Starting phenix.real_space_refine on Fri Sep 11 20:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6see_10153/09_2026/6see_10153.cif Found real_map, /net/cci-nas-00/data/ceres_data/6see_10153/09_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_10153/09_2026/6see_10153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6see_10153/09_2026/6see_10153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6see_10153/09_2026/6see_10153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6see_10153/09_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-2.2.1-6174/lib/python3.11/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: 2.64, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 358.9 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: 1.73 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: 2.28 Time building geometry restraints manager: 1.39 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 -62 " pdb=" O3' DC I -62 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.95e+01 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" C3' DG J 2 " pdb=" C2' DG J 2 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.64e+01 bond pdb=" C3' DC J -58 " pdb=" C2' DC J -58 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.61e+01 ... (remaining 12756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 17989 2.69 - 5.38: 438 5.38 - 8.07: 46 8.07 - 10.75: 1 10.75 - 13.44: 2 Bond angle restraints: 18476 Sorted by residual: angle pdb=" O4' DG I 26 " pdb=" C1' DG I 26 " pdb=" N9 DG I 26 " ideal model delta sigma weight residual 108.00 103.88 4.12 7.00e-01 2.04e+00 3.46e+01 angle pdb=" O4' DT I 68 " pdb=" C1' DT I 68 " pdb=" N1 DT I 68 " ideal model delta sigma weight residual 108.00 112.04 -4.04 7.00e-01 2.04e+00 3.34e+01 angle pdb=" O4' DT J -61 " pdb=" C4' DT J -61 " pdb=" C3' DT J -61 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.56e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 111.54 -3.54 7.00e-01 2.04e+00 2.55e+01 angle pdb=" O4' DA I 57 " pdb=" C1' DA I 57 " pdb=" N9 DA I 57 " ideal model delta sigma weight residual 108.00 104.51 3.49 7.00e-01 2.04e+00 2.48e+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: 1503 0.065 - 0.130: 505 0.130 - 0.195: 74 0.195 - 0.260: 8 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=" C3' DT J 54 " pdb=" C4' DT J 54 " pdb=" O3' DT J 54 " pdb=" C2' DT J 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' DC I -29 " pdb=" C4' DC I -29 " pdb=" O3' DC I -29 " pdb=" C2' DC I -29 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.31e+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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 0.057 12761 Z= 0.750 Angle : 1.052 13.444 18476 Z= 0.835 Chirality : 0.063 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/Z covalent geometry : bond 0.00830 / 0.75 (12761) covalent geometry : angle 1.05157 / 0.83 (18476) hydrogen bonds : bond 0.12847 / 8.60 ( 732) hydrogen bonds : angle 4.13660 / 2.93 ( 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 : 0.299 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: 0.9341 (mmtm) cc_final: 0.8984 (pttp) REVERT: A 67 PHE cc_start: 0.9233 (t80) cc_final: 0.9025 (t80) REVERT: A 83 ASP cc_start: 0.6939 (t70) cc_final: 0.6490 (t0) REVERT: A 86 TRP cc_start: 0.8802 (m100) cc_final: 0.8489 (m-10) REVERT: A 87 GLN cc_start: 0.7942 (mt0) cc_final: 0.7714 (mt0) REVERT: A 89 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8266 (mm-40) REVERT: A 95 GLN cc_start: 0.9341 (tt0) cc_final: 0.8566 (tt0) REVERT: A 96 GLU cc_start: 0.8607 (tp30) cc_final: 0.8377 (tp30) REVERT: A 99 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 104 HIS cc_start: 0.8917 (m-70) cc_final: 0.8610 (t-170) REVERT: A 107 GLU cc_start: 0.8469 (pp20) cc_final: 0.8134 (pp20) REVERT: A 111 LEU cc_start: 0.9375 (mm) cc_final: 0.9017 (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: 0.8687 (tm-30) REVERT: B 79 LYS cc_start: 0.9403 (mttp) cc_final: 0.9091 (mtmt) REVERT: C 38 ASN cc_start: 0.8818 (m-40) cc_final: 0.7986 (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: 0.8423 (m-70) REVERT: C 95 LYS cc_start: 0.9487 (tttm) cc_final: 0.9125 (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: 0.8922 (tpp) REVERT: D 65 ASP cc_start: 0.9180 (t0) cc_final: 0.8915 (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: 0.8128 (mtm180) REVERT: E 55 GLN cc_start: 0.9177 (mt0) cc_final: 0.8522 (mm-40) REVERT: E 87 GLN cc_start: 0.8693 (mt0) cc_final: 0.7996 (mt0) REVERT: E 89 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8374 (pm20) REVERT: E 95 GLN cc_start: 0.9159 (tt0) cc_final: 0.8930 (tt0) REVERT: E 104 HIS cc_start: 0.9414 (m-70) cc_final: 0.9121 (m90) REVERT: E 127 GLN cc_start: 0.9386 (tp-100) cc_final: 0.8845 (tm-30) REVERT: F 45 ARG cc_start: 0.9268 (mtp85) cc_final: 0.8945 (mmm-85) REVERT: F 64 ASN cc_start: 0.9248 (t0) cc_final: 0.8335 (m-40) REVERT: F 67 ARG cc_start: 0.9361 (ttm170) cc_final: 0.9123 (tmm-80) REVERT: F 68 ASP cc_start: 0.8965 (m-30) cc_final: 0.7262 (m-30) REVERT: F 70 VAL cc_start: 0.8761 (p) cc_final: 0.8005 (p) REVERT: F 71 THR cc_start: 0.8773 (p) cc_final: 0.8120 (p) REVERT: F 81 VAL cc_start: 0.9554 (t) cc_final: 0.9170 (t) REVERT: F 88 TYR cc_start: 0.9087 (m-10) cc_final: 0.8526 (m-80) REVERT: F 90 LEU cc_start: 0.9782 (mt) cc_final: 0.9580 (mp) REVERT: F 97 LEU cc_start: 0.9178 (mm) cc_final: 0.8967 (mm) REVERT: G 25 PHE cc_start: 0.8320 (m-80) cc_final: 0.7976 (m-80) REVERT: G 36 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8671 (mmmt) REVERT: G 56 GLU cc_start: 0.9539 (tm-30) cc_final: 0.9250 (tm-30) REVERT: G 68 ASN cc_start: 0.8930 (m-40) cc_final: 0.8623 (m-40) REVERT: G 87 ILE cc_start: 0.9037 (mm) cc_final: 0.8678 (mm) REVERT: G 89 ASN cc_start: 0.8546 (m-40) cc_final: 0.8332 (m110) REVERT: G 94 ASN cc_start: 0.9313 (t0) cc_final: 0.9068 (m-40) REVERT: H 62 MET cc_start: 0.9312 (mmm) cc_final: 0.9034 (mmm) REVERT: H 68 ASP cc_start: 0.8998 (t70) cc_final: 0.8779 (t0) REVERT: H 71 GLU cc_start: 0.8888 (tp30) cc_final: 0.8620 (tm-30) REVERT: H 90 THR cc_start: 0.8345 (p) cc_final: 0.8130 (p) REVERT: H 106 LEU cc_start: 0.9371 (mt) cc_final: 0.8869 (mt) REVERT: H 120 LYS cc_start: 0.9518 (tttt) cc_final: 0.9122 (tttm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1534 time to fit residues: 61.3181 Evaluate side-chains 215 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 59 HIS B 64 ASN B 75 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.052440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039355 restraints weight = 82635.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040557 restraints weight = 44685.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041451 restraints weight = 29492.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.042055 restraints weight = 21997.