Starting phenix.real_space_refine on Sun Jul 5 01:10:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gw2_51643/07_2026/9gw2_51643.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gw2_51643/07_2026/9gw2_51643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gw2_51643/07_2026/9gw2_51643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gw2_51643/07_2026/9gw2_51643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gw2_51643/07_2026/9gw2_51643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gw2_51643/07_2026/9gw2_51643.map" } resolution = 4.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 250 5.49 5 S 32 5.16 5 C 7442 2.51 5 N 2440 2.21 5 O 2950 1.98 5 H 11011 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24125 Number of models: 1 Model: "" Number of chains: 12 Chain: "N" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 3982 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "O" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 3923 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "T" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 3949 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "a" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1684 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "b" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "c" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1711 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "d" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1458 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1601 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "f" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1283 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1645 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "h" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1401 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "j" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 205 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 3.20, per 1000 atoms: 0.13 Number of scatterers: 24125 At special positions: 0 Unit cell: (84, 119.7, 139.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 250 15.00 O 2950 8.00 N 2440 7.00 C 7442 6.00 H 11011 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 491.8 milliseconds 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 16 sheets defined 61.1% alpha, 6.3% beta 125 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'O' and resid 1452 through 1455 Processing helix chain 'O' and resid 1456 through 1466 Processing helix chain 'O' and resid 1488 through 1491 Processing helix chain 'O' and resid 1492 through 1497 Processing helix chain 'O' and resid 1505 through 1512 Processing helix chain 'O' and resid 1522 through 1526 Processing helix chain 'O' and resid 1535 through 1539 removed outlier: 3.557A pdb=" N CYS O1539 " --> pdb=" O GLY O1536 " (cutoff:3.500A) Processing helix chain 'O' and resid 1585 through 1599 Processing helix chain 'O' and resid 1622 through 1627 Processing helix chain 'a' and resid 45 through 58 Processing helix chain 'a' and resid 64 through 77 Processing helix chain 'a' and resid 86 through 115 removed outlier: 3.548A pdb=" N LEU a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 133 Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.517A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 23 Processing helix chain 'c' and resid 28 through 37 Processing helix chain 'c' and resid 47 through 74 removed outlier: 3.639A pdb=" N LEU c 66 " --> pdb=" O GLU c 62 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 91 Processing helix chain 'c' and resid 91 through 98 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 123 removed outlier: 4.092A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 58 Processing helix chain 'e' and resid 64 through 78 removed outlier: 3.530A pdb=" N PHE e 68 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP e 78 " --> pdb=" O GLU e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 115 Processing helix chain 'e' and resid 121 through 133 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.761A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.520A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 23 Processing helix chain 'g' and resid 28 through 38 Processing helix chain 'g' and resid 46 through 74 removed outlier: 4.439A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 90 Processing helix chain 'g' and resid 91 through 98 removed outlier: 3.640A pdb=" N LYS g 96 " --> pdb=" O GLU g 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.630A pdb=" N LYS h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 Processing helix chain 'j' and resid 940 through 945 removed outlier: 3.737A pdb=" N GLU j 944 " --> pdb=" O GLU j 940 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 1474 through 1475 removed outlier: 5.751A pdb=" N ASP O1474 " --> pdb=" O GLY O1621 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'O' and resid 1480 through 1481 removed outlier: 7.323A pdb=" N VAL O1480 " --> pdb=" O VAL O1583 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU O1613 " --> pdb=" O LEU O1609 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 1552 through 1556 Processing sheet with id=AA4, first strand: chain 'O' and resid 1575 through 1578 removed outlier: 6.651A pdb=" N PHE O1650 " --> pdb=" O VAL O1576 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU O1578 " --> pdb=" O VAL O1648 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL O1648 " --> pdb=" O GLU O1578 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 1628 through 1629 removed outlier: 6.462A pdb=" N ASN O1628 " --> pdb=" O PHE O1664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 1669 through 1670 Processing sheet with id=AA7, first strand: chain 'a' and resid 84 through 85 removed outlier: 7.151A pdb=" N ARG a 84 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.297A pdb=" N THR b 96 " --> pdb=" O THR g 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'c' and resid 43 through 44 removed outlier: 7.079A pdb=" N ARG c 43 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'c' and resid 78 through 79 Processing sheet with id=AB3, first strand: chain 'c' and resid 102 through 103 removed outlier: 6.726A pdb=" N THR c 102 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'e' and resid 84 through 85 removed outlier: 6.984A pdb=" N ARG e 84 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'e' and resid 119 through 120 Processing sheet with id=AB6, first strand: chain 'g' and resid 43 through 44 removed outlier: 7.250A pdb=" N ARG g 43 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'g' and resid 78 through 79 457 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 10995 1.02 - 1.22: 73 1.22 - 1.42: 6039 1.42 - 1.62: 7711 1.62 - 1.82: 49 Bond restraints: 24867 Sorted by residual: bond pdb=" C3' DC N 48 " pdb=" O3' DC N 48 " ideal model delta sigma weight residual 1.435 1.543 -0.108 1.30e-02 5.92e+03 6.87e+01 bond pdb=" C1' DT N 78 " pdb=" N1 DT N 78 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C5' DT N 6 " pdb=" C4' DT N 6 " ideal model delta sigma weight residual 1.512 1.546 -0.034 7.00e-03 2.04e+04 2.31e+01 bond pdb=" C5' DC N 110 " pdb=" C4' DC N 110 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.07e+01 bond pdb=" C3' DC T 116 " pdb=" O3' DC T 116 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.01e+01 ... (remaining 24862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.92: 44988 15.92 - 31.83: 0 31.83 - 47.75: 0 47.75 - 63.66: 0 63.66 - 79.58: 1 Bond angle restraints: 44989 Sorted by residual: angle pdb=" O3' DC N 48 " pdb=" P DT N 49 " pdb=" OP1 DT N 49 " ideal model delta sigma weight residual 108.00 28.42 79.58 3.00e+00 1.11e-01 7.04e+02 angle pdb=" O4' DC N 3 " pdb=" C1' DC N 3 " pdb=" N1 DC N 3 " ideal model delta