Starting phenix.real_space_refine on Tue Jul 29 18:20:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6see_10153/07_2025/6see_10153.cif Found real_map, /net/cci-nas-00/data/ceres_data/6see_10153/07_2025/6see_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6see_10153/07_2025/6see_10153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6see_10153/07_2025/6see_10153.map" model { file = "/net/cci-nas-00/data/ceres_data/6see_10153/07_2025/6see_10153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6see_10153/07_2025/6see_10153.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.18, per 1000 atoms: 0.60 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: 3.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 6.31 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: 4.77 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2239 1.33 - 1.45: 4367 1.45 - 1.57: 5561 1.57 - 1.69: 576 1.69 - 1.81: 18 Bond restraints: 12761 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.71e+00 bond pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.25e+00 ... (remaining 12756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 18145 2.69 - 5.38: 304 5.38 - 8.07: 24 8.07 - 10.75: 1 10.75 - 13.44: 2 Bond angle restraints: 18476 Sorted by residual: angle pdb=" CA LEU G 116 " pdb=" CB LEU G 116 " pdb=" CG LEU G 116 " ideal model delta sigma weight residual 116.30 129.74 -13.44 3.50e+00 8.16e-02 1.48e+01 angle pdb=" C3' DG I -30 " pdb=" O3' DG I -30 " pdb=" P DC I -29 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sigma weight residual 120.20 125.45 -5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " pdb=" P DT J 22 " ideal model delta sigma weight residual 120.20 125.41 -5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " pdb=" P DT I -28 " ideal model delta sigma weight residual 120.20 125.36 -5.16 1.50e+00 4.44e-01 1.18e+01 ... (remaining 18471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 5514 35.82 - 71.64: 1344 71.64 - 107.46: 15 107.46 - 143.29: 6 143.29 - 179.11: 2 Dihedral angle restraints: 6881 sinusoidal: 4708 harmonic: 2173 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 39.11 -179.11 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.64 144.36 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 93.35 126.65 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 6878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1652 0.065 - 0.130: 389 0.130 - 0.195: 43 0.195 - 0.260: 6 0.260 - 0.325: 1 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CB ILE V 523 " pdb=" CA ILE V 523 " pdb=" CG1 ILE V 523 " pdb=" CG2 ILE V 523 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' DT I 68 " pdb=" O4' DT I 68 " pdb=" C2' DT I 68 " pdb=" N1 DT I 68 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2088 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.052 2.00e-02 2.50e+03 2.39e-02 1.72e+01 pdb=" N9 DG I 26 " 0.061 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.016 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.040 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" N9 DG I 28 " 0.043 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.018 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 95 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C VAL D 95 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL D 95 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG D 96 " 0.017 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2368 2.78 - 3.31: 10294 3.31 - 3.84: 24661 3.84 - 4.37: 27163 4.37 - 4.90: 38345 Nonbonded interactions: 102831 Sorted by model distance: nonbonded pdb=" N2 DG I -58 " pdb=" O2 DC J 58 " model vdw 2.252 2.496 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.258 3.040 nonbonded pdb=" O2 DC I -4 " pdb=" N2 DG J 4 " model vdw 2.271 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.274 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.279 2.496 ... (remaining 102826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 110) } ncs_group { reference = (chain 'D' and resid 32 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.170 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 12761 Z= 0.345 Angle : 0.935 13.444 18476 Z= 0.540 Chirality : 0.055 0.325 2091 Planarity : 0.006 0.035 1328 Dihedral : 27.452 179.107 5481 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.003 TRP V 531 HIS 0.010 0.002 HIS H 49 PHE 0.020 0.003 PHE E 84 TYR 0.018 0.003 TYR F 72 ARG 0.006 0.001 ARG G 11 Details of bonding type rmsd hydrogen bonds : bond 0.12847 ( 732) hydrogen bonds : angle 4.13660 ( 1787) covalent geometry : bond 0.00764 (12761) covalent geometry : angle 0.93549 (18476) *********************** 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 : 1.088 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: 0.9342 (mmtm) cc_final: 0.8984 (pttp) REVERT: A 67 PHE cc_start: 0.9233 (t80) cc_final: 0.9029 (t80) REVERT: A 83 ASP cc_start: 0.6939 (t70) cc_final: 0.6475 (t0) REVERT: A 86 TRP cc_start: 0.8802 (m100) cc_final: 0.8502 (m-10) REVERT: A 95 GLN cc_start: 0.9341 (tt0) cc_final: 0.8566 (tt0) REVERT: A 96 GLU cc_start: 0.8607 (tp30) cc_final: 0.8368 (tp30) REVERT: A 99 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 104 HIS cc_start: 0.8917 (m-70) cc_final: 0.8611 (t-170) REVERT: A 107 GLU cc_start: 0.8469 (pp20) cc_final: 0.8136 (pp20) REVERT: A 111 LEU cc_start: 0.9375 (mm) cc_final: 0.9020 (mm) REVERT: A 130 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8450 (ttt-90) REVERT: B 31 LYS cc_start: 0.9316 (mttp) cc_final: 0.9116 (ttpt) REVERT: B 63 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8684 (tm-30) REVERT: B 79 LYS cc_start: 0.9403 (mttp) cc_final: 0.9029 (mtmt) REVERT: C 38 ASN cc_start: 0.8818 (m-40) cc_final: 0.7530 (p0) REVERT: C 73 ASN cc_start: 0.9059 (t0) cc_final: 0.8587 (t0) REVERT: C 82 HIS cc_start: 0.8710 (m170) cc_final: 0.8425 (m-70) REVERT: C 95 LYS cc_start: 0.9487 (tttm) cc_final: 0.9124 (mttm) REVERT: D 39 TYR cc_start: 0.8793 (t80) cc_final: 0.8183 (t80) REVERT: D 43 LYS cc_start: 0.9079 (tttt) cc_final: 0.8683 (tppt) REVERT: D 56 MET cc_start: 0.9129 (tpp) cc_final: 0.8923 (tpp) REVERT: D 65 ASP cc_start: 0.9180 (t0) cc_final: 0.8913 (t0) REVERT: D 68 GLU cc_start: 0.9034 (tt0) cc_final: 0.8169 (tm-30) REVERT: D 69 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8131 (mtm180) REVERT: E 55 GLN