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.042431 restraints weight = 17968.863| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12761 Z= 0.197 Angle : 0.783 9.845 18476 Z= 0.439 Chirality : 0.050 0.281 2091 Planarity : 0.006 0.066 1328 Dihedral : 31.453 179.808 4002 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.48 % Allowed : 4.16 % Favored : 95.36 % 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: -0.45 (0.28), residues: 738 helix: 0.42 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.97 (0.36), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 35 TYR 0.021 0.002 TYR E 110 PHE 0.015 0.002 PHE E 106 TRP 0.010 0.002 TRP E 47 HIS 0.006 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.20 (12761) covalent geometry : angle 0.78295 / 0.44 (18476) hydrogen bonds : bond 0.08030 / 5.34 ( 732) hydrogen bonds : angle 3.49516 / 2.45 ( 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 274 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 271 time to evaluate : 0.321 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: 0.9351 (mmtm) cc_final: 0.9037 (pttp) REVERT: A 64 LYS cc_start: 0.8957 (mppt) cc_final: 0.8715 (mmtm) REVERT: A 67 PHE cc_start: 0.9368 (t80) cc_final: 0.9110 (t80) REVERT: A 83 ASP cc_start: 0.6769 (t70) cc_final: 0.6436 (t0) REVERT: A 86 TRP cc_start: 0.9002 (m100) cc_final: 0.8534 (m-10) REVERT: A 89 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8555 (mm-40) REVERT: A 104 HIS cc_start: 0.8903 (m-70) cc_final: 0.8604 (t-170) REVERT: A 107 GLU cc_start: 0.8509 (pp20) cc_final: 0.8108 (pp20) REVERT: A 110 TYR cc_start: 0.8645 (t80) cc_final: 0.8051 (t80) REVERT: A 130 ARG cc_start: 0.9014 (mtp180) cc_final: 0.8618 (ttt-90) REVERT: B 27 GLN cc_start: 0.8926 (pt0) cc_final: 0.8574 (pp30) REVERT: B 63 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8843 (tm-30) REVERT: B 79 LYS cc_start: 0.9402 (mttp) cc_final: 0.9067 (mtmt) REVERT: B 98 TYR cc_start: 0.8286 (m-10) cc_final: 0.8025 (m-80) REVERT: C 38 ASN cc_start: 0.8856 (m-40) cc_final: 0.8571 (m-40) REVERT: C 64 GLU cc_start: 0.8909 (tp30) cc_final: 0.8694 (tp30) REVERT: C 81 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8293 (tpp80) REVERT: C 89 ASN cc_start: 0.8482 (m-40) cc_final: 0.7997 (m110) REVERT: C 95 LYS cc_start: 0.9485 (tttm) cc_final: 0.9030 (mttm) REVERT: D 39 TYR cc_start: 0.8978 (t80) cc_final: 0.8357 (t80) REVERT: D 43 LYS cc_start: 0.9088 (tttt) cc_final: 0.8705 (tppt) REVERT: D 44 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8994 (tm-30) REVERT: D 65 ASP cc_start: 0.9358 (t0) cc_final: 0.9084 (t0) REVERT: D 68 GLU cc_start: 0.9106 (tt0) cc_final: 0.8267 (tm-30) REVERT: D 69 ARG cc_start: 0.8738 (mtp180) cc_final: 0.8524 (ptp-110) REVERT: D 77 LEU cc_start: 0.9561 (tt) cc_final: 0.9118 (tt) REVERT: E 50 GLU cc_start: 0.9221 (tt0) cc_final: 0.8958 (tt0) REVERT: E 55 GLN cc_start: 0.9318 (mt0) cc_final: 0.8756 (mm110) REVERT: E 87 GLN cc_start: 0.8887 (mt0) cc_final: 0.7832 (mt0) REVERT: E 89 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8275 (pm20) REVERT: E 95 GLN cc_start: 0.9199 (tt0) cc_final: 0.8904 (tt0) REVERT: E 127 GLN cc_start: 0.9508 (tp40) cc_final: 0.9298 (tm-30) REVERT: F 50 ILE cc_start: 0.9625 (mm) cc_final: 0.9413 (mm) REVERT: F 58 LEU cc_start: 0.9586 (tp) cc_final: 0.9330 (pp) REVERT: F 64 ASN cc_start: 0.9269 (t0) cc_final: 0.8251 (m-40) REVERT: F 67 ARG cc_start: 0.9362 (ttm170) cc_final: 0.9056 (tmm-80) REVERT: F 68 ASP cc_start: 0.8903 (m-30) cc_final: 0.8387 (m-30) REVERT: F 70 VAL cc_start: 0.8719 (p) cc_final: 0.8057 (p) REVERT: F 71 THR cc_start: 0.8699 (p) cc_final: 0.8187 (p) REVERT: F 74 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8759 (mt-10) REVERT: F 81 VAL cc_start: 0.9557 (t) cc_final: 0.8945 (t) REVERT: G 25 PHE cc_start: 0.8658 (m-80) cc_final: 0.8220 (m-80) REVERT: G 36 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8699 (mmmt) REVERT: G 56 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9347 (tm-30) REVERT: G 73 ASN cc_start: 0.9078 (m110) cc_final: 0.8868 (m110) REVERT: G 87 ILE cc_start: 0.8979 (mm) cc_final: 0.8620 (mm) REVERT: G 89 ASN cc_start: 0.8594 (m-40) cc_final: 0.8357 (m110) REVERT: G 94 ASN cc_start: 0.9333 (t0) cc_final: 0.9035 (m-40) REVERT: H 47 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8969 (tm-30) REVERT: H 59 MET cc_start: 0.8905 (tpp) cc_final: 0.8514 (tpt) REVERT: H 62 MET cc_start: 0.9351 (mmm) cc_final: 0.9051 (mmm) REVERT: H 116 LYS cc_start: 0.9377 (ptmt) cc_final: 0.9142 (pttm) REVERT: H 120 LYS cc_start: 0.9544 (tttt) cc_final: 0.9208 (tttp) outliers start: 3 outliers final: 1 residues processed: 272 average time/residue: 0.1322 time to fit residues: 48.3348 Evaluate side-chains 218 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 40.0000 chunk 12 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 40.0000 chunk 35 optimal weight: 40.0000 chunk 92 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 95 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.050952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.037905 restraints weight = 87615.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039054 restraints weight = 47801.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039946 restraints weight = 31803.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040531 restraints weight = 23878.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040928 restraints weight = 19609.365| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12761 Z= 0.233 Angle : 0.765 9.886 18476 Z= 0.432 Chirality : 0.048 0.271 2091 Planarity : 0.005 0.055 1328 Dihedral : 31.630 177.912 4002 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.72 % 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: 0.12 (0.29), residues: 738 helix: 0.89 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -1.86 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 83 TYR 0.021 0.002 TYR H 40 PHE 0.019 0.002 PHE E 106 TRP 0.006 0.001 TRP E 47 HIS 0.005 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.23 (12761) covalent geometry : angle 0.76532 / 0.43 (18476) hydrogen bonds : bond 0.08437 / 5.56 ( 732) hydrogen bonds : angle 3.57547 / 2.51 ( 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 250 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.271 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: A 49 LYS cc_start: 0.9322 (mmtm) cc_final: 0.9044 (pttp) REVERT: A 64 LYS cc_start: 0.9159 (mppt) cc_final: 0.8901 (mmtm) REVERT: A 83 ASP cc_start: 0.7121 (t70) cc_final: 0.6737 (t0) REVERT: A 86 TRP cc_start: 0.9121 (m100) cc_final: 0.8868 (m100) REVERT: A 89 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8578 (mm-40) REVERT: A 96 GLU cc_start: 0.8660 (tp30) cc_final: 0.8292 (tp30) REVERT: A 99 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8060 (mt-10) REVERT: A 104 HIS cc_start: 0.8759 (m-70) cc_final: 0.8489 (t-170) REVERT: A 107 GLU cc_start: 0.8470 (pp20) cc_final: 0.8072 (pp20) REVERT: A 130 ARG cc_start: 0.9104 (mtp180) cc_final: 0.8724 (ttt-90) REVERT: B 27 GLN cc_start: 0.8781 (pt0) cc_final: 0.8439 (pp30) REVERT: B 31 LYS cc_start: 0.9481 (mtmt) cc_final: 0.9265 (mtmm) REVERT: B 63 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8869 (tm-30) REVERT: B 79 LYS cc_start: 0.9405 (mttp) cc_final: 0.9071 (mtmt) REVERT: B 98 TYR cc_start: 0.8529 (m-10) cc_final: 0.8088 (m-80) REVERT: C 38 ASN cc_start: 0.8860 (m-40) cc_final: 0.8227 (p0) REVERT: C 89 ASN cc_start: 0.8449 (m-40) cc_final: 0.7965 (m110) REVERT: C 95 LYS cc_start: 0.9504 (tttm) cc_final: 0.9191 (mttm) REVERT: D 39 TYR cc_start: 0.8976 (t80) cc_final: 0.8441 (t80) REVERT: D 43 LYS cc_start: 0.9080 (tttt) cc_final: 0.8671 (tppt) REVERT: D 65 ASP cc_start: 0.9414 (t0) cc_final: 0.9117 (t0) REVERT: D 68 GLU cc_start: 0.9089 (tt0) cc_final: 0.8396 (tm-30) REVERT: D 77 LEU cc_start: 0.9567 (tt) cc_final: 0.9125 (tt) REVERT: D 90 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8365 (mm-30) REVERT: E 50 GLU cc_start: 0.9116 (tt0) cc_final: 0.8864 (tt0) REVERT: E 55 GLN cc_start: 0.9354 (mt0) cc_final: 0.9106 (mt0) REVERT: E 74 ILE cc_start: 0.9070 (tp) cc_final: 0.8868 (tp) REVERT: E 87 GLN cc_start: 0.8769 (mt0) cc_final: 0.7517 (mt0) REVERT: E 89 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8377 (pm20) REVERT: E 108 ASP cc_start: 0.8924 (m-30) cc_final: 0.8196 (m-30) REVERT: E 115 HIS cc_start: 0.8417 (t-90) cc_final: 0.8206 (t-90) REVERT: E 124 LYS cc_start: 0.9181 (mppt) cc_final: 0.8820 (tmmt) REVERT: E 127 GLN cc_start: 0.9507 (tp40) cc_final: 0.9237 (tm-30) REVERT: F 64 ASN cc_start: 0.9242 (t0) cc_final: 0.8133 (m-40) REVERT: F 67 ARG cc_start: 0.9394 (ttm170) cc_final: 0.9103 (tmm-80) REVERT: F 68 ASP cc_start: 0.9299 (m-30) cc_final: 0.8402 (m-30) REVERT: F 70 VAL cc_start: 0.8721 (p) cc_final: 0.8090 (p) REVERT: F 71 THR cc_start: 0.8722 (p) cc_final: 0.8245 (p) REVERT: F 81 VAL cc_start: 0.9551 (t) cc_final: 0.9176 (t) REVERT: F 88 TYR cc_start: 0.9014 (m-10) cc_final: 0.8779 (m-10) REVERT: G 25 PHE cc_start: 0.8649 (m-80) cc_final: 0.8294 (m-80) REVERT: G 36 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8763 (mmmt) REVERT: G 56 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9343 (tm-30) REVERT: G 89 ASN cc_start: 0.8557 (m-40) cc_final: 0.8300 (m110) REVERT: G 92 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8607 (mt-10) REVERT: G 94 ASN cc_start: 0.9372 (t0) cc_final: 0.9026 (m110) REVERT: H 47 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8986 (tm-30) REVERT: H 62 MET cc_start: 0.9384 (mmm) cc_final: 0.9044 (mmm) REVERT: H 116 LYS cc_start: 0.9417 (ptmt) cc_final: 0.9144 (pttm) REVERT: H 120 LYS cc_start: 0.9588 (tttt) cc_final: 0.9238 (tttm) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.1337 time to fit residues: 44.6274 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 : 0.236 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 72 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.051315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.038419 restraints weight = 87153.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.039545 restraints weight = 46898.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040417 restraints weight = 31059.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040975 restraints weight = 23292.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041388 restraints weight = 19228.728| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12761 Z= 0.191 Angle : 0.722 9.679 18476 Z= 0.409 Chirality : 0.047 0.259 2091 Planarity : 0.004 0.044 1328 Dihedral : 31.640 176.684 4002 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 0.39 (0.30), residues: 738 helix: 1.09 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.79 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.012 0.002 TYR C 39 PHE 0.022 0.002 PHE G 25 TRP 0.007 0.001 TRP V 531 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.19 (12761) covalent geometry : angle 0.72201 / 0.41 (18476) hydrogen bonds : bond 0.07545 / 5.02 ( 732) hydrogen bonds : angle 3.49894 / 2.48 ( 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 246 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.315 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: 0.9362 (mmtm) cc_final: 0.9056 (pttp) REVERT: A 83 ASP cc_start: 0.7085 (t70) cc_final: 0.6714 (t0) REVERT: A 86 TRP cc_start: 0.9118 (m100) cc_final: 0.8834 (m100) REVERT: A 89 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8578 (mm-40) REVERT: A 95 GLN cc_start: 0.9348 (tt0) cc_final: 0.9098 (tt0) REVERT: A 96 GLU cc_start: 0.8728 (tp30) cc_final: 0.8521 (tp30) REVERT: A 99 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 104 HIS cc_start: 0.8889 (m-70) cc_final: 0.8588 (t-170) REVERT: A 107 GLU cc_start: 0.8543 (pp20) cc_final: 0.8135 (pp20) REVERT: A 130 ARG cc_start: 0.9136 (mtp180) cc_final: 0.8686 (ttt-90) REVERT: B 31 LYS cc_start: 0.9492 (mtmt) cc_final: 0.9180 (ttpt) REVERT: B 63 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8835 (tm-30) REVERT: B 74 GLU cc_start: 0.9479 (tt0) cc_final: 0.8933 (pt0) REVERT: B 79 LYS cc_start: 0.9399 (mttp) cc_final: 0.9033 (mtmt) REVERT: C 38 ASN cc_start: 0.8873 (m-40) cc_final: 0.8298 (p0) REVERT: C 68 ASN cc_start: 0.8687 (m-40) cc_final: 0.8478 (m110) REVERT: C 81 ARG cc_start: 0.8743 (tpp80) cc_final: 0.8115 (tpp80) REVERT: C 89 ASN cc_start: 0.8392 (m110) cc_final: 0.8039 (m110) REVERT: C 95 LYS cc_start: 0.9504 (tttm) cc_final: 0.9129 (mttm) REVERT: C 104 GLN cc_start: 0.8364 (tp-100) cc_final: 0.6845 (tp-100) REVERT: D 39 TYR cc_start: 0.8953 (t80) cc_final: 0.8548 (t80) REVERT: D 43 LYS cc_start: 0.9074 (tttt) cc_final: 0.8670 (tppt) REVERT: D 65 ASP cc_start: 0.9449 (t0) cc_final: 0.9049 (t0) REVERT: D 68 GLU cc_start: 0.9114 (tt0) cc_final: 0.8511 (tm-30) REVERT: E 50 GLU cc_start: 0.9099 (tt0) cc_final: 0.8872 (tt0) REVERT: E 55 GLN cc_start: 0.9316 (mt0) cc_final: 0.9055 (mt0) REVERT: E 87 GLN cc_start: 0.8800 (mt0) cc_final: 0.7620 (mt0) REVERT: E 89 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8313 (pm20) REVERT: E 115 HIS cc_start: 0.8395 (t-90) cc_final: 0.7961 (t70) REVERT: E 124 LYS cc_start: 0.9179 (mppt) cc_final: 0.8836 (tmmt) REVERT: E 125 ASP cc_start: 0.8794 (m-30) cc_final: 0.8305 (m-30) REVERT: E 127 GLN cc_start: 0.9527 (tp40) cc_final: 0.9252 (tm-30) REVERT: F 64 ASN cc_start: 0.9222 (t0) cc_final: 0.8092 (m-40) REVERT: F 67 ARG cc_start: 0.9404 (ttm170) cc_final: 0.9104 (tmm-80) REVERT: F 68 ASP cc_start: 0.9276 (m-30) cc_final: 0.8097 (m-30) REVERT: F 70 VAL cc_start: 0.8755 (p) cc_final: 0.8113 (p) REVERT: F 71 THR cc_start: 0.8695 (p) cc_final: 0.8199 (p) REVERT: F 74 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8911 (mt-10) REVERT: F 81 VAL cc_start: 0.9524 (t) cc_final: 0.8874 (t) REVERT: G 25 PHE cc_start: 0.8779 (m-10) cc_final: 0.8512 (m-80) REVERT: G 36 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8760 (mmmt) REVERT: G 56 GLU cc_start: 0.9575 (tm-30) cc_final: 0.9254 (tm-30) REVERT: G 59 THR cc_start: 0.9425 (t) cc_final: 0.9121 (t) REVERT: G 89 ASN cc_start: 0.8565 (m-40) cc_final: 0.8322 (m110) REVERT: G 94 ASN cc_start: 0.9396 (t0) cc_final: 0.9023 (m-40) REVERT: H 59 MET cc_start: 0.8829 (tpp) cc_final: 0.8497 (tpp) REVERT: H 62 MET cc_start: 0.9390 (mmm) cc_final: 0.8978 (mmm) REVERT: H 79 ARG cc_start: 0.9267 (ptp90) cc_final: 0.8999 (ptp-110) REVERT: H 116 LYS cc_start: 0.9400 (ptmt) cc_final: 0.9150 (pttm) REVERT: H 120 LYS cc_start: 0.9583 (tttt) cc_final: 0.9253 (tttm) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1341 time to fit residues: 44.4159 Evaluate side-chains 204 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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: 10.0000 chunk 54 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 84 optimal weight: 50.0000 chunk 75 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 84 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.051061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.038009 restraints weight = 87283.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039162 restraints weight = 47667.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.040032 restraints weight = 31810.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.040613 restraints weight = 23987.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040996 restraints weight = 19748.386| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12761 Z= 0.195 Angle : 0.721 10.786 18476 Z= 0.408 Chirality : 0.046 0.258 2091 Planarity : 0.004 0.044 1328 Dihedral : 31.598 175.970 4002 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.30), residues: 738 helix: 1.16 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.77 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.029 0.002 TYR B 98 PHE 0.026 0.002 PHE A 67 TRP 0.007 0.001 TRP V 531 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.19 (12761) covalent geometry : angle 0.72059 / 0.41 (18476) hydrogen bonds : bond 0.07636 / 5.07 ( 732) hydrogen bonds : angle 3.49233 / 2.48 ( 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 239 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.281 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: 0.9355 (mmtm) cc_final: 0.9052 (pttp) REVERT: A 83 ASP cc_start: 0.7088 (t70) cc_final: 0.6735 (t0) REVERT: A 86 TRP cc_start: 0.9070 (m100) cc_final: 0.8768 (m100) REVERT: A 95 GLN cc_start: 0.9254 (tt0) cc_final: 0.8958 (tt0) REVERT: A 96 GLU cc_start: 0.8857 (tp30) cc_final: 0.8537 (tp30) REVERT: A 99 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 104 HIS cc_start: 0.8775 (m-70) cc_final: 0.8482 (t-170) REVERT: A 107 GLU cc_start: 0.8488 (pp20) cc_final: 0.8112 (pp20) REVERT: A 130 ARG cc_start: 0.9127 (mtp180) cc_final: 0.8699 (ttt-90) REVERT: B 27 GLN cc_start: 0.8807 (pt0) cc_final: 0.8142 (pm20) REVERT: B 31 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9127 (ttpt) REVERT: B 63 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8826 (tm-30) REVERT: B 79 LYS cc_start: 0.9403 (mttp) cc_final: 0.8993 (mtmt) REVERT: B 98 TYR cc_start: 0.8794 (m-80) cc_final: 0.7681 (m-80) REVERT: C 38 ASN cc_start: 0.8859 (m-40) cc_final: 0.8315 (p0) REVERT: C 84 GLN cc_start: 0.9273 (tp40) cc_final: 0.8635 (mt0) REVERT: C 89 ASN cc_start: 0.8390 (m110) cc_final: 0.8049 (m110) REVERT: C 95 LYS cc_start: 0.9543 (tttm) cc_final: 0.9161 (mttm) REVERT: C 104 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7684 (tp-100) REVERT: C 107 VAL cc_start: 0.8560 (t) cc_final: 0.8273 (t) REVERT: D 39 TYR cc_start: 0.8948 (t80) cc_final: 0.8551 (t80) REVERT: D 43 LYS cc_start: 0.9097 (tttt) cc_final: 0.8675 (tppt) REVERT: D 65 ASP cc_start: 0.9436 (t0) cc_final: 0.9078 (t0) REVERT: D 68 GLU cc_start: 0.9099 (tt0) cc_final: 0.8530 (tm-30) REVERT: D 110 GLU cc_start: 0.8878 (tt0) cc_final: 0.8404 (tt0) REVERT: E 50 GLU cc_start: 0.9054 (tt0) cc_final: 0.8825 (tt0) REVERT: E 55 GLN cc_start: 0.9355 (mt0) cc_final: 0.9106 (mt0) REVERT: E 84 PHE cc_start: 0.9171 (m-10) cc_final: 0.8971 (m-10) REVERT: E 87 GLN cc_start: 0.8768 (mt0) cc_final: 0.7517 (mt0) REVERT: E 89 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8338 (pm20) REVERT: E 115 HIS cc_start: 0.8522 (t-90) cc_final: 0.8062 (t70) REVERT: E 124 LYS cc_start: 0.9183 (mppt) cc_final: 0.8821 (tmmt) REVERT: E 125 ASP cc_start: 0.8820 (m-30) cc_final: 0.8347 (m-30) REVERT: E 127 GLN cc_start: 0.9520 (tp40) cc_final: 0.9257 (tm-30) REVERT: F 35 ARG cc_start: 0.9289 (ttm110) cc_final: 0.9066 (ttp-110) REVERT: F 63 GLU cc_start: 0.9182 (tp30) cc_final: 0.8971 (tp30) REVERT: F 64 ASN cc_start: 0.9201 (t0) cc_final: 0.8117 (m-40) REVERT: F 67 ARG cc_start: 0.9344 (ttm170) cc_final: 0.9104 (tmm-80) REVERT: F 68 ASP cc_start: 0.9209 (m-30) cc_final: 0.8077 (m-30) REVERT: F 70 VAL cc_start: 0.8766 (p) cc_final: 0.8138 (p) REVERT: F 71 THR cc_start: 0.8679 (p) cc_final: 0.8129 (p) REVERT: F 74 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8902 (mt-10) REVERT: F 81 VAL cc_start: 0.9511 (t) cc_final: 0.8904 (t) REVERT: F 88 TYR cc_start: 0.8487 (m-80) cc_final: 0.7982 (m-10) REVERT: G 36 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8766 (mmmt) REVERT: G 56 GLU cc_start: 0.9543 (tm-30) cc_final: 0.9309 (tm-30) REVERT: G 59 THR cc_start: 0.9449 (t) cc_final: 0.9198 (t) REVERT: G 89 ASN cc_start: 0.8532 (m-40) cc_final: 0.8281 (m110) REVERT: G 92 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8399 (mt-10) REVERT: G 94 ASN cc_start: 0.9380 (t0) cc_final: 0.9010 (m-40) REVERT: H 62 MET cc_start: 0.9364 (mmm) cc_final: 0.9054 (mmm) REVERT: H 116 LYS cc_start: 0.9397 (ptmt) cc_final: 0.9143 (pttm) REVERT: H 120 LYS cc_start: 0.9582 (tttt) cc_final: 0.9242 (tttm) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1297 time to fit residues: 42.2517 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 : 0.304 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 40.0000 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 93 optimal weight: 40.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** 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 = 0.3265 r_free = 0.3265 target = 0.051945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038998 restraints weight = 84013.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040232 restraints weight = 45006.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.041126 restraints weight = 29576.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041755 restraints weight = 22014.