sigma weight residual 108.00 116.07 -8.07 7.00e-01 2.04e+00 1.33e+02 angle pdb=" C3' DC N 48 " pdb=" O3' DC N 48 " pdb=" P DT N 49 " ideal model delta sigma weight residual 120.20 132.89 -12.69 1.50e+00 4.44e-01 7.16e+01 angle pdb=" O4' DC T 179 " pdb=" C1' DC T 179 " pdb=" N1 DC T 179 " ideal model delta sigma weight residual 108.00 113.67 -5.67 7.00e-01 2.04e+00 6.57e+01 angle pdb=" O4' DC N 114 " pdb=" C1' DC N 114 " pdb=" N1 DC N 114 " ideal model delta sigma weight residual 108.00 113.54 -5.54 7.00e-01 2.04e+00 6.27e+01 ... (remaining 44984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 9236 35.14 - 70.27: 1372 70.27 - 105.41: 17 105.41 - 140.54: 2 140.54 - 175.68: 1 Dihedral angle restraints: 10628 sinusoidal: 7331 harmonic: 3297 Sorted by residual: dihedral pdb=" C4' DG T 130 " pdb=" C3' DG T 130 " pdb=" O3' DG T 130 " pdb=" P DC T 131 " ideal model delta sinusoidal sigma weight residual 220.00 44.32 175.68 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CD ARG c 82 " pdb=" NE ARG c 82 " pdb=" CZ ARG c 82 " pdb=" NH1 ARG c 82 " ideal model delta sinusoidal sigma weight residual 0.00 32.61 -32.61 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" C4' DC T 118 " pdb=" C3' DC T 118 " pdb=" O3' DC T 118 " pdb=" P DG T 119 " ideal model delta sinusoidal sigma weight residual 220.00 81.57 138.43 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 10625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1656 0.103 - 0.206: 305 0.206 - 0.309: 161 0.309 - 0.412: 72 0.412 - 0.515: 19 Chirality restraints: 2213 Sorted by residual: chirality pdb=" P DT N 49 " pdb=" OP1 DT N 49 " pdb=" OP2 DT N 49 " pdb=" O5' DT N 49 " both_signs ideal model delta sigma weight residual True 2.34 1.82 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" P DT T 165 " pdb=" OP1 DT T 165 " pdb=" OP2 DT T 165 " pdb=" O5' DT T 165 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" P DT N 6 " pdb=" OP1 DT N 6 " pdb=" OP2 DT N 6 " pdb=" O5' DT N 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 2210 not shown) Planarity restraints: 2813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG c 82 " 0.492 9.50e-02 1.11e+02 1.65e-01 3.42e+01 pdb=" NE ARG c 82 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG c 82 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG c 82 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG c 82 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG c 82 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG c 82 " 0.014 2.00e-02 2.50e+03 pdb="HH21 ARG c 82 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG c 82 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG c 33 " 0.375 9.50e-02 1.11e+02 1.28e-01 3.02e+01 pdb=" NE ARG c 33 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG c 33 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG c 33 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG c 33 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG c 33 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG c 33 " 0.030 2.00e-02 2.50e+03 pdb="HH21 ARG c 33 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG c 33 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG g 18 " 0.134 9.50e-02 1.11e+02 5.63e-02 2.85e+01 pdb=" NE ARG g 18 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG g 18 " -0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG g 18 " -0.049 2.00e-02 2.50e+03 pdb=" NH2 ARG g 18 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG g 18 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG g 18 " 0.045 2.00e-02 2.50e+03 pdb="HH21 ARG g 18 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG g 18 " 0.036 2.00e-02 2.50e+03 ... (remaining 2810 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.42: 10006 2.42 - 2.97: 49680 2.97 - 3.51: 59693 3.51 - 4.06: 84909 4.06 - 4.60: 121696 Nonbonded interactions: 325984 Sorted by model distance: nonbonded pdb=" O TYR c 40 " pdb=" HG SER d 