cc_start: 0.9177 (mt0) cc_final: 0.8526 (mm-40) REVERT: E 87 GLN cc_start: 0.8693 (mt0) cc_final: 0.7995 (mt0) REVERT: E 89 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8374 (pm20) REVERT: E 95 GLN cc_start: 0.9160 (tt0) cc_final: 0.8931 (tt0) REVERT: E 104 HIS cc_start: 0.9414 (m-70) cc_final: 0.9120 (m90) REVERT: E 127 GLN cc_start: 0.9386 (tp-100) cc_final: 0.8844 (tm-30) REVERT: F 35 ARG cc_start: 0.8873 (ttp-110) cc_final: 0.8473 (ttp-110) REVERT: F 39 ARG cc_start: 0.8440 (mmt90) cc_final: 0.7739 (mmt180) REVERT: F 64 ASN cc_start: 0.9248 (t0) cc_final: 0.8331 (m-40) REVERT: F 67 ARG cc_start: 0.9361 (ttm170) cc_final: 0.9121 (tmm-80) REVERT: F 68 ASP cc_start: 0.8965 (m-30) cc_final: 0.7263 (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: 0.8116 (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: 0.8529 (m-80) REVERT: F 90 LEU cc_start: 0.9782 (mt) cc_final: 0.9579 (mp) REVERT: F 97 LEU cc_start: 0.9178 (mm) cc_final: 0.8969 (mm) REVERT: G 25 PHE cc_start: 0.8319 (m-80) cc_final: 0.7978 (m-80) REVERT: G 36 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8667 (mmmt) REVERT: G 56 GLU cc_start: 0.9539 (tm-30) cc_final: 0.9254 (tm-30) 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: 0.8330 (m110) REVERT: G 94 ASN cc_start: 0.9313 (t0) cc_final: 0.9069 (m-40) REVERT: H 68 ASP cc_start: 0.8998 (t70) cc_final: 0.8785 (t0) REVERT: H 71 GLU cc_start: 0.8888 (tp30) cc_final: 0.8622 (tm-30) REVERT: H 106 LEU cc_start: 0.9371 (mt) cc_final: 0.8884 (mt) REVERT: H 120 LYS cc_start: 0.9518 (tttt) cc_final: 0.9124 (tttm) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.4243 time to fit residues: 167.2238 Evaluate side-chains 211 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 59 HIS B 64 ASN B 93 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN G 31 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.051277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.038288 restraints weight = 86329.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.039438 restraints weight = 47427.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040305 restraints weight = 31592.662| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12761 Z= 0.246 Angle : 0.678 9.843 18476 Z= 0.392 Chirality : 0.037 0.178 2091 Planarity : 0.004 0.031 1328 Dihedral : 31.140 176.342 4002 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.16 % Allowed : 4.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.29), residues: 738 helix: 0.83 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.91 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.008 0.001 HIS B 75 PHE 0.013 0.002 PHE B 100 TYR 0.019 0.002 TYR E 110 ARG 0.009 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.07342 ( 732) hydrogen bonds : angle 3.38473 ( 1787) covalent geometry : bond 0.00533 (12761) covalent geometry : angle 0.67844 (18476) *********************** 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 269 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.082 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: 0.9341 (mmtm) cc_final: 0.9010 (pttm) REVERT: A 64 LYS cc_start: 0.9140 (mppt) cc_final: 0.8901 (mmtm) REVERT: A 67 PHE cc_start: 0.9367 (t80) cc_final: 0.9127 (t80) REVERT: A 83 ASP cc_start: 0.6975 (t70) cc_final: 0.6651 (t0) REVERT: A 86 TRP cc_start: 0.9072 (m100) cc_final: 0.8715 (m100) REVERT: A 104 HIS cc_start: 0.8911 (m-70) cc_final: 0.8584 (t-170) REVERT: A 107 GLU cc_start: 0.8579 (pp20) cc_final: 0.8182 (pp20) REVERT: A 110 TYR cc_start: 0.8597 (t80) cc_final: 0.8206 (t80) REVERT: A 130 ARG cc_start: 0.9009 (mtp180) cc_final: 0.8534 (ttt-90) REVERT: B 27 GLN cc_start: 0.8789 (pt0) cc_final: 0.8425 (pp30) REVERT: B 31 LYS cc_start: 0.9400 (mttp) cc_final: 0.9191 (ttpt) REVERT: B 63 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8808 (tm-30) REVERT: B 79 LYS cc_start: 0.9341 (mttp) cc_final: 0.8880 (mtmt) REVERT: B 98 TYR cc_start: 0.8417 (m-10) cc_final: 0.8128 (m-80) REVERT: C 81 ARG cc_start: 0.8767 (tpp80) cc_final: 0.8237 (tpp80) REVERT: C 95 LYS cc_start: 0.9485 (tttm) cc_final: 0.9088 (mttm) REVERT: D 39 TYR cc_start: 0.8903 (t80) cc_final: 0.8460 (t80) REVERT: D 43 LYS cc_start: 0.9085 (tttt) cc_final: 0.8687 (tppt) REVERT: D 65 ASP cc_start: 0.9403 (t0) cc_final: 0.9090 (t0) REVERT: D 68 GLU cc_start: 0.9139 (tt0) cc_final: 0.8394 (tm-30) REVERT: D 69 ARG cc_start: 0.8714 (mtp180) cc_final: 0.8391 (ptm160) REVERT: D 77 LEU cc_start: 0.9622 (tt) cc_final: 0.9298 (tt) REVERT: D 110 GLU cc_start: 0.8918 (tt0) cc_final: 0.8418 (tt0) REVERT: E 55 GLN cc_start: 0.9331 (mt0) cc_final: 0.9099 (mt0) REVERT: E 87 GLN cc_start: 0.8770 (mt0) cc_final: 0.8440 (mt0) REVERT: E 95 GLN cc_start: 0.9260 (tt0) cc_final: 0.8973 (tt0) REVERT: E 104 HIS cc_start: 0.9397 (m-70) cc_final: 0.9123 (m90) REVERT: E 108 ASP cc_start: 0.8978 (m-30) cc_final: 0.8775 (m-30) REVERT: E 127 GLN cc_start: 0.9480 (tp40) cc_final: 0.9171 (tm-30) REVERT: E 133 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7856 (ttm-80) REVERT: F 35 ARG cc_start: 0.8932 (ttp-110) cc_final: 0.8359 (ttp-110) REVERT: F 39 ARG cc_start: 0.8559 (mmt90) cc_final: 0.7698 (mmt180) REVERT: F 44 LYS cc_start: 0.8631 (tptp) cc_final: 0.8000 (tptt) REVERT: F 63 GLU cc_start: 0.9105 (tp30) cc_final: 0.8886 (tp30) REVERT: F 64 ASN cc_start: 0.9059 (t0) cc_final: 0.7965 (m-40) REVERT: F 67 ARG cc_start: 0.9370 (ttm170) cc_final: 0.9137 (tmm-80) REVERT: F 68 ASP cc_start: 0.8922 (m-30) cc_final: 0.8104 (m-30) REVERT: F 70 VAL cc_start: 0.8737 (p) cc_final: 0.8095 (p) REVERT: F 71 THR cc_start: 0.8676 (p) cc_final: 0.8151 (p) REVERT: F 74 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8689 (mt-10) REVERT: F 81 VAL cc_start: 0.9466 (t) cc_final: 0.9083 (t) REVERT: G 25 PHE cc_start: 0.8662 (m-80) cc_final: 0.8182 (m-80) REVERT: G 36 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8756 (mmmt) REVERT: G 56 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9330 (tm-30) REVERT: G 73 ASN cc_start: 0.9161 (m110) cc_final: 0.8956 (m110) REVERT: G 89 ASN cc_start: 0.8517 (m-40) cc_final: 0.8260 (m110) REVERT: G 94 ASN cc_start: 0.9364 (t0) cc_final: 0.9034 (m110) REVERT: H 43 LYS cc_start: 0.9604 (mtpp) cc_final: 0.9396 (pttp) REVERT: H 47 GLN cc_start: 0.9279 (tm-30) cc_final: 0.9072 (tm-30) REVERT: H 62 MET cc_start: 0.9364 (mmm) cc_final: 0.9034 (mmm) REVERT: H 116 LYS cc_start: 0.9403 (ptmt) cc_final: 0.9159 (pttm) REVERT: H 120 LYS cc_start: 0.9547 (tttt) cc_final: 0.9232 (tttm) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.4385 time to fit residues: 156.7280 Evaluate side-chains 210 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 95 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.050048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.037133 restraints weight = 88884.