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.042146 restraints weight = 17819.363| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12761 Z= 0.153 Angle : 0.683 10.024 18476 Z= 0.390 Chirality : 0.045 0.264 2091 Planarity : 0.004 0.033 1328 Dihedral : 31.484 174.692 4002 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.34 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: 0.52 (0.30), residues: 738 helix: 1.17 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.72 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 83 TYR 0.017 0.002 TYR F 88 PHE 0.026 0.002 PHE A 67 TRP 0.008 0.001 TRP V 531 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (12761) covalent geometry : angle 0.68330 / 0.39 (18476) hydrogen bonds : bond 0.06828 / 4.59 ( 732) hydrogen bonds : angle 3.33599 / 2.37 ( 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 242 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.303 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: A 49 LYS cc_start: 0.9332 (mmtm) cc_final: 0.9023 (pttp) REVERT: A 83 ASP cc_start: 0.6881 (t70) cc_final: 0.6630 (t0) REVERT: A 86 TRP cc_start: 0.9064 (m100) cc_final: 0.8754 (m100) REVERT: A 95 GLN cc_start: 0.9249 (tt0) cc_final: 0.8919 (tt0) REVERT: A 96 GLU cc_start: 0.8947 (tp30) cc_final: 0.8678 (tp30) REVERT: A 99 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 104 HIS cc_start: 0.8736 (m-70) cc_final: 0.8465 (t-170) REVERT: A 107 GLU cc_start: 0.8481 (pp20) cc_final: 0.8131 (pp20) REVERT: A 111 LEU cc_start: 0.9290 (mm) cc_final: 0.8946 (mm) REVERT: A 130 ARG cc_start: 0.9092 (mtp180) cc_final: 0.8677 (ttt-90) REVERT: B 31 LYS cc_start: 0.9478 (mtmt) cc_final: 0.9138 (ttpt) REVERT: B 63 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8890 (tm-30) REVERT: B 74 GLU cc_start: 0.9396 (tt0) cc_final: 0.8909 (pt0) REVERT: B 79 LYS cc_start: 0.9403 (mttp) cc_final: 0.8983 (mtmt) REVERT: B 98 TYR cc_start: 0.8573 (m-80) cc_final: 0.7612 (m-80) REVERT: C 32 ARG cc_start: 0.8591 (ptt90) cc_final: 0.8044 (ttp80) REVERT: C 38 ASN cc_start: 0.8790 (m-40) cc_final: 0.8198 (p0) REVERT: C 71 ARG cc_start: 0.9158 (tmm160) cc_final: 0.8954 (ttp80) REVERT: C 84 GLN cc_start: 0.9307 (tp40) cc_final: 0.8662 (mt0) REVERT: C 89 ASN cc_start: 0.8361 (m110) cc_final: 0.7991 (m110) REVERT: C 95 LYS cc_start: 0.9500 (tttm) cc_final: 0.9007 (mttm) REVERT: C 104 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7519 (tp-100) REVERT: C 107 VAL cc_start: 0.8508 (t) cc_final: 0.8249 (t) REVERT: D 39 TYR cc_start: 0.8895 (t80) cc_final: 0.8510 (t80) REVERT: D 43 LYS cc_start: 0.9072 (tttt) cc_final: 0.8691 (tppt) REVERT: D 44 GLN cc_start: 0.9255 (tm-30) cc_final: 0.9053 (tm-30) REVERT: D 65 ASP cc_start: 0.9458 (t0) cc_final: 0.9083 (t0) REVERT: D 68 GLU cc_start: 0.9095 (tt0) cc_final: 0.8525 (tm-30) REVERT: D 82 LYS cc_start: 0.9219 (mppt) cc_final: 0.9016 (mmtm) REVERT: D 110 GLU cc_start: 0.8955 (tt0) cc_final: 0.8337 (tt0) REVERT: E 50 GLU cc_start: 0.9070 (tt0) cc_final: 0.8812 (tt0) REVERT: E 55 GLN cc_start: 0.9313 (mt0) cc_final: 0.9019 (mt0) REVERT: E 84 PHE cc_start: 0.9152 (m-10) cc_final: 0.8910 (m-10) REVERT: E 87 GLN cc_start: 0.8804 (mt0) cc_final: 0.7550 (mt0) REVERT: E 89 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8340 (pm20) REVERT: E 108 ASP cc_start: 0.9151 (m-30) cc_final: 0.8925 (m-30) REVERT: E 115 HIS cc_start: 0.8391 (t-90) cc_final: 0.7909 (t70) REVERT: E 124 LYS cc_start: 0.9157 (mppt) cc_final: 0.8805 (tmmt) REVERT: E 125 ASP cc_start: 0.8800 (m-30) cc_final: 0.8292 (m-30) REVERT: E 127 GLN cc_start: 0.9500 (tp40) cc_final: 0.9260 (tm-30) REVERT: F 63 GLU cc_start: 0.9203 (tp30) cc_final: 0.8767 (tp30) REVERT: F 64 ASN cc_start: 0.9176 (t0) cc_final: 0.8202 (m-40) REVERT: F 67 ARG cc_start: 0.9393 (ttm170) cc_final: 0.9092 (tmm-80) REVERT: F 68 ASP cc_start: 0.9150 (m-30) cc_final: 0.8069 (m-30) REVERT: F 70 VAL cc_start: 0.8714 (p) cc_final: 0.8039 (p) REVERT: F 71 THR cc_start: 0.8658 (p) cc_final: 0.8122 (p) REVERT: F 74 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8791 (mt-10) REVERT: F 81 VAL cc_start: 0.9567 (t) cc_final: 0.8926 (t) REVERT: F 88 TYR cc_start: 0.8440 (m-80) cc_final: 0.7953 (m-10) REVERT: F 95 ARG cc_start: 0.8190 (mpp80) cc_final: 0.7917 (mtt-85) REVERT: G 36 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8750 (mmmt) REVERT: G 56 GLU cc_start: 0.9513 (tm-30) cc_final: 0.9235 (tm-30) REVERT: G 89 ASN cc_start: 0.8509 (m-40) cc_final: 0.8258 (m110) REVERT: G 92 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8165 (mt-10) REVERT: G 94 ASN cc_start: 0.9370 (t0) cc_final: 0.8983 (m-40) REVERT: H 62 MET cc_start: 0.9401 (mmm) cc_final: 0.9071 (mmm) REVERT: H 79 ARG cc_start: 0.9204 (ptp90) cc_final: 0.8808 (ptp-110) REVERT: H 116 LYS cc_start: 0.9402 (ptmt) cc_final: 0.9136 (pttm) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1322 time to fit residues: 43.0884 Evaluate side-chains 206 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 50.0000 chunk 25 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.3244 r_free = 0.3244 target = 0.051057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038228 restraints weight = 87150.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039373 restraints weight = 46935.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040249 restraints weight = 31131.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040835 restraints weight = 23308.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041195 restraints weight = 19074.620| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12761 Z= 0.191 Angle : 0.709 9.953 18476 Z= 0.402 Chirality : 0.045 0.253 2091 Planarity : 0.004 0.045 1328 Dihedral : 31.460 174.226 4002 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: 0.70 (0.30), residues: 738 helix: 1.31 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.67 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 76 TYR 0.017 0.002 TYR G 50 PHE 0.025 0.002 PHE A 67 TRP 0.006 0.001 TRP A 47 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.19 (12761) covalent geometry : angle 0.70889 / 0.40 (18476) hydrogen bonds : bond 0.07596 / 5.02 ( 732) hydrogen bonds : angle 3.42548 / 2.44 ( 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 231 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.289 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: 0.9332 (mmtm) cc_final: 0.9026 (pttp) REVERT: A 83 ASP cc_start: 0.7118 (t70) cc_final: 0.6772 (t0) REVERT: A 86 TRP cc_start: 0.9044 (m100) cc_final: 0.8739 (m100) REVERT: A 95 GLN cc_start: 0.9214 (tt0) cc_final: 0.8877 (tt0) REVERT: A 96 GLU cc_start: 0.8948 (tp30) cc_final: 0.8694 (tp30) REVERT: A 99 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 104 HIS cc_start: 0.8664 (m-70) cc_final: 0.8389 (t70) REVERT: A 107 GLU cc_start: 0.8442 (pp20) cc_final: 0.8142 (pp20) REVERT: A 130 ARG cc_start: 0.9119 (mtp180) cc_final: 0.8647 (ttt-90) REVERT: B 31 LYS cc_start: 0.9460 (mtmt) cc_final: 0.9176 (mtmm) REVERT: B 63 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8901 (tm-30) REVERT: B 79 LYS cc_start: 0.9419 (mttp) cc_final: 0.8975 (mtmt) REVERT: C 38 ASN cc_start: 0.8886 (m-40) cc_final: 0.8301 (p0) REVERT: C 84 GLN cc_start: 0.9310 (tp40) cc_final: 0.8738 (mt0) REVERT: C 89 ASN cc_start: 0.8469 (m110) cc_final: 0.8120 (m110) REVERT: C 95 LYS cc_start: 0.9525 (tttm) cc_final: 0.9023 (mttm) REVERT: C 104 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7758 (tp-100) REVERT: C 107 VAL cc_start: 0.8500 (t) cc_final: 0.8232 (t) REVERT: D 39 TYR cc_start: 0.8874 (t80) cc_final: 0.8503 (t80) REVERT: D 43 LYS cc_start: 0.9087 (tttt) cc_final: 0.8698 (tppt) REVERT: D 65 ASP cc_start: 0.9458 (t0) cc_final: 0.9083 (t0) REVERT: D 68 GLU cc_start: 0.9083 (tt0) cc_final: 0.8548 (tm-30) REVERT: E 50 GLU cc_start: 0.9086 (tt0) cc_final: 0.8825 (tt0) REVERT: E 55 GLN cc_start: 0.9376 (mt0) cc_final: 0.9153 (mt0) REVERT: E 84 PHE cc_start: 0.9193 (m-10) cc_final: 0.8943 (m-10) REVERT: E 87 GLN cc_start: 0.8757 (mt0) cc_final: 0.7589 (mt0) REVERT: E 89 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8358 (pm20) REVERT: E 108 ASP cc_start: 0.9116 (m-30) cc_final: 0.8397 (m-30) REVERT: E 115 HIS cc_start: 0.8404 (t-90) cc_final: 0.8074 (t70) REVERT: E 124 LYS cc_start: 0.9179 (mppt) cc_final: 0.8781 (tmmt) REVERT: E 125 ASP cc_start: 0.8813 (m-30) cc_final: 0.8336 (m-30) REVERT: E 127 GLN cc_start: 0.9496 (tp40) cc_final: 0.9266 (tm-30) REVERT: F 63 GLU cc_start: 0.9217 (tp30) cc_final: 0.8707 (tp30) REVERT: F 64 ASN cc_start: 0.9163 (t0) cc_final: 0.8202 (m-40) REVERT: F 67 ARG cc_start: 0.9386 (ttm170) cc_final: 0.9081 (tmm-80) REVERT: F 68 ASP cc_start: 0.9122 (m-30) cc_final: 0.8045 (m-30) REVERT: F 70 VAL cc_start: 0.8754 (p) cc_final: 0.8086 (p) REVERT: F 71 THR cc_start: 0.8651 (p) cc_final: 0.8108 (p) REVERT: F 74 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8837 (mt-10) REVERT: F 81 VAL cc_start: 0.9579 (t) cc_final: 0.8896 (t) REVERT: F 88 TYR cc_start: 0.8534 (m-80) cc_final: 0.7982 (m-10) REVERT: G 36 LYS cc_start: 0.9206 (mtpt) cc_final: 0.8794 (mmmt) REVERT: G 56 GLU cc_start: 0.9520 (tm-30) cc_final: 0.9236 (tm-30) REVERT: G 89 ASN cc_start: 0.8462 (m-40) cc_final: 0.8214 (m110) REVERT: G 92 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8133 (mt-10) REVERT: G 94 ASN cc_start: 0.9397 (t0) cc_final: 0.9000 (m-40) REVERT: H 62 MET cc_start: 0.9397 (mmm) cc_final: 0.9051 (mmm) REVERT: H 116 LYS cc_start: 0.9394 (ptmt) cc_final: 0.9133 (pttm) REVERT: H 120 LYS cc_start: 0.9576 (tttt) cc_final: 0.9237 (tttm) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1306 time to fit residues: 40.8543 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 : 0.300 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 94 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** 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 = 0.3252 r_free = 0.3252 target = 0.051522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038778 restraints weight = 87588.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.039915 restraints weight = 47353.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.040810 restraints weight = 31500.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.041401 restraints weight = 23652.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.041786 restraints weight = 19357.189| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12761 Z= 0.172 Angle : 0.690 10.142 18476 Z= 0.394 Chirality : 0.044 0.257 2091 Planarity : 0.004 0.040 1328 Dihedral : 31.445 173.335 4002 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: 0.73 (0.30), residues: 738 helix: 1.30 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 131 TYR 0.034 0.002 TYR B 98 PHE 0.020 0.002 PHE A 67 TRP 0.006 0.001 TRP V 531 HIS 0.008 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (12761) covalent geometry : angle 0.68984 / 0.39 (18476) hydrogen bonds : bond 0.07004 / 4.67 ( 732) hydrogen bonds : angle 3.38861 / 2.42 ( 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 236 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.323 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: 0.9333 (mmtm) cc_final: 0.9026 (pttp) REVERT: A 77 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8033 (pttp) REVERT: A 83 ASP cc_start: 0.6860 (t70) cc_final: 0.6608 (t0) REVERT: A 86 TRP cc_start: 0.9040 (m100) cc_final: 0.8737 (m100) REVERT: A 95 GLN cc_start: 0.9240 (tt0) cc_final: 0.8895 (tt0) REVERT: A 96 GLU cc_start: 0.8947 (tp30) cc_final: 0.8700 (tp30) REVERT: A 99 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7982 (mt-10) REVERT: A 104 HIS cc_start: 0.8671 (m-70) cc_final: 0.8400 (t70) REVERT: A 107 GLU cc_start: 0.8439 (pp20) cc_final: 0.8097 (pp20) REVERT: A 130 ARG cc_start: 0.9093 (mtp180) cc_final: 0.8536 (ttt-90) REVERT: B 31 LYS cc_start: 0.9461 (mtmt) cc_final: 0.9177 (mtmm) REVERT: B 63 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8867 (tm-30) REVERT: B 79 LYS cc_start: 0.9409 (mttp) cc_final: 0.8937 (mtmt) REVERT: B 98 TYR cc_start: 0.8496 (m-80) cc_final: 0.7230 (m-80) REVERT: C 38 ASN cc_start: 0.8864 (m-40) cc_final: 0.8288 (p0) REVERT: C 84 GLN cc_start: 0.9322 (tp40) cc_final: 0.8686 (mt0) REVERT: C 89 ASN cc_start: 0.8461 (m110) cc_final: 0.8072 (m-40) REVERT: C 95 LYS cc_start: 0.9540 (tttm) cc_final: 0.9060 (mttm) REVERT: C 104 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7684 (tp-100) REVERT: C 107 VAL cc_start: 0.8558 (t) cc_final: 0.8304 (t) REVERT: D 39 TYR cc_start: 0.8884 (t80) cc_final: 0.8528 (t80) REVERT: D 43 LYS cc_start: 0.9083 (tttt) cc_final: 0.8706 (tppt) REVERT: D 65 ASP cc_start: 0.9478 (t0) cc_final: 0.9155 (t0) REVERT: D 68 GLU cc_start: 0.9087 (tt0) cc_final: 0.8428 (tm-30) REVERT: D 69 ARG cc_start: 0.9019 (ptp-170) cc_final: 0.8634 (ptm160) REVERT: E 50 GLU cc_start: 0.9081 (tt0) cc_final: 0.8819 (tt0) REVERT: E 55 GLN cc_start: 0.9386 (mt0) cc_final: 0.9151 (mt0) REVERT: E 87 GLN cc_start: 0.8810 (mt0) cc_final: 0.7645 (mt0) REVERT: E 89 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8385 (pm20) REVERT: E 108 ASP cc_start: 0.9126 (m-30) cc_final: 0.8558 (m-30) REVERT: E 110 TYR cc_start: 0.8671 (t80) cc_final: 0.8293 (t80) REVERT: E 115 HIS cc_start: 0.8313 (t-90) cc_final: 0.7835 (t70) REVERT: E 124 LYS cc_start: 0.9175 (mppt) cc_final: 0.8783 (tmmt) REVERT: E 125 ASP cc_start: 0.8792 (m-30) cc_final: 0.8327 (m-30) REVERT: E 127 GLN cc_start: 0.9494 (tp40) cc_final: 0.9274 (tm-30) REVERT: F 29 ILE cc_start: 0.9446 (mm) cc_final: 0.9197 (pt) REVERT: F 63 GLU cc_start: 0.9205 (tp30) cc_final: 0.8637 (tp30) REVERT: F 64 ASN cc_start: 0.9148 (t0) cc_final: 0.8199 (m-40) REVERT: F 67 ARG cc_start: 0.9373 (ttm170) cc_final: 0.9079 (tmm-80) REVERT: F 68 ASP cc_start: 0.9060 (m-30) cc_final: 0.7906 (m-30) REVERT: F 70 VAL cc_start: 0.8762 (p) cc_final: 0.8084 (p) REVERT: F 71 THR cc_start: 0.8650 (p) cc_final: 0.8088 (p) REVERT: F 