78 " model vdw 1.877 2.450 nonbonded pdb=" HG1 THR d 90 " pdb=" OE1 GLU d 93 " model vdw 1.878 2.450 nonbonded pdb=" H2' DC N 46 " pdb=" H6 DC N 46 " model vdw 1.887 2.270 nonbonded pdb="HD12 LEU a 62 " pdb="HH21 ARG b 40 " model vdw 1.891 2.270 nonbonded pdb=" O LEU e 104 " pdb=" HG1 THR e 108 " model vdw 1.897 2.450 ... (remaining 325979 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' and resid 40 through 134) selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 118) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 35 through 123) 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: 1.890 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.020 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 0.108 13856 Z= 0.641 Angle : 1.871 79.578 19760 Z= 1.046 Chirality : 0.125 0.515 2213 Planarity : 0.017 0.217 1657 Dihedral : 23.821 175.677 5850 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.71 % Allowed : 2.00 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 983 helix: 0.69 (0.20), residues: 592 sheet: -1.64 (0.89), residues: 28 loop : -1.00 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.005 ARG c 82 TYR 0.037 0.007 TYR O1604 PHE 0.041 0.005 PHE j 948 TRP 0.037 0.006 TRP O1562 HIS 0.021 0.004 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.64 (13856) covalent geometry : angle 1.87109 / 1.05 (19760) hydrogen bonds : bond 0.12309 / 13.37 ( 776) hydrogen bonds : angle 4.81830 / 6.27 ( 1961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 467 time to evaluate : 0.568 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1452 ASP cc_start: 0.5855 (m-30) cc_final: 0.5068 (m-30) REVERT: O 1478 GLU cc_start: 0.7814 (pt0) cc_final: 0.7540 (pt0) REVERT: O 1482 LEU cc_start: 0.8103 (mp) cc_final: 0.6728 (tt) REVERT: O 1498 GLN cc_start: 0.8642 (tp40) cc_final: 0.8308 (tp40) REVERT: O 1526 MET cc_start: 0.8541 (mtm) cc_final: 0.8000 (mtm) REVERT: O 1574 THR cc_start: 0.7955 (m) cc_final: 0.7450 (m) REVERT: O 1587 LYS cc_start: 0.7549 (tttt) cc_final: 0.7269 (mttt) REVERT: O 1589 PHE cc_start: 0.7321 (t80) cc_final: 0.6971 (t80) REVERT: O 1595 GLU cc_start: 0.8620 (tt0) cc_final: 0.8214 (tt0) REVERT: O 1596 TYR cc_start: 0.5565 (m-10) cc_final: 0.5121 (m-10) REVERT: O 1612 ASP cc_start: 0.7656 (t0) cc_final: 0.7143 (t0) REVERT: O 1616 ASP cc_start: 0.5625 (t0) cc_final: 0.4493 (t0) REVERT: a 38 LYS cc_start: 0.7218 (pttp) cc_final: 0.6957 (pttt) REVERT: a 60 GLU cc_start: 0.8121 (pt0) cc_final: 0.7839 (pt0) REVERT: a 63 ILE cc_start: 0.8521 (mt) cc_final: 0.8306 (mm) REVERT: a 100 TYR cc_start: 0.7888 (t80) cc_final: 0.7616 (t80) REVERT: a 104 LEU cc_start: 0.8074 (tp) cc_final: 0.7812 (tt) REVERT: a 108 THR cc_start: 0.8578 (m) cc_final: 0.8072 (m) REVERT: a 130 ARG cc_start: 0.8479 (tpt90) cc_final: 0.8144 (tpt90) REVERT: b 25 ASN cc_start: 0.8854 (m-40) cc_final: 0.8626 (m110) REVERT: b 26 ILE cc_start: 0.8678 (tp) cc_final: 0.8184 (mt) REVERT: b 43 VAL cc_start: 0.8488 (t) cc_final: 0.8060 (m) REVERT: b 68 ASP cc_start: 0.8293 (m-30) cc_final: 0.7830 (m-30) REVERT: b 84 MET cc_start: 0.7072 (mmm) cc_final: 0.6827 (mmt) REVERT: c 43 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7686 (mtp85) REVERT: c 44 VAL cc_start: 0.8882 (t) cc_final: 0.8450 (p) REVERT: c 57 GLU cc_start: 0.7773 (tt0) cc_final: 0.7360 (tm-30) REVERT: c 62 GLU cc_start: 0.8210 (tp30) cc_final: 0.7679 (tp30) REVERT: c 85 GLN cc_start: 0.7580 (tp40) cc_final: 0.7310 (tp40) REVERT: d 41 VAL cc_start: 0.8124 (t) cc_final: 0.7758 (t) REVERT: d 45 LEU cc_start: 0.8766 (tp) cc_final: 0.8528 (tp) REVERT: d 52 THR cc_start: 0.8072 (m) cc_final: 0.7860 (m) REVERT: d 71 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7395 (tm-30) REVERT: d 85 LYS cc_start: 0.8248 (mttp) cc_final: 0.7702 (mtpt) REVERT: d 87 SER cc_start: 0.8571 (m) cc_final: 0.8126 (p) REVERT: d 120 LYS cc_start: 0.8391 (mttt) cc_final: 0.7982 (tptp) REVERT: e 56 GLN cc_start: 0.8499 (mt0) cc_final: 0.8192 (mt0) REVERT: e 57 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8059 (tmtt) REVERT: e 63 ILE cc_start: 0.8614 (mt) cc_final: 0.8207 (mt) REVERT: e 74 GLU cc_start: 0.7622 (tt0) cc_final: 0.7309 (tt0) REVERT: e 94 GLN cc_start: 0.8312 (tt0) cc_final: 0.7819 (tt0) REVERT: e 126 GLN cc_start: 0.8457 (mt0) cc_final: 0.8256 (mm-40) REVERT: f 25 ASN cc_start: 0.8455 (m-40) cc_final: 0.8208 (m-40) REVERT: f 74 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8397 (mm-30) REVERT: g 25 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8952 (mm-40) REVERT: g 36 ARG cc_start: 0.8646 (mtm110) cc_final: 0.8209 (ttp-110) REVERT: g 43 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7461 (mtm-85) REVERT: g 56 LEU cc_start: 0.8325 (mt) cc_final: 0.8065 (mt) REVERT: g 60 THR cc_start: 0.8978 (m) cc_final: 0.8777 (p) REVERT: g 62 GLU cc_start: 0.8861 (tp30) cc_final: 0.8644 (tp30) REVERT: g 85 GLN cc_start: 0.7287 (tp40) cc_final: 0.6978 (tp40) REVERT: g 93 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7230 (mt-10) REVERT: g 96 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8192 (tptt) REVERT: g 97 LEU cc_start: 0.9099 (tp) cc_final: 0.8893 (tt) REVERT: g 105 GLN cc_start: 0.7144 (mm-40) cc_final: 0.5899 (tp-100) REVERT: h 62 MET cc_start: 0.6944 (mmm) cc_final: 0.6702 (mmm) REVERT: h 85 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8139 (mptt) REVERT: h 86 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7470 (mmm-85) REVERT: h 105 GLU cc_start: 0.7405 (tp30) cc_final: 0.7116 (tp30) REVERT: h 121 TYR cc_start: 0.8763 (t80) cc_final: 0.8549 (t80) outliers start: 6 outliers final: 2 residues processed: 470 average time/residue: 0.3604 time to fit residues: 222.3811 Evaluate side-chains 297 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 86 GLN f 93 GLN g 25 GLN j 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.087709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.060324 restraints weight = 80657.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.062999 restraints weight = 37213.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.064786 restraints weight = 23717.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.065864 restraints weight = 18402.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.066457 restraints weight = 15988.937| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 13856 Z= 0.246 Angle : 0.840 25.751 19760 Z= 0.495 Chirality : 0.070 2.279 2213 Planarity : 0.007 0.078 1657 Dihedral : 28.316 176.821 3850 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 983 helix: 1.08 (0.20), residues: 587 sheet: -1.00 (1.15), residues: 18 loop : -1.10 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG g 18 TYR 0.027 0.003 TYR f 88 PHE 0.026 0.002 PHE O1668 TRP 0.006 0.001 TRP O1562 HIS 0.007 0.002 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.25 (13856) covalent geometry : angle 0.84008 / 0.49 (19760) hydrogen bonds : bond 0.06384 / 7.04 ( 776) hydrogen bonds : angle 4.22771 / 5.53 ( 1961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 0.558 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: 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: O 1482 LEU cc_start: 0.8436 (mp) cc_final: 0.7272 (tt) REVERT: O 1538 TYR cc_start: 0.7905 (m-80) cc_final: 0.7704 (m-80) REVERT: O 1587 LYS cc_start: 0.7607 (tttt) cc_final: 0.7214 (mttt) REVERT: O 1595 GLU cc_start: 0.8477 (tt0) cc_final: 0.8168 (tt0) REVERT: O 1614 ILE cc_start: 0.6804 (mp) cc_final: 0.5853 (mp) REVERT: a 60 GLU cc_start: 0.8251 (pt0) cc_final: 0.7974 (pt0) REVERT: a 74 GLU cc_start: 0.7657 (tt0) cc_final: 0.7438 (tt0) REVERT: a 94 GLN cc_start: 0.8350 (tt0) cc_final: 0.7135 (tp40) REVERT: a 100 TYR cc_start: 0.8027 (t80) cc_final: 0.7776 (t80) REVERT: a 108 THR cc_start: 0.8617 (m) cc_final: 0.8295 (m) REVERT: a 118 VAL cc_start: 0.9024 (t) cc_final: 0.8752 (p) REVERT: a 130 ARG cc_start: 0.8703