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.038221 restraints weight = 49103.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039043 restraints weight = 33101.332| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12761 Z= 0.269 Angle : 0.675 9.928 18476 Z= 0.392 Chirality : 0.038 0.163 2091 Planarity : 0.004 0.050 1328 Dihedral : 31.177 175.873 4002 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.30), residues: 738 helix: 1.19 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.85 (0.35), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 531 HIS 0.005 0.002 HIS F 75 PHE 0.016 0.002 PHE B 100 TYR 0.024 0.002 TYR H 83 ARG 0.008 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.07508 ( 732) hydrogen bonds : angle 3.44775 ( 1787) covalent geometry : bond 0.00581 (12761) covalent geometry : angle 0.67548 (18476) *********************** 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 248 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 2.213 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: 0.9344 (mmtm) cc_final: 0.9039 (pttp) REVERT: A 64 LYS cc_start: 0.9353 (mppt) cc_final: 0.9063 (mmtm) REVERT: A 83 ASP cc_start: 0.7299 (t70) cc_final: 0.6926 (t0) REVERT: A 86 TRP cc_start: 0.9038 (m100) cc_final: 0.8746 (m100) REVERT: A 104 HIS cc_start: 0.8842 (m-70) cc_final: 0.8557 (t-170) REVERT: A 107 GLU cc_start: 0.8525 (pp20) cc_final: 0.8206 (pp20) REVERT: A 111 LEU cc_start: 0.9248 (mm) cc_final: 0.8916 (mm) REVERT: A 130 ARG cc_start: 0.9166 (mtp180) cc_final: 0.8733 (ttt-90) REVERT: B 27 GLN cc_start: 0.8773 (pt0) cc_final: 0.8152 (pm20) REVERT: B 44 LYS cc_start: 0.9234 (tttt) cc_final: 0.8742 (tptt) REVERT: B 63 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8886 (tm-30) REVERT: B 74 GLU cc_start: 0.9383 (tt0) cc_final: 0.8956 (pt0) REVERT: B 79 LYS cc_start: 0.9332 (mttp) cc_final: 0.8822 (mtmt) REVERT: B 98 TYR cc_start: 0.8449 (m-10) cc_final: 0.8180 (m-80) REVERT: C 32 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8254 (ttp-110) REVERT: C 81 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8093 (tpp80) REVERT: C 84 GLN cc_start: 0.9364 (tp40) cc_final: 0.9002 (tp40) REVERT: C 89 ASN cc_start: 0.8477 (m110) cc_final: 0.8109 (m110) REVERT: C 95 LYS cc_start: 0.9584 (tttm) cc_final: 0.9087 (mttm) REVERT: D 39 TYR cc_start: 0.8893 (t80) cc_final: 0.8507 (t80) REVERT: D 43 LYS cc_start: 0.9101 (tttt) cc_final: 0.8706 (tppt) REVERT: D 65 ASP cc_start: 0.9373 (t0) cc_final: 0.9101 (t0) REVERT: D 68 GLU cc_start: 0.9089 (tt0) cc_final: 0.8444 (tm-30) REVERT: D 77 LEU cc_start: 0.9538 (tt) cc_final: 0.9277 (tt) REVERT: E 62 ILE cc_start: 0.9385 (mm) cc_final: 0.9178 (mm) REVERT: E 87 GLN cc_start: 0.8625 (mt0) cc_final: 0.7932 (mt0) REVERT: E 104 HIS cc_start: 0.9359 (m-70) cc_final: 0.9113 (m90) REVERT: E 115 HIS cc_start: 0.8278 (t-90) cc_final: 0.7987 (t70) REVERT: F 46 ILE cc_start: 0.9480 (mp) cc_final: 0.9211 (pt) REVERT: F 64 ASN cc_start: 0.9104 (t0) cc_final: 0.7973 (m-40) REVERT: F 67 ARG cc_start: 0.9362 (ttm170) cc_final: 0.9136 (tmm-80) REVERT: F 68 ASP cc_start: 0.9112 (m-30) cc_final: 0.8431 (m-30) REVERT: F 70 VAL cc_start: 0.8807 (p) cc_final: 0.8242 (p) REVERT: F 71 THR cc_start: 0.8666 (p) cc_final: 0.8190 (p) REVERT: F 81 VAL cc_start: 0.9529 (t) cc_final: 0.8912 (t) REVERT: F 95 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7974 (mtt180) REVERT: G 36 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8820 (mmmt) REVERT: G 56 GLU cc_start: 0.9584 (tm-30) cc_final: 0.9205 (tm-30) REVERT: G 59 THR cc_start: 0.9433 (t) cc_final: 0.9205 (t) REVERT: G 89 ASN cc_start: 0.8507 (m-40) cc_final: 0.8228 (m110) REVERT: G 92 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8519 (mt-10) REVERT: G 94 ASN cc_start: 0.9427 (t0) cc_final: 0.9092 (m-40) REVERT: H 43 LYS cc_start: 0.9554 (mtpp) cc_final: 0.9337 (ttpp) REVERT: H 62 MET cc_start: 0.9431 (mmm) cc_final: 0.9097 (mmm) REVERT: H 116 LYS cc_start: 0.9395 (ptmt) cc_final: 0.9129 (pttm) REVERT: H 120 LYS cc_start: 0.9591 (tttt) cc_final: 0.9268 (tttm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.5171 time to fit residues: 169.5434 Evaluate side-chains 198 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 84 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 = 0.050384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.037608 restraints weight = 87440.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038760 restraints weight = 47827.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.039649 restraints weight = 31622.578| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12761 Z= 0.231 Angle : 0.644 9.923 18476 Z= 0.376 Chirality : 0.036 0.156 2091 Planarity : 0.004 0.046 1328 Dihedral : 31.151 173.910 4002 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.30), residues: 738 helix: 1.33 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.60 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 531 HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE H 70 TYR 0.033 0.002 TYR H 83 ARG 0.007 0.001 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.06857 ( 732) hydrogen bonds : angle 3.32178 ( 1787) covalent geometry : bond 0.00499 (12761) covalent geometry : angle 0.64426 (18476) *********************** 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 245 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9041 (pttp) REVERT: A 64 LYS cc_start: 0.9412 (mppt) cc_final: 0.9082 (mmtm) REVERT: A 73 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8935 (tm-30) REVERT: A 74 ILE cc_start: 0.9513 (pt) cc_final: 0.9232 (pt) REVERT: A 83 ASP cc_start: 0.7249 (t70) cc_final: 0.6899 (t0) REVERT: A 86 TRP cc_start: 0.9042 (m100) cc_final: 0.8761 (m100) REVERT: A 95 GLN cc_start: 0.9276 (tt0) cc_final: 0.8904 (tt0) REVERT: A 99 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8130 (mt-10) REVERT: A 104 HIS cc_start: 0.8861 (m-70) cc_final: 0.8509 (t-90) REVERT: A 107 GLU cc_start: 0.8488 (pp20) cc_final: 0.8134 (pp20) REVERT: A 130 ARG cc_start: 0.9188 (mtp180) cc_final: 0.8863 (mmm160) REVERT: B 27 GLN cc_start: 0.8767 (pt0) cc_final: 0.8042 (pm20) REVERT: B 44 LYS cc_start: 0.9263 (tttt) cc_final: 0.8929 (tptm) REVERT: B 63 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8835 (tm-30) REVERT: B 72 TYR cc_start: 0.9214 (m-80) cc_final: 0.8946 (m-10) REVERT: B 74 GLU cc_start: 0.9399 (tt0) cc_final: 0.8952 (pt0) REVERT: B 79 LYS cc_start: 0.9356 (mttp) cc_final: 0.8837 (mtmt) REVERT: B 98 TYR cc_start: 0.8487 (m-10) cc_final: 0.8153 (m-80) REVERT: C 32 ARG cc_start: 0.8716 (ttp-110) cc_final: 0.8396 (ttp80) REVERT: C 84 GLN cc_start: 0.9340 (tp40) cc_final: 0.8922 (tp40) REVERT: C 95 LYS cc_start: 0.9565 (tttm) cc_final: 0.9063 (mttm) REVERT: C 102 ILE cc_start: 0.9364 (mp) cc_final: 0.8977 (mp) REVERT: C 104 GLN cc_start: 0.8489 (tp-100) cc_final: 0.7590 (tp-100) REVERT: D 39 TYR cc_start: 0.8874 (t80) cc_final: 0.8503 (t80) REVERT: D 43 LYS cc_start: 0.9109 (tttt) cc_final: 0.8678 (tppt) REVERT: D 65 ASP cc_start: 0.9424 (t0) cc_final: 0.9103 (t0) REVERT: D 68 GLU cc_start: 0.9080 (tt0) cc_final: 0.8363 (tm-30) REVERT: D 105 LYS cc_start: 0.9446 (mppt) cc_final: 0.9245 (mtmm) REVERT: E 87 GLN cc_start: 0.8615 (mt0) cc_final: 0.8217 (mt0) REVERT: E 104 HIS cc_start: 0.9430 (m-70) cc_final: 0.9209 (m90) REVERT: E 108 ASP cc_start: 0.9222 (m-30) cc_final: 0.8808 (m-30) REVERT: E 115 HIS cc_start: 0.8381 (t-90) cc_final: 0.8060 (t70) REVERT: E 127 GLN cc_start: 0.9408 (tm-30) cc_final: 0.9130 (tm-30) REVERT: F 44 LYS cc_start: 0.8424 (tptp) cc_final: 0.8208 (tptt) REVERT: F 58 LEU cc_start: 0.9416 (tp) cc_final: 0.9169 (pp) REVERT: F 68 ASP cc_start: 0.9267 (m-30) cc_final: 0.8886 (m-30) REVERT: F 70 VAL cc_start: 0.8820 (p) cc_final: 0.8129 (p) REVERT: F 71 THR cc_start: 0.8712 (p) cc_final: 0.8174 (p) REVERT: F 81 VAL cc_start: 0.9510 (t) cc_final: 0.9053 (t) REVERT: F 100 PHE cc_start: 0.8401 (m-80) cc_final: 0.8060 (m-80) REVERT: G 25 PHE cc_start: 0.8551 (m-80) cc_final: 0.8117 (m-80) REVERT: G 36 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8798 (mmmt) REVERT: G 56 GLU cc_start: 0.9537 (tm-30) cc_final: 0.9199 (tm-30) REVERT: G 68 ASN cc_start: 0.9103 (m-40) cc_final: 0.8900 (m-40) REVERT: G 89 ASN cc_start: 0.8504 (m-40) cc_final: 0.8258 (m110) REVERT: G 94 ASN cc_start: 0.9421 (t0) cc_final: 0.9085 (m-40) REVERT: H 62 MET cc_start: 0.9404 (mmm) cc_final: 0.9071 (mmm) REVERT: H 73 ILE cc_start: 0.9066 (pt) cc_final: 0.8748 (pt) REVERT: H 83 TYR cc_start: 0.8853 (m-80) cc_final: 0.8576 (m-10) REVERT: H 120 LYS cc_start: 0.9568 (tttt) cc_final: 0.9210 (tttp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5699 time to fit residues: 190.8008 Evaluate side-chains 202 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.051844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.038834 restraints weight = 86470.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.040007 restraints weight = 46810.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040924 restraints weight = 31027.216| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12761 Z= 0.175 Angle : 0.618 10.141 18476 Z= 0.358 Chirality : 0.035 0.160 2091 Planarity : 0.003 0.030 1328 Dihedral : 30.990 171.805 4002 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 738 helix: 1.46 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 531 HIS 0.005 0.001 HIS D 106 PHE 0.015 0.001 PHE B 100 TYR 0.025 0.002 TYR H 83 ARG 0.006 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.06182 ( 732) hydrogen bonds : angle 3.15914 ( 1787) covalent geometry : bond 0.00376 (12761) covalent geometry : angle 0.61814 (18476) *********************** 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 248 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.458 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: 0.9336 (mmtm) cc_final: 0.8969 (pttp) REVERT: A 50 GLU cc_start: 0.9293 (mp0) cc_final: 0.8992 (mp0) REVERT: A 64 LYS cc_start: 0.9387 (mppt) cc_final: 0.9025 (mmtm) REVERT: A 73 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8975 (tm-30) REVERT: A 83 ASP cc_start: 0.7027 (t70) cc_final: 0.6687 (t0) REVERT: A 86 TRP cc_start: 0.8983 (m100) cc_final: 0.8639 (m100) REVERT: A 95 GLN cc_start: 0.9265 (tt0) cc_final: 0.8956 (tt0) REVERT: A 99 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 104 HIS cc_start: 0.8562 (m-70) cc_final: 0.8336 (t-170) REVERT: A 107 GLU cc_start: 0.8501 (pp20) cc_final: 0.8153 (pp20) REVERT: A 111 LEU cc_start: 0.9130 (mm) cc_final: 0.8848 (mm) REVERT: A 130 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8657 (mmm160) REVERT: B 27 GLN cc_start: 0.8863 (pt0) cc_final: 0.8141 (pm20) REVERT: B 63 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8847 (tm-30) REVERT: B 74 GLU cc_start: 0.9358 (tt0) cc_final: 0.8884 (pt0) REVERT: B 79 LYS cc_start: 0.9367 (mttp) cc_final: 0.8872 (mtmt) REVERT: C 71 ARG cc_start: 0.9146 (tmm160) cc_final: 0.8942 (ttp80) REVERT: C 84 GLN cc_start: 0.9315 (tp40) cc_final: 0.8755 (mt0) REVERT: C 89 ASN cc_start: 0.8395 (m110) cc_final: 0.7950 (m110) REVERT: C 95 LYS cc_start: 0.9596 (tttm) cc_final: 0.9045 (mttm) REVERT: C 104 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7768 (tp-100) REVERT: C 107 VAL cc_start: 0.8691 (t) cc_final: 0.8427 (t) REVERT: D 39 TYR cc_start: 0.8860 (t80) cc_final: 0.8514 (t80) REVERT: D 43 LYS cc_start: 0.9098 (tttt) cc_final: 0.8701 (tppt) REVERT: D 65 ASP cc_start: 0.9444 (t0) cc_final: 0.9076 (t0) REVERT: D 68 GLU cc_start: 0.9047 (tt0) cc_final: 0.8303 (tm-30) REVERT: D 69 ARG cc_start: 0.9058 (ptp-170) cc_final: 0.8533 (ptm160) REVERT: D 110 GLU cc_start: 0.9016 (tt0) cc_final: 0.8454 (tm-30) REVERT: E 84 PHE cc_start: 0.8725 (m-10) cc_final: 0.8448 (m-10) REVERT: E 87 GLN cc_start: 0.8661 (mt0) cc_final: 0.7939 (mt0) REVERT: E 104 HIS cc_start: 0.9372 (m-70) cc_final: 0.9153 (m90) REVERT: E 108 ASP cc_start: 0.9007 (m-30) cc_final: 0.8791 (m-30) REVERT: E 110 TYR cc_start: 0.8626 (t80) cc_final: 0.8188 (t80) REVERT: E 115 HIS cc_start: 0.8248 (t-90) cc_final: 0.7914 (t70) REVERT: E 124 LYS cc_start: 0.9115 (mppt) cc_final: 0.8829 (tmmt) REVERT: E 125 ASP cc_start: 0.9047 (m-30) cc_final: 0.8764 (m-30) REVERT: E 127 GLN cc_start: 0.9539 (tm-30) cc_final: 0.9223 (tm-30) REVERT: E 137 GLU cc_start: 0.5026 (mp0) cc_final: 