81 VAL cc_start: 0.9538 (t) cc_final: 0.8875 (t) REVERT: F 88 TYR cc_start: 0.8655 (m-80) cc_final: 0.8066 (m-10) REVERT: F 95 ARG cc_start: 0.8305 (mpp80) cc_final: 0.8092 (mtt-85) REVERT: G 36 LYS cc_start: 0.9204 (mtpt) cc_final: 0.8810 (mmmt) REVERT: G 56 GLU cc_start: 0.9528 (tm-30) cc_final: 0.9240 (tm-30) REVERT: G 87 ILE cc_start: 0.8919 (mm) cc_final: 0.8635 (pt) REVERT: G 92 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8398 (mt-10) REVERT: H 59 MET cc_start: 0.8824 (tpp) cc_final: 0.8500 (tpp) REVERT: H 62 MET cc_start: 0.9374 (mmm) cc_final: 0.9009 (mmm) REVERT: H 85 LYS cc_start: 0.9672 (mttt) cc_final: 0.9465 (mmtm) REVERT: H 116 LYS cc_start: 0.9401 (ptmt) cc_final: 0.9163 (pttm) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1329 time to fit residues: 42.5192 Evaluate side-chains 201 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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: 40.0000 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 86 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 40.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.051690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.039016 restraints weight = 85428.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040234 restraints weight = 45834.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.041138 restraints weight = 30036.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.041693 restraints weight = 22254.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.042161 restraints weight = 18203.381| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12761 Z= 0.161 Angle : 0.691 10.244 18476 Z= 0.393 Chirality : 0.045 0.260 2091 Planarity : 0.004 0.036 1328 Dihedral : 31.399 172.787 4002 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % 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: 0.72 (0.30), residues: 738 helix: 1.28 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.46 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.030 0.002 TYR E 110 PHE 0.019 0.002 PHE H 70 TRP 0.007 0.001 TRP V 531 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (12761) covalent geometry : angle 0.69074 / 0.39 (18476) hydrogen bonds : bond 0.06843 / 4.55 ( 732) hydrogen bonds : angle 3.34434 / 2.39 ( 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 232 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.293 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: 0.9339 (mmtm) cc_final: 0.9031 (pttp) REVERT: A 83 ASP cc_start: 0.6968 (t70) cc_final: 0.6648 (t0) REVERT: A 86 TRP cc_start: 0.9037 (m100) cc_final: 0.8707 (m100) REVERT: A 95 GLN cc_start: 0.9261 (tt0) cc_final: 0.8973 (tt0) REVERT: A 96 GLU cc_start: 0.8955 (tp30) cc_final: 0.8730 (tp30) REVERT: A 99 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7990 (mt-10) REVERT: A 104 HIS cc_start: 0.8508 (m-70) cc_final: 0.8271 (t-170) REVERT: A 107 GLU cc_start: 0.8414 (pp20) cc_final: 0.8105 (pp20) REVERT: A 130 ARG cc_start: 0.9080 (mtp180) cc_final: 0.8707 (ttt-90) REVERT: B 63 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8844 (tm-30) REVERT: B 68 ASP cc_start: 0.8329 (m-30) cc_final: 0.7864 (t0) REVERT: B 74 GLU cc_start: 0.9430 (tt0) cc_final: 0.8933 (pt0) REVERT: B 79 LYS cc_start: 0.9418 (mttp) cc_final: 0.8952 (mtmt) REVERT: B 98 TYR cc_start: 0.8379 (m-80) cc_final: 0.7237 (m-80) REVERT: C 32 ARG cc_start: 0.8896 (ptt90) cc_final: 0.8322 (ttp80) REVERT: C 38 ASN cc_start: 0.8835 (m-40) cc_final: 0.8231 (p0) REVERT: C 71 ARG cc_start: 0.9137 (tmm160) cc_final: 0.8933 (ttp80) REVERT: C 84 GLN cc_start: 0.9304 (tp40) cc_final: 0.8665 (mt0) REVERT: C 89 ASN cc_start: 0.8593 (m-40) cc_final: 0.8114 (m-40) REVERT: C 95 LYS cc_start: 0.9532 (tttm) cc_final: 0.9048 (mttm) REVERT: C 104 GLN cc_start: 0.8357 (tp-100) cc_final: 0.7763 (tp-100) REVERT: C 107 VAL cc_start: 0.8566 (t) cc_final: 0.8316 (t) REVERT: D 39 TYR cc_start: 0.8898 (t80) cc_final: 0.8558 (t80) REVERT: D 43 LYS cc_start: 0.9080 (tttt) cc_final: 0.8673 (tppt) REVERT: D 44 GLN cc_start: 0.9275 (tm-30) cc_final: 0.9064 (tm-30) REVERT: D 65 ASP cc_start: 0.9494 (t0) cc_final: 0.9094 (t0) REVERT: D 68 GLU cc_start: 0.9036 (tt0) cc_final: 0.8327 (tm-30) REVERT: D 69 ARG cc_start: 0.9009 (ptp-170) cc_final: 0.8521 (ptm160) REVERT: D 90 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8380 (tp30) REVERT: D 97 LEU cc_start: 0.9157 (pp) cc_final: 0.8957 (pp) REVERT: E 50 GLU cc_start: 0.9089 (tt0) cc_final: 0.8791 (tt0) REVERT: E 55 GLN cc_start: 0.9387 (mt0) cc_final: 0.9164 (mt0) REVERT: E 87 GLN cc_start: 0.8819 (mt0) cc_final: 0.7658 (mt0) REVERT: E 89 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8351 (pm20) REVERT: E 108 ASP cc_start: 0.9127 (m-30) cc_final: 0.8656 (m-30) REVERT: E 110 TYR cc_start: 0.8651 (t80) cc_final: 0.8223 (t80) REVERT: E 115 HIS cc_start: 0.8329 (t-90) cc_final: 0.7876 (t70) REVERT: E 124 LYS cc_start: 0.9165 (mppt) cc_final: 0.8763 (tmmt) REVERT: E 125 ASP cc_start: 0.8799 (m-30) cc_final: 0.8325 (m-30) REVERT: E 127 GLN cc_start: 0.9498 (tp40) cc_final: 0.9290 (tm-30) REVERT: F 29 ILE cc_start: 0.9453 (mm) cc_final: 0.9188 (pt) REVERT: F 63 GLU cc_start: 0.9214 (tp30) cc_final: 0.8604 (tp30) REVERT: F 64 ASN cc_start: 0.9164 (t0) cc_final: 0.8257 (m-40) REVERT: F 67 ARG cc_start: 0.9348 (ttm170) cc_final: 0.9091 (tmm-80) REVERT: F 68 ASP cc_start: 0.9056 (m-30) cc_final: 0.7891 (m-30) REVERT: F 70 VAL cc_start: 0.8801 (p) cc_final: 0.8100 (p) REVERT: F 71 THR cc_start: 0.8660 (p) cc_final: 0.8103 (p) REVERT: F 81 VAL cc_start: 0.9527 (t) cc_final: 0.8829 (t) REVERT: F 88 TYR cc_start: 0.8699 (m-80) cc_final: 0.8091 (m-10) REVERT: F 95 ARG cc_start: 0.8316 (mpp80) cc_final: 0.8081 (mtt-85) REVERT: G 36 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8792 (mmmt) REVERT: G 56 GLU cc_start: 0.9535 (tm-30) cc_final: 0.9254 (tm-30) REVERT: G 87 ILE cc_start: 0.8905 (mm) cc_final: 0.8370 (pt) REVERT: G 94 ASN cc_start: 0.9392 (t0) cc_final: 0.8966 (m-40) REVERT: H 59 MET cc_start: 0.8788 (tpp) cc_final: 0.8486 (tpp) REVERT: H 62 MET cc_start: 0.9390 (mmm) cc_final: 0.9003 (mmm) REVERT: H 79 ARG cc_start: 0.9209 (ptp90) cc_final: 0.8905 (ptp-110) REVERT: H 85 LYS cc_start: 0.9662 (mttt) cc_final: 0.9459 (mmtm) REVERT: H 116 LYS cc_start: 0.9422 (ptmt) cc_final: 0.9172 (pttm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1330 time to fit residues: 41.7394 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 : 0.296 ------------------------------------------------------------------------------- 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: 7.9990 chunk 17 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 chunk 85 optimal weight: 40.0000 chunk 97 optimal weight: 50.0000 chunk 59 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 35 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 GLN ** 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 = 0.3255 r_free = 0.3255 target = 0.051621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.039035 restraints weight = 84800.