4002 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.30), residues: 738 helix: 1.53 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.77 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 76 TYR 0.033 0.003 TYR H 83 PHE 0.035 0.002 PHE A 67 TRP 0.005 0.001 TRP V 531 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00453 (12761) covalent geometry : angle 0.65668 (18476) hydrogen bonds : bond 0.06641 ( 732) hydrogen bonds : angle 3.39185 ( 1787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.333 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8892 (pttp) REVERT: A 64 LYS cc_start: 0.9458 (mppt) cc_final: 0.9175 (mmtm) REVERT: A 83 ASP cc_start: 0.7067 (t70) cc_final: 0.6668 (t0) REVERT: A 86 TRP cc_start: 0.8925 (m100) cc_final: 0.8645 (m100) REVERT: A 95 GLN cc_start: 0.9236 (tt0) cc_final: 0.8923 (tt0) REVERT: A 96 GLU cc_start: 0.8735 (tp30) cc_final: 0.8424 (tp30) REVERT: A 99 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8005 (mt-10) REVERT: A 104 HIS cc_start: 0.8695 (m-70) cc_final: 0.8218 (t-170) REVERT: A 107 GLU cc_start: 0.8440 (pp20) cc_final: 0.8100 (pp20) REVERT: A 130 ARG cc_start: 0.9131 (mtp180) cc_final: 0.8730 (ttt-90) REVERT: B 63 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8989 (tm-30) REVERT: B 74 GLU cc_start: 0.9394 (tt0) cc_final: 0.8899 (pt0) REVERT: B 79 LYS cc_start: 0.9419 (mttp) cc_final: 0.8959 (mtmt) REVERT: B 98 TYR cc_start: 0.8740 (m-80) cc_final: 0.8086 (m-80) REVERT: C 38 ASN cc_start: 0.8854 (m-40) cc_final: 0.8183 (p0) REVERT: C 84 GLN cc_start: 0.9257 (tp40) cc_final: 0.8620 (mt0) REVERT: C 89 ASN cc_start: 0.8172 (m-40) cc_final: 0.7784 (m110) REVERT: C 93 LEU cc_start: 0.9541 (mt) cc_final: 0.9247 (mt) REVERT: C 95 LYS cc_start: 0.9575 (tttm) cc_final: 0.9064 (mttm) REVERT: C 104 GLN cc_start: 0.8646 (tp-100) cc_final: 0.7975 (tp-100) REVERT: D 39 TYR cc_start: 0.8865 (t80) cc_final: 0.8495 (t80) REVERT: D 43 LYS cc_start: 0.9026 (tttt) cc_final: 0.8697 (tppt) REVERT: D 65 ASP cc_start: 0.9476 (t0) cc_final: 0.9067 (t0) REVERT: D 68 GLU cc_start: 0.9004 (tt0) cc_final: 0.8544 (tm-30) REVERT: D 69 ARG cc_start: 0.9019 (ptp-170) cc_final: 0.8286 (ptm160) REVERT: D 99 LEU cc_start: 0.8664 (tp) cc_final: 0.8463 (tp) REVERT: E 50 GLU cc_start: 0.9107 (tt0) cc_final: 0.8835 (tt0) REVERT: E 62 ILE cc_start: 0.9301 (mm) cc_final: 0.9080 (mm) REVERT: E 73 GLU cc_start: 0.9304 (mp0) cc_final: 0.9041 (mp0) REVERT: E 74 ILE cc_start: 0.9246 (tp) cc_final: 0.8907 (tt) REVERT: E 87 GLN cc_start: 0.8830 (mt0) cc_final: 0.8292 (mt0) REVERT: E 95 GLN cc_start: 0.9185 (tt0) cc_final: 0.8917 (tt0) REVERT: E 104 HIS cc_start: 0.9437 (m-70) cc_final: 0.9079 (m90) REVERT: E 107 GLU cc_start: 0.8960 (pm20) cc_final: 0.8752 (pm20) REVERT: E 108 ASP cc_start: 0.9003 (m-30) cc_final: 0.8331 (m-30) REVERT: E 110 TYR cc_start: 0.8592 (t80) cc_final: 0.8310 (t80) REVERT: E 115 HIS cc_start: 0.8209 (t-90) cc_final: 0.7875 (t70) REVERT: E 125 ASP cc_start: 0.8936 (m-30) cc_final: 0.8712 (m-30) REVERT: E 133 ARG cc_start: 0.8907 (ttt180) cc_final: 0.8656 (ttt180) REVERT: F 34 ILE cc_start: 0.9486 (mt) cc_final: 0.9267 (mm) REVERT: F 44 LYS cc_start: 0.8845 (tptp) cc_final: 0.8132 (tptt) REVERT: F 46 ILE cc_start: 0.9491 (mp) cc_final: 0.9161 (pt) REVERT: F 58 LEU cc_start: 0.9494 (tp) cc_final: 0.9193 (pp) REVERT: F 62 LEU cc_start: 0.9271 (mm) cc_final: 0.9001 (mm) REVERT: F 63 GLU cc_start: 0.9235 (tp30) cc_final: 0.8894 (tp30) REVERT: F 68 ASP cc_start: 0.8969 (m-30) cc_final: 0.7908 (m-30) REVERT: F 71 THR cc_start: 0.8795 (p) cc_final: 0.8320 (p) REVERT: F 79 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7640 (mtmm) REVERT: F 81 VAL cc_start: 0.9337 (t) cc_final: 0.8797 (t) REVERT: G 25 PHE cc_start: 0.8826 (m-10) cc_final: 0.8318 (m-80) REVERT: G 36 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8790 (mmmt) REVERT: G 56 GLU cc_start: 0.9572 (tm-30) cc_final: 0.9291 (tm-30) REVERT: G 68 ASN cc_start: 0.8943 (m-40) cc_final: 0.8743 (m-40) REVERT: G 87 ILE cc_start: 0.8968 (mm) cc_final: 0.8492 (pt) REVERT: G 89 ASN cc_start: 0.8554 (m-40) cc_final: 0.8308 (m110) REVERT: G 94 ASN cc_start: 0.9362 (t0) cc_final: 0.9041 (m-40) REVERT: H 57 LYS cc_start: 0.9288 (mtpt) cc_final: 0.9084 (mtpt) REVERT: H 62 MET cc_start: 0.9202 (mmm) cc_final: 0.8951 (mmm) REVERT: H 85 LYS cc_start: 0.9649 (mttt) cc_final: 0.9399 (mmmm) REVERT: H 120 LYS cc_start: 0.9505 (tttt) cc_final: 0.9196 (ttpp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1452 time to fit residues: 44.9899 Evaluate side-chains 198 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.037997 restraints weight = 89314.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039147 restraints weight = 48667.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040047 restraints weight = 32280.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040639 restraints weight = 24199.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041019 restraints weight = 19798.558| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12761 Z= 0.205 Angle : 0.657 10.189 18476 Z= 0.377 Chirality : 0.037 0.231 2091 Planarity : 0.004 0.051 1328 Dihedral : 30.992 163.244 4002 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.30), residues: 738 helix: 1.52 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.76 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.018 0.002 TYR E 110 PHE 0.038 0.002 PHE A 67 TRP 0.007 0.001 TRP A 47 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00444 (12761) covalent geometry : angle 0.65703 (18476) hydrogen bonds : bond 0.06595 ( 732) hydrogen bonds : angle 3.34123 ( 1787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.324 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8864 (pttp) REVERT: A 64 LYS cc_start: 0.9479 (mppt) cc_final: 0.9214 (mmtm) REVERT: A 83 ASP cc_start: 0.7127 (t70) cc_final: 0.6729 (t0) REVERT: A 86 TRP cc_start: 0.8925 (m100) cc_final: 0.8648 (m100) REVERT: A 95 GLN cc_start: 0.9237 (tt0) cc_final: 0.8930 (tt0) REVERT: A 96 GLU cc_start: 0.8687 (tp30) cc_final: 0.8380 (tp30) REVERT: A 99 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 104 HIS cc_start: 0.8684 (m-70) cc_final: 0.8387 (t-90) REVERT: A 130 ARG cc_start: 0.9113 (mtp180) cc_final: 0.8670 (ttt-90) REVERT: B 63 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8979 (tm-30) REVERT: B 74 GLU cc_start: 0.9410 (tt0) cc_final: 0.8918 (pt0) REVERT: B 79 LYS cc_start: 0.9433 (mttp) cc_final: 0.8972 (mtmt) REVERT: B 98 TYR cc_start: 0.8639 (m-80) cc_final: 0.8061 (m-80) REVERT: C 38 ASN cc_start: 0.8866 (m-40) cc_final: 0.8185 (p0) REVERT: C 84 GLN cc_start: 0.9265 (tp40) cc_final: 0.8633 (mt0) REVERT: C 89 ASN cc_start: 0.8243 (m-40) cc_final: 0.7863 (m-40) REVERT: C 93 LEU cc_start: 0.9530 (mt) cc_final: 0.9237 (mt) REVERT: C 95 LYS cc_start: 0.9603 (tttm) cc_final: 0.9071 (mttm) REVERT: C 104 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8045 (tp-100) REVERT: D 39 TYR cc_start: 0.8840 (t80) cc_final: 0.8476 (t80) REVERT: D 43 LYS cc_start: 0.9042 (tttt) cc_final: 0.8707 (tppt) REVERT: D 65 ASP cc_start: 