0.4790 (mp0) REVERT: F 44 LYS cc_start: 0.8831 (tptp) cc_final: 0.8224 (tptt) REVERT: F 58 LEU cc_start: 0.9356 (tp) cc_final: 0.9124 (pp) REVERT: F 63 GLU cc_start: 0.9143 (tp30) cc_final: 0.8625 (tp30) REVERT: F 64 ASN cc_start: 0.9229 (m-40) cc_final: 0.8587 (m-40) REVERT: F 67 ARG cc_start: 0.9306 (ttm170) cc_final: 0.9093 (ttp80) REVERT: F 68 ASP cc_start: 0.8935 (m-30) cc_final: 0.7623 (m-30) REVERT: F 70 VAL cc_start: 0.8806 (p) cc_final: 0.8077 (p) REVERT: F 71 THR cc_start: 0.8654 (p) cc_final: 0.8052 (p) REVERT: F 81 VAL cc_start: 0.9495 (t) cc_final: 0.8843 (t) REVERT: F 100 PHE cc_start: 0.8409 (m-80) cc_final: 0.8034 (m-80) REVERT: G 36 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8778 (mmmt) REVERT: G 56 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9147 (tm-30) REVERT: G 73 ASN cc_start: 0.9179 (m110) cc_final: 0.8945 (m110) REVERT: G 87 ILE cc_start: 0.9068 (mm) cc_final: 0.8691 (pt) REVERT: G 89 ASN cc_start: 0.8581 (m-40) cc_final: 0.8355 (m110) REVERT: G 94 ASN cc_start: 0.9367 (t0) cc_final: 0.9106 (m-40) REVERT: G 104 GLN cc_start: 0.9289 (mt0) cc_final: 0.9087 (mt0) REVERT: H 62 MET cc_start: 0.9379 (mmm) cc_final: 0.9059 (mmm) REVERT: H 86 ARG cc_start: 0.8692 (mtt-85) cc_final: 0.8445 (mmt-90) REVERT: H 120 LYS cc_start: 0.9519 (tttt) cc_final: 0.9092 (tttm) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.4198 time to fit residues: 139.0575 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 : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 60 optimal weight: 0.0870 chunk 87 optimal weight: 10.0000 overall best weight: 1.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039587 restraints weight = 86264.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040752 restraints weight = 46810.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041667 restraints weight = 31101.946| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3740 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= 0.160 Angle : 0.598 10.156 18476 Z= 0.348 Chirality : 0.034 0.149 2091 Planarity : 0.003 0.033 1328 Dihedral : 30.755 169.395 4002 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.16 % Allowed : 1.60 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 738 helix: 1.49 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 531 HIS 0.003 0.001 HIS B 75 PHE 0.024 0.001 PHE A 67 TYR 0.027 0.002 TYR D 80 ARG 0.003 0.000 ARG F 39 Details of bonding type rmsd hydrogen bonds : bond 0.06004 ( 732) hydrogen bonds : angle 3.00798 ( 1787) covalent geometry : bond 0.00342 (12761) covalent geometry : angle 0.59768 (18476) *********************** 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 253 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9323 (mmtm) cc_final: 0.8963 (pttp) REVERT: A 50 GLU cc_start: 0.9272 (mp0) cc_final: 0.8974 (mp0) REVERT: A 64 LYS cc_start: 0.9385 (mppt) cc_final: 0.9032 (mmtm) REVERT: A 73 GLU cc_start: 0.9264 (tm-30) cc_final: 0.9025 (tm-30) REVERT: A 83 ASP cc_start: 0.6972 (t70) cc_final: 0.6134 (t0) REVERT: A 86 TRP cc_start: 0.8995 (m100) cc_final: 0.8642 (m100) REVERT: A 104 HIS cc_start: 0.8599 (m-70) cc_final: 0.8367 (t-170) REVERT: A 107 GLU cc_start: 0.8542 (pp20) cc_final: 0.8131 (pp20) REVERT: A 130 ARG cc_start: 0.9014 (mtp180) cc_final: 0.8614 (ttt-90) REVERT: B 27 GLN cc_start: 0.8928 (pt0) cc_final: 0.8227 (pm20) REVERT: B 63 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8802 (tm-30) REVERT: B 79 LYS cc_start: 0.9371 (mttp) cc_final: 0.8794 (tttt) REVERT: B 98 TYR cc_start: 0.8285 (m-10) cc_final: 0.7501 (m-80) REVERT: C 71 ARG cc_start: 0.9129 (tmm160) cc_final: 0.8911 (ttp80) REVERT: C 84 GLN cc_start: 0.9308 (tp40) cc_final: 0.8694 (mt0) REVERT: C 89 ASN cc_start: 0.8469 (m-40) cc_final: 0.7982 (m110) REVERT: C 95 LYS cc_start: 0.9589 (tttm) cc_final: 0.9046 (mttm) REVERT: C 104 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7815 (tp-100) REVERT: D 39 TYR cc_start: 0.8836 (t80) cc_final: 0.8424 (t80) REVERT: D 43 LYS cc_start: 0.9061 (tttt) cc_final: 0.8692 (tppt) REVERT: D 65 ASP cc_start: 0.9469 (t0) cc_final: 0.9181 (t0) REVERT: D 68 GLU cc_start: 0.8984 (tt0) cc_final: 0.8370 (tm-30) REVERT: D 69 ARG cc_start: 0.9039 (ptp-170) cc_final: 0.8561 (ptm160) REVERT: E 87 GLN cc_start: 0.8751 (mt0) cc_final: 0.8069 (mt0) REVERT: E 95 GLN cc_start: 0.8915 (tt0) cc_final: 0.8608 (tt0) REVERT: E 104 HIS cc_start: 0.9296 (m-70) cc_final: 0.8777 (m90) REVERT: E 108 ASP cc_start: 0.8954 (m-30) cc_final: 0.8223 (m-30) REVERT: E 115 HIS cc_start: 0.8240 (t-90) cc_final: 0.7911 (t70) REVERT: E 124 LYS cc_start: 0.9184 (mppt) cc_final: 0.8925 (ptmm) REVERT: F 44 LYS cc_start: 0.8742 (tptp) cc_final: 0.8243 (tptt) REVERT: F 58 LEU cc_start: 0.9391 (tp) cc_final: 0.9161 (pp) REVERT: F 64 ASN cc_start: 0.9240 (m-40) cc_final: 0.8633 (m-40) REVERT: F 68 ASP cc_start: 0.8851 (m-30) cc_final: 0.7852 (m-30) REVERT: F 70 VAL cc_start: 0.8810 (p) cc_final: 0.8100 (p) REVERT: F 71 THR cc_start: 0.8597 (p) cc_final: 0.7999 (p) REVERT: F 81 VAL cc_start: 0.9481 (t) cc_final: 0.8796 (t) REVERT: F 100 PHE cc_start: 0.8405 (m-80) cc_final: 0.8008 (m-80) REVERT: G 36 LYS cc_start: 0.9201 (mtpt) cc_final: 0.8774 (mmmt) REVERT: G 56 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9143 (tm-30) REVERT: G 73 ASN cc_start: 0.9138 (m110) cc_final: 0.8881 (m110) REVERT: G 87 ILE cc_start: 0.8917 (mm) cc_final: 0.8586 (pt) REVERT: G 89 ASN cc_start: 0.8507 (m-40) cc_final: 0.8296 (m110) REVERT: G 94 ASN cc_start: 0.9308 (t0) cc_final: 0.9023 (m-40) REVERT: G 102 ILE cc_start: 0.9381 (mt) cc_final: 0.9098 (mt) REVERT: H 59 MET cc_start: 0.8701 (tpp) cc_final: 0.8498 (tpp) REVERT: H 86 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8352 (ttm170) REVERT: H 120 LYS cc_start: 0.9481 (tttt) cc_final: 0.9064 (tttm) outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.3080 time to fit residues: 102.2618 Evaluate side-chains 207 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 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 = 0.3213 r_free = 0.3213 target = 0.050090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037284 restraints weight = 89635.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038364 restraints weight = 49372.