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040219 restraints weight = 45036.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.041119 restraints weight = 29287.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.041691 restraints weight = 21561.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.042147 restraints weight = 17569.104| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12761 Z= 0.163 Angle : 0.691 10.182 18476 Z= 0.393 Chirality : 0.044 0.260 2091 Planarity : 0.004 0.045 1328 Dihedral : 31.379 172.133 4002 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: 0.72 (0.30), residues: 738 helix: 1.28 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.49 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 133 TYR 0.025 0.002 TYR E 110 PHE 0.021 0.002 PHE A 67 TRP 0.006 0.001 TRP V 531 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (12761) covalent geometry : angle 0.69143 / 0.39 (18476) hydrogen bonds : bond 0.06823 / 4.52 ( 732) hydrogen bonds : angle 3.33612 / 2.39 ( 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 230 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.291 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: 0.9340 (mmtm) cc_final: 0.9025 (pttp) REVERT: A 83 ASP cc_start: 0.6961 (t70) cc_final: 0.6641 (t0) REVERT: A 86 TRP cc_start: 0.9049 (m100) cc_final: 0.8747 (m100) REVERT: A 95 GLN cc_start: 0.9270 (tt0) cc_final: 0.8880 (tt0) REVERT: A 96 GLU cc_start: 0.8962 (tp30) cc_final: 0.8749 (tp30) REVERT: A 99 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7982 (mt-10) REVERT: A 104 HIS cc_start: 0.8491 (m-70) cc_final: 0.8244 (t-170) REVERT: A 107 GLU cc_start: 0.8390 (pp20) cc_final: 0.8066 (pp20) REVERT: A 130 ARG cc_start: 0.9080 (mtp180) cc_final: 0.8725 (ttt-90) REVERT: B 27 GLN cc_start: 0.8957 (pt0) cc_final: 0.8606 (pp30) REVERT: B 63 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8902 (tm-30) REVERT: B 74 GLU cc_start: 0.9452 (tt0) cc_final: 0.8939 (pt0) REVERT: B 79 LYS cc_start: 0.9453 (mttp) cc_final: 0.9039 (mtmt) REVERT: B 98 TYR cc_start: 0.8529 (m-80) cc_final: 0.7477 (m-80) REVERT: C 38 ASN cc_start: 0.8894 (m-40) cc_final: 0.8259 (p0) REVERT: C 71 ARG cc_start: 0.9144 (tmm160) cc_final: 0.8942 (ttp80) REVERT: C 84 GLN cc_start: 0.9292 (tp40) cc_final: 0.8652 (mt0) REVERT: C 89 ASN cc_start: 0.8613 (m-40) cc_final: 0.8134 (m-40) REVERT: C 95 LYS cc_start: 0.9527 (tttm) cc_final: 0.9035 (mttm) REVERT: C 104 GLN cc_start: 0.8377 (tp-100) cc_final: 0.7790 (tp-100) REVERT: C 107 VAL cc_start: 0.8584 (t) cc_final: 0.8339 (t) REVERT: D 39 TYR cc_start: 0.8870 (t80) cc_final: 0.8527 (t80) REVERT: D 43 LYS cc_start: 0.9075 (tttt) cc_final: 0.8687 (tppt) REVERT: D 65 ASP cc_start: 0.9495 (t0) cc_final: 0.9084 (t0) REVERT: D 68 GLU cc_start: 0.9013 (tt0) cc_final: 0.8305 (tm-30) REVERT: D 69 ARG cc_start: 0.8966 (ptp-170) cc_final: 0.8496 (ptm160) REVERT: D 82 LYS cc_start: 0.9339 (mppt) cc_final: 0.9105 (mmtm) REVERT: D 90 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8148 (tp30) REVERT: D 110 GLU cc_start: 0.9073 (tt0) cc_final: 0.8460 (tm-30) REVERT: E 50 GLU cc_start: 0.9144 (tt0) cc_final: 0.8843 (tt0) REVERT: E 55 GLN cc_start: 0.9396 (mt0) cc_final: 0.9155 (mt0) REVERT: E 87 GLN cc_start: 0.8847 (mt0) cc_final: 0.7659 (mt0) REVERT: E 89 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8371 (pm20) REVERT: E 108 ASP cc_start: 0.9202 (m-30) cc_final: 0.8505 (m-30) REVERT: E 110 TYR cc_start: 0.8629 (t80) cc_final: 0.8235 (t80) REVERT: E 115 HIS cc_start: 0.8325 (t-90) cc_final: 0.7909 (t70) REVERT: E 124 LYS cc_start: 0.9151 (mppt) cc_final: 0.8854 (tmmt) REVERT: E 125 ASP cc_start: 0.8792 (m-30) cc_final: 0.8239 (m-30) REVERT: F 29 ILE cc_start: 0.9427 (mm) cc_final: 0.9196 (pt) REVERT: F 63 GLU cc_start: 0.9180 (tp30) cc_final: 0.8606 (tp30) REVERT: F 64 ASN cc_start: 0.9165 (t0) cc_final: 0.8384 (m-40) REVERT: F 67 ARG cc_start: 0.9353 (ttm170) cc_final: 0.9092 (ttp80) REVERT: F 68 ASP cc_start: 0.9118 (m-30) cc_final: 0.7736 (m-30) REVERT: F 70 VAL cc_start: 0.8779 (p) cc_final: 0.8089 (p) REVERT: F 71 THR cc_start: 0.8655 (p) cc_final: 0.8093 (p) REVERT: F 81 VAL cc_start: 0.9528 (t) cc_final: 0.8854 (t) REVERT: F 88 TYR cc_start: 0.8699 (m-80) cc_final: 0.8094 (m-10) REVERT: F 95 ARG cc_start: 0.8363 (mpp80) cc_final: 0.8095 (mtt-85) REVERT: G 36 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8779 (mmmt) REVERT: G 56 GLU cc_start: 0.9502 (tm-30) cc_final: 0.9222 (tm-30) REVERT: G 73 ASN cc_start: 0.9160 (m110) cc_final: 0.8926 (m110) REVERT: G 87 ILE cc_start: 0.8888 (mm) cc_final: 0.8378 (pt) REVERT: G 92 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8510 (mt-10) REVERT: G 94 ASN cc_start: 0.9395 (t0) cc_final: 0.8962 (m-40) REVERT: H 59 MET cc_start: 0.8831 (tpp) cc_final: 0.8546 (tpp) REVERT: H 62 MET cc_start: 0.9393 (mmm) cc_final: 0.9038 (mmm) REVERT: H 79 ARG cc_start: 0.9183 (ptp90) cc_final: 0.8762 (ptp-110) REVERT: H 116 LYS cc_start: 0.9398 (ptmt) cc_final: 0.9165 (pttm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1346 time to fit residues: 41.8335 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 : 0.384 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 chunk 75 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 74 optimal weight: 40.0000 chunk 82 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 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 = 0.3229 r_free = 0.3229 target = 0.050673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037918 restraints weight = 89672.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.039053 restraints weight = 48516.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039933 restraints weight = 32206.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040510 restraints weight = 24080.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040889 restraints weight = 19723.292| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12761 Z= 0.210 Angle : 0.729 10.015 18476 Z= 0.414 Chirality : 0.045 0.251 2091 Planarity : 0.005 0.077 1328 Dihedral : 31.456 171.841 4002 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % 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: 0.58 (0.30), residues: 738 helix: 1.18 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 133 TYR 0.025 0.003 TYR E 110 PHE 0.019 0.002 PHE A 67 TRP 0.008 0.001 TRP A 47 HIS 0.004 0.001 HIS A 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.21 (12761) covalent geometry : angle 0.72870 / 0.41 (18476) hydrogen bonds : bond 0.07699 / 5.06 ( 732) hydrogen bonds : angle 3.52502 / 2.54 ( 1787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.94 seconds wall clock time: 33 minutes 1.26 seconds (1981.26 seconds total)