0.9452 (t0) cc_final: 0.9204 (p0) REVERT: D 68 GLU cc_start: 0.9028 (tt0) cc_final: 0.8572 (tm-30) REVERT: D 69 ARG cc_start: 0.9035 (ptp-170) cc_final: 0.8529 (ptm160) REVERT: E 50 GLU cc_start: 0.9138 (tt0) cc_final: 0.8912 (tt0) REVERT: E 62 ILE cc_start: 0.9305 (mm) cc_final: 0.9067 (mm) REVERT: E 73 GLU cc_start: 0.9328 (mp0) cc_final: 0.9003 (mp0) REVERT: E 74 ILE cc_start: 0.9257 (tp) cc_final: 0.8920 (tt) REVERT: E 87 GLN cc_start: 0.8845 (mt0) cc_final: 0.8309 (mt0) REVERT: E 95 GLN cc_start: 0.9175 (tt0) cc_final: 0.8840 (tt0) REVERT: E 104 HIS cc_start: 0.9401 (m-70) cc_final: 0.9071 (m90) REVERT: E 107 GLU cc_start: 0.8928 (pm20) cc_final: 0.8712 (pm20) REVERT: E 108 ASP cc_start: 0.9000 (m-30) cc_final: 0.8287 (m-30) REVERT: E 110 TYR cc_start: 0.8615 (t80) cc_final: 0.8334 (t80) REVERT: E 115 HIS cc_start: 0.8191 (t-90) cc_final: 0.7858 (t70) REVERT: E 133 ARG cc_start: 0.8900 (ttt180) cc_final: 0.8640 (ttt180) REVERT: F 34 ILE cc_start: 0.9472 (mt) cc_final: 0.9268 (mm) REVERT: F 44 LYS cc_start: 0.8844 (tptp) cc_final: 0.8079 (tptt) REVERT: F 58 LEU cc_start: 0.9506 (tp) cc_final: 0.9196 (pp) REVERT: F 62 LEU cc_start: 0.9313 (mm) cc_final: 0.9060 (mm) REVERT: F 63 GLU cc_start: 0.9223 (tp30) cc_final: 0.8876 (tp30) REVERT: F 68 ASP cc_start: 0.8986 (m-30) cc_final: 0.7967 (m-30) REVERT: F 71 THR cc_start: 0.8826 (p) cc_final: 0.8390 (p) REVERT: F 79 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7651 (mtmm) REVERT: F 81 VAL cc_start: 0.9260 (t) cc_final: 0.8808 (t) REVERT: G 25 PHE cc_start: 0.8826 (m-10) cc_final: 0.8324 (m-80) REVERT: G 36 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8785 (mmmt) REVERT: G 56 GLU cc_start: 0.9577 (tm-30) cc_final: 0.9279 (tm-30) REVERT: G 68 ASN cc_start: 0.9013 (m-40) cc_final: 0.8756 (m-40) REVERT: G 87 ILE cc_start: 0.8927 (mm) cc_final: 0.8466 (pt) REVERT: G 89 ASN cc_start: 0.8523 (m-40) cc_final: 0.8307 (m110) REVERT: G 94 ASN cc_start: 0.9364 (t0) cc_final: 0.9027 (m-40) REVERT: H 57 LYS cc_start: 0.9336 (mtpt) cc_final: 0.9127 (mtpt) REVERT: H 62 MET cc_start: 0.9157 (mmm) cc_final: 0.8906 (mmm) REVERT: H 85 LYS cc_start: 0.9651 (mttt) cc_final: 0.9403 (mmmm) REVERT: H 120 LYS cc_start: 0.9501 (tttt) cc_final: 0.9206 (ttpp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1454 time to fit residues: 44.7661 Evaluate side-chains 192 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.051002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.038119 restraints weight = 88978.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039307 restraints weight = 48543.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040201 restraints weight = 32052.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040791 restraints weight = 23972.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041136 restraints weight = 19618.183| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12761 Z= 0.204 Angle : 0.656 10.214 18476 Z= 0.376 Chirality : 0.036 0.155 2091 Planarity : 0.004 0.050 1328 Dihedral : 31.004 161.231 4002 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.30), residues: 738 helix: 1.54 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 76 TYR 0.035 0.003 TYR F 88 PHE 0.038 0.002 PHE A 67 TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00442 (12761) covalent geometry : angle 0.65571 (18476) hydrogen bonds : bond 0.06575 ( 732) hydrogen bonds : angle 3.32045 ( 1787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.75 seconds wall clock time: 34 minutes 38.90 seconds (2078.90 seconds total)