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.039212 restraints weight = 33213.110| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 12761 Z= 0.256 Angle : 0.665 9.989 18476 Z= 0.383 Chirality : 0.038 0.171 2091 Planarity : 0.004 0.049 1328 Dihedral : 31.007 167.881 4002 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 738 helix: 1.38 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.57 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS A 59 PHE 0.015 0.002 PHE E 84 TYR 0.029 0.002 TYR F 88 ARG 0.007 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.07273 ( 732) hydrogen bonds : angle 3.30860 ( 1787) covalent geometry : bond 0.00555 (12761) covalent geometry : angle 0.66461 (18476) *********************** 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 236 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.826 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: 0.9298 (mmtm) cc_final: 0.8948 (pttm) REVERT: A 64 LYS cc_start: 0.9512 (mppt) cc_final: 0.9156 (mmtm) REVERT: A 67 PHE cc_start: 0.9436 (t80) cc_final: 0.9225 (t80) REVERT: A 73 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8983 (tm-30) REVERT: A 83 ASP cc_start: 0.7131 (t70) cc_final: 0.6844 (t0) REVERT: A 86 TRP cc_start: 0.8944 (m100) cc_final: 0.8593 (m100) REVERT: A 99 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 104 HIS cc_start: 0.8672 (m-70) cc_final: 0.8365 (t70) REVERT: A 107 GLU cc_start: 0.8508 (pp20) cc_final: 0.8184 (pp20) REVERT: A 130 ARG cc_start: 0.9142 (mtp180) cc_final: 0.8722 (ttt-90) REVERT: B 63 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8934 (tm-30) REVERT: B 74 GLU cc_start: 0.9329 (tt0) cc_final: 0.8832 (pt0) REVERT: B 79 LYS cc_start: 0.9399 (mttp) cc_final: 0.8885 (mtmt) REVERT: B 98 TYR cc_start: 0.8413 (m-10) cc_final: 0.7841 (m-80) REVERT: C 64 GLU cc_start: 0.8943 (tp30) cc_final: 0.8694 (tp30) REVERT: C 84 GLN cc_start: 0.9325 (tp40) cc_final: 0.8797 (mt0) REVERT: C 90 ASP cc_start: 0.7514 (t0) cc_final: 0.7216 (t70) REVERT: C 93 LEU cc_start: 0.9572 (mt) cc_final: 0.9184 (mt) REVERT: C 104 GLN cc_start: 0.8530 (tp-100) cc_final: 0.7842 (tp-100) REVERT: C 107 VAL cc_start: 0.8711 (t) cc_final: 0.8480 (t) REVERT: D 39 TYR cc_start: 0.8857 (t80) cc_final: 0.8470 (t80) REVERT: D 43 LYS cc_start: 0.9100 (tttt) cc_final: 0.8747 (tppt) REVERT: D 65 ASP cc_start: 0.9450 (t0) cc_final: 0.9094 (t0) REVERT: D 68 GLU cc_start: 0.9075 (tt0) cc_final: 0.8549 (tm-30) REVERT: D 69 ARG cc_start: 0.9039 (ptp-170) cc_final: 0.8394 (ptm160) REVERT: E 62 ILE cc_start: 0.9240 (mm) cc_final: 0.9022 (mm) REVERT: E 74 ILE cc_start: 0.9245 (tp) cc_final: 0.8877 (tt) REVERT: E 87 GLN cc_start: 0.8612 (mt0) cc_final: 0.7979 (mt0) REVERT: E 95 GLN cc_start: 0.8977 (tt0) cc_final: 0.8732 (tt0) REVERT: E 104 HIS cc_start: 0.9372 (m-70) cc_final: 0.8802 (m90) REVERT: E 108 ASP cc_start: 0.8646 (m-30) cc_final: 0.8077 (m-30) REVERT: E 115 HIS cc_start: 0.8400 (t-90) cc_final: 0.8089 (t70) REVERT: E 124 LYS cc_start: 0.9107 (mppt) cc_final: 0.8904 (ptmm) REVERT: E 125 ASP cc_start: 0.9021 (m-30) cc_final: 0.8808 (m-30) REVERT: E 127 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9235 (tm-30) REVERT: E 133 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8490 (mtt90) REVERT: F 29 ILE cc_start: 0.9476 (mm) cc_final: 0.9185 (pt) REVERT: F 44 LYS cc_start: 0.8797 (tptp) cc_final: 0.8276 (tptt) REVERT: F 63 GLU cc_start: 0.9167 (tp30) cc_final: 0.8956 (tp30) REVERT: F 64 ASN cc_start: 0.9213 (m-40) cc_final: 0.8939 (m-40) REVERT: F 68 ASP cc_start: 0.9134 (m-30) cc_final: 0.7722 (m-30) REVERT: F 71 THR cc_start: 0.8708 (p) cc_final: 0.8195 (p) REVERT: F 81 VAL cc_start: 0.9393 (t) cc_final: 0.8580 (t) REVERT: F 88 TYR cc_start: 0.8736 (m-80) cc_final: 0.8151 (m-10) REVERT: G 36 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8830 (mmmt) REVERT: G 56 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9234 (tm-30) REVERT: G 87 ILE cc_start: 0.8912 (mm) cc_final: 0.8538 (pt) REVERT: G 89 ASN cc_start: 0.8577 (m-40) cc_final: 0.8330 (m110) REVERT: G 94 ASN cc_start: 0.9409 (t0) cc_final: 0.9122 (m-40) REVERT: H 59 MET cc_start: 0.8685 (tpp) cc_final: 0.8438 (tpp) REVERT: H 62 MET cc_start: 0.9402 (mmm) cc_final: 0.8905 (mmm) REVERT: H 120 LYS cc_start: 0.9517 (tttt) cc_final: 0.9108 (tttp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3023 time to fit residues: 94.1372 Evaluate side-chains 191 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 115 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3181 r_free = 0.3181 target = 0.049151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.036224 restraints weight = 92261.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.037344 restraints weight = 50812.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.038163 restraints weight = 34133.053| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12761 Z= 0.295 Angle : 0.708 9.706 18476 Z= 0.408 Chirality : 0.040 0.156 2091 Planarity : 0.005 0.058 1328 Dihedral : 31.273 167.308 4002 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 17.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.30), residues: 738 helix: 1.11 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.007 0.002 HIS E 104 PHE 0.017 0.002 PHE A 106 TYR 0.020 0.003 TYR F 88 ARG 0.005 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.07972 ( 732) hydrogen bonds : angle 3.63372 ( 1787) covalent geometry : bond 0.00638 (12761) covalent geometry : angle 0.70838 (18476) *********************** 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 224 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.9327 (mmtm) cc_final: 0.9007 (pttp) REVERT: A 64 LYS cc_start: 0.9471 (mppt) cc_final: 0.9237 (mmtm) REVERT: A 67 PHE cc_start: 0.9415 (t80) cc_final: 0.9210 (t80) REVERT: A 73 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8984 (tm-30) REVERT: A 83 ASP cc_start: 0.7155 (t70) cc_final: 0.6806 (t0) REVERT: A 86 TRP cc_start: 0.8980 (m100) cc_final: 0.8655 (m100) REVERT: A 96 GLU cc_start: 0.8773 (tt0) cc_final: 0.8523 (tt0) REVERT: A 99 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 130 ARG cc_start: 0.9286 (mtp180) cc_final: 0.8986 (mmm160) REVERT: B 74 GLU cc_start: 0.9391 (tt0) cc_final: 0.8923 (pt0) REVERT: B 79 LYS cc_start: 0.9402 (mttp) cc_final: 0.8889 (mtmt) REVERT: B 98 TYR cc_start: 0.8606 (m-10) cc_final: 0.7985 (m-80) REVERT: C 90 ASP cc_start: 0.7587 (t0) cc_final: 0.7277 (t70) REVERT: C 93 LEU cc_start: 0.9561 (mt) cc_final: 0.9182 (mt) REVERT: C 104 GLN cc_start: 0.8615 (tp-100) cc_final: 0.7987 (tp-100) REVERT: D 39 TYR cc_start: 0.8902 (t80) cc_final: 0.8502 (t80) REVERT: D 43 LYS cc_start: 0.9104 (tttt) cc_final: 0.8718 (tppt) REVERT: D 65 ASP cc_start: 0.9429 (t0) cc_final: 0.9066 (t0) REVERT: D 68 GLU cc_start: 0.9078 (tt0) cc_final: 0.8554 (tm-30) REVERT: D 69 ARG cc_start: 0.9099 (ptp-170) cc_final: 0.8508 (ptm160) REVERT: D 117 LYS cc_start: 0.9565 (ptmm) cc_final: 0.9346 (ptmm) REVERT: E 62 ILE cc_start: 0.9228 (mm) cc_final: 0.8975 (mm) REVERT: E 74 ILE cc_start: 0.9309 (tp) cc_final: 0.8988 (tt) REVERT: E 87 GLN cc_start: 0.8738 (mt0) cc_final: 0.8327 (mt0) REVERT: E 95 GLN cc_start: 0.9019 (tt0) cc_final: 0.8805 (tt0) REVERT: E 104 HIS cc_start: 0.9437 (m-70) cc_final: 0.8986 (m90) REVERT: E 108 ASP cc_start: 0.9125 (m-30) cc_final: 0.8536 (m-30) REVERT: E 115 HIS cc_start: 0.8393 (t-90) cc_final: 0.8086 (t70) REVERT: E 133 ARG cc_start: 0.8706 (ttt180) cc_final: 0.8504 (ttt180) REVERT: F 29 ILE cc_start: 0.9527 (mm) cc_final: 0.9241 (pt) REVERT: F 44 LYS cc_start: 0.8902 (tptp) cc_final: 0.8235 (tptt) REVERT: F 63 GLU cc_start: 0.9187 (tp30) cc_final: 0.8964 (tp30) REVERT: F 68 ASP cc_start: 0.8941 (m-30) cc_final: 0.7820 (m-30) REVERT: F 81 VAL cc_start: 0.9251 (t) cc_final: 0.8887 (t) REVERT: F 88 TYR cc_start: 0.8817 (m-80) cc_final: 0.8293 (m-80) REVERT: G 25 PHE cc_start: 0.8775 (m-80) cc_final: 0.8353 (m-80) REVERT: G 36 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8823 (mmmt) REVERT: G 56 GLU cc_start: 0.9546 (tm-30) cc_final: 0.9259 (tm-30) REVERT: G 87 ILE cc_start: 0.9123 (mm) cc_final: 0.8628 (pt) REVERT: G 89 ASN cc_start: 0.8495 (m-40) cc_final: 0.8243 (m110) REVERT: G 90 ASP cc_start: 0.9018 (t0) cc_final: 0.8803 (t0) REVERT: G 94 ASN cc_start: 0.9467 (t0) cc_final: 0.9135 (m-40) REVERT: H 59 MET cc_start: 0.8618 (tpp) cc_final: 0.8377 (tpp) REVERT: H 62 MET cc_start: 0.9395 (mmm) cc_final: 0.8897 (mmm) REVERT: H 120 LYS cc_start: 0.9566 (tttt) cc_final: 0.9133 (tttm) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3099 time to fit residues: 91.4499 Evaluate side-chains 186 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 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 = 0.050925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038253 restraints weight = 87628.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039364 restraints weight = 47257.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040226 restraints weight = 31478.442| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12761 Z= 0.190 Angle : 0.647 10.156 18476 Z= 0.372 Chirality : 0.037 0.184 2091 Planarity : 0.004 0.033 1328 Dihedral : 31.087 164.786 4002 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.30), residues: 738 helix: 1.38 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.75 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.009 0.001 HIS A 104 PHE 0.020 0.001 PHE H 70 TYR 0.022 0.002 TYR G 50 ARG 0.005 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.06534 ( 732) hydrogen bonds : angle 3.25655 ( 1787) covalent geometry : bond 0.00409 (12761) covalent geometry : angle 0.64703 (18476) *********************** 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 : 0.915 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: 0.9298 (mmtm) cc_final: 0.8966 (pttp) REVERT: A 64 LYS cc_start: 0.9444 (mppt) cc_final: 0.9191 (mmtm) REVERT: A 73 GLU cc_start: 0.9243 (tm-30) cc_final: 0.9010 (tm-30) REVERT: A 83 ASP cc_start: 0.7134 (t70) cc_final: 0.6813 (t0) REVERT: A 86 TRP cc_start: 0.8955 (m100) cc_final: 0.8630 (m100) REVERT: A 96 GLU cc_start: 0.8780 (tt0) cc_final: 0.8435 (tt0) REVERT: A 99 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8007 (mt-10) REVERT: B 74 GLU cc_start: 0.9383 (tt0) cc_final: 0.8851 (pt0) REVERT: B 79 LYS cc_start: 0.9383 (mttp) cc_final: 0.8912 (mtmt) REVERT: B 98 TYR cc_start: 0.8421 (m-10) cc_final: 0.7860 (m-80) REVERT: C 39 TYR cc_start: 0.8808 (m-80) cc_final: 0.8571 (m-10) REVERT: C 90 ASP cc_start: 0.7478 (t0) cc_final: 0.7162 (t70) REVERT: C 93 LEU cc_start: 0.9520 (mt) cc_final: 0.9106 (mt) REVERT: C 104 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8030 (tp-100) REVERT: D 39 TYR cc_start: 0.8916 (t80) cc_final: 0.8553 (t80) REVERT: D 43 LYS cc_start: 0.9103 (tttt) cc_final: 0.8740 (tppt) REVERT: D 65 ASP cc_start: 0.9494 (t0) cc_final: 0.9209 (p0) REVERT: D 68 GLU cc_start: 0.9074 (tt0) cc_final: 0.8499 (tm-30) REVERT: D 69 ARG cc_start: 0.9079 (ptp-170) cc_final: 0.8601 (ptm160) REVERT: D 102 GLU cc_start: 0.8418 (pp20) cc_final: 0.8076 (pp20) REVERT: D 117 LYS cc_start: 0.9538 (ptmm) cc_final: 0.9336 (ptmm) REVERT: E 62 ILE cc_start: 0.9126 (mm) cc_final: 0.8811 (mm) REVERT: E 87 GLN cc_start: 0.8859 (mt0) cc_final: 0.8510 (mt0) REVERT: E 95 GLN cc_start: 0.9021 (tt0) cc_final: 0.8800 (tt0) REVERT: E 104 HIS cc_start: 0.9397 (m-70) cc_final: 0.8946 (m90) REVERT: E 108 ASP cc_start: 0.9061 (m-30) cc_final: 0.8453 (m-30) REVERT: E 110 TYR cc_start: 0.8593 (t80) cc_final: 0.8327 (t80) REVERT: E 115 HIS cc_start: 0.8378 (t-90) cc_final: 0.8040 (t70) REVERT: F 29 ILE cc_start: 0.9526 (mm) cc_final: 0.9192 (pt) REVERT: F 44 LYS cc_start: 0.8858 (tptp) cc_final: 0.8253 (tptt) REVERT: F 55 ARG cc_start: 0.8530 (mtt180) cc_final: 0.7700 (mtt-85) REVERT: F 64 ASN cc_start: 0.9301 (m-40) cc_final: 0.8991 (m-40) REVERT: F 68 ASP cc_start: 0.8953 (m-30) cc_final: 0.7927 (m-30) REVERT: F 79 LYS cc_start: 0.8715 (mppt) cc_final: 0.8512 (mmtp) REVERT: F 81 VAL cc_start: 0.9264 (t) cc_final: 0.8869 (t) REVERT: F 88 TYR cc_start: 0.8767 (m-80) cc_final: 0.8235 (m-80) REVERT: G 25 PHE cc_start: 0.8751 (m-80) cc_final: 0.8318 (m-80) REVERT: G 36 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8812 (mmmt) REVERT: G 56 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9245 (tm-30) REVERT: G 73 ASN cc_start: 0.9165 (m110) cc_final: 0.8876 (m110) REVERT: G 87 ILE cc_start: 0.9037 (mm) cc_final: 0.8552 (pt) REVERT: G 89 ASN cc_start: 0.8519 (m-40) cc_final: 0.8296 (m110) REVERT: G 94 ASN cc_start: 0.9381 (t0) cc_final: 0.9077 (m-40) REVERT: H 59 MET cc_start: 0.8632 (tpp) cc_final: 0.8361 (tpp) REVERT: H 62 MET cc_start: 0.9420 (mmm) cc_final: 0.8917 (mmm) REVERT: H 76 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9098 (mm-30) REVERT: H 85 LYS cc_start: 0.9644 (mttt) cc_final: 0.9364 (mmmm) REVERT: H 86 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.8498 (mmt-90) REVERT: H 120 LYS cc_start: 0.9516 (tttt) cc_final: 0.9094 (tttm) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3103 time to fit residues: 94.6531 Evaluate side-chains 191 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039625 restraints weight = 85998.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040846 restraints weight = 46228.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041770 restraints weight = 30369.836| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12761 Z= 0.163 Angle : 0.631 10.368 18476 Z= 0.362 Chirality : 0.035 0.153 2091 Planarity : 0.003 0.034 1328 Dihedral : 30.843 160.597 4002 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 738 helix: 1.53 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.76 (0.36), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.007 0.001 HIS A 104 PHE 0.037 0.001 PHE A 67 TYR 0.018 0.002 TYR E 110 ARG 0.004 0.000 ARG E 133 Details of bonding type rmsd hydrogen bonds : bond 0.06130 ( 732) hydrogen bonds : angle 3.09294 ( 1787) covalent geometry : bond 0.00350 (12761) covalent geometry : angle 0.63091 (18476) ********************** 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 236 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.504 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: 0.9260 (mmtm) cc_final: 0.8874 (pttp) REVERT: A 50 GLU cc_start: 0.9281 (mp0) cc_final: 0.9022 (mp0) REVERT: A 64 LYS cc_start: 0.9463 (mppt) cc_final: 0.9118 (mmtm) REVERT: A 73 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8993 (tm-30) REVERT: A 83 ASP cc_start: 0.7050 (t70) cc_final: 0.6744 (t0) REVERT: A 86 TRP cc_start: 0.8889 (m100) cc_final: 0.8593 (m100) REVERT: A 96 GLU cc_start: 0.8779 (tt0) cc_final: 0.8550 (tt0) REVERT: A 99 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7976 (mt-10) REVERT: A 107 GLU cc_start: 0.8550 (pp20) cc_final: 0.8345 (pp20) REVERT: A 130 ARG cc_start: 0.9171 (mtp180) cc_final: 0.8792 (mmm160) REVERT: B 74 GLU cc_start: 0.9317 (tt0) cc_final: 0.8913 (pt0) REVERT: B 79 LYS cc_start: 0.9375 (mttp) cc_final: 0.8868 (mtmt) REVERT: C 71 ARG cc_start: 0.9119 (tmm160) cc_final: 0.8902 (ttp80) REVERT: C 84 GLN cc_start: 0.9238 (tp40) cc_final: 0.8957 (tp40) REVERT: C 89 ASN cc_start: 0.8385 (m-40) cc_final: 0.7946 (m110) REVERT: C 90 ASP cc_start: 0.7604 (t0) cc_final: 0.7345 (t0) REVERT: C 93 LEU cc_start: 0.9542 (mt) cc_final: 0.9262 (mt) REVERT: C 104 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8085 (tp-100) REVERT: D 39 TYR cc_start: 0.8878 (t80) cc_final: 0.8506 (t80) REVERT: D 43 LYS cc_start: 0.8990 (tttt) cc_final: 0.8702 (tppt) REVERT: D 44 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9077 (tm-30) REVERT: D 65 ASP cc_start: 0.9479 (t0) cc_final: 0.9191 (p0) REVERT: D 68 GLU cc_start: 0.9093 (tt0) cc_final: 0.8472 (tm-30) REVERT: D 69 ARG cc_start: 0.9098 (ptp-170) cc_final: 0.8629 (ptm160) REVERT: D 102 GLU cc_start: 0.8397 (pp20) cc_final: 0.8085 (pp20) REVERT: D 117 LYS cc_start: 0.9566 (ptmm) cc_final: 0.9357 (ptmm) REVERT: E 74 ILE cc_start: 0.9236 (tp) cc_final: 0.8980 (tt) REVERT: E 87 GLN cc_start: 0.8790 (mt0) cc_final: 0.8222 (mt0) REVERT: E 95 GLN cc_start: 0.9045 (tt0) cc_final: 0.8837 (tt0) REVERT: E 104 HIS cc_start: 0.9352 (m-70) cc_final: 0.9056 (m90) REVERT: E 108 ASP cc_start: 0.8919 (m-30) cc_final: 0.8597 (m-30) REVERT: E 110 TYR cc_start: 0.8607 (t80) cc_final: 0.8371 (t80) REVERT: E 115 HIS cc_start: 0.8243 (t-90) cc_final: 0.7896 (t70) REVERT: F 29 ILE cc_start: 0.9498 (mm) cc_final: 0.9193 (pt) REVERT: F 44 LYS cc_start: 0.8763 (tptp) cc_final: 0.8251 (tptt) REVERT: F 55 ARG cc_start: 0.8290 (mtt180) cc_final: 0.8011 (mtt-85) REVERT: F 63 GLU cc_start: 0.9291 (tp30) cc_final: 0.8990 (tp30) REVERT: F 68 ASP cc_start: 0.8939 (m-30) cc_final: 0.7930 (m-30) REVERT: F 71 THR cc_start: 0.8718 (p) cc_final: 0.8234 (p) REVERT: F 81 VAL cc_start: 0.9255 (t) cc_final: 0.8735 (t) REVERT: F 88 TYR cc_start: 0.8672 (m-80) cc_final: 0.8101 (m-10) REVERT: G 25 PHE cc_start: 0.8654 (m-80) cc_final: 0.8232 (m-80) REVERT: G 36 LYS cc_start: 0.9219 (mtpt) cc_final: 0.8790 (mmmt) REVERT: G 41 GLU cc_start: 0.8547 (mp0) cc_final: 0.8343 (mp0) REVERT: G 56 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9197 (tm-30) REVERT: G 68 ASN cc_start: 0.8995 (m110) cc_final: 0.8777 (m110) REVERT: G 73 ASN cc_start: 0.9116 (m110) cc_final: 0.8815 (m110) REVERT: G 87 ILE cc_start: 0.8909 (mm) cc_final: 0.8497 (pt) REVERT: G 89 ASN cc_start: 0.8511 (m-40) cc_final: 0.8302 (m110) REVERT: G 94 ASN cc_start: 0.9329 (t0) cc_final: 0.9028 (m-40) REVERT: H 59 MET cc_start: 0.8665 (tpp) cc_final: 0.8422 (tpp) REVERT: H 62 MET cc_start: 0.9443 (mmm) cc_final: 0.8891 (mmm) REVERT: H 76 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9109 (mm-30) REVERT: H 85 LYS cc_start: 0.9608 (mttt) cc_final: 0.9345 (mmmm) REVERT: H 86 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8422 (mmt-90) REVERT: H 120 LYS cc_start: 0.9493 (tttt) cc_final: 0.9127 (tttp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3270 time to fit residues: 102.5729 Evaluate side-chains 197 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 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 = 0.3242 r_free = 0.3242 target = 0.051305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038575 restraints weight = 87155.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.039764 restraints weight = 47491.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040674 restraints weight = 31496.141| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12761 Z= 0.204 Angle : 0.656 10.288 18476 Z= 0.376 Chirality : 0.036 0.185 2091 Planarity : 0.004 0.056 1328 Dihedral : 30.937 157.659 4002 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 738 helix: 1.43 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.73 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.007 0.001 HIS A 104 PHE 0.035 0.002 PHE A 67 TYR 0.017 0.002 TYR B 88 ARG 0.007 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.06549 ( 732) hydrogen bonds : angle 3.25522 ( 1787) covalent geometry : bond 0.00445 (12761) covalent geometry : angle 0.65650 (18476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4156.98 seconds wall clock time: 79 minutes 21.86 seconds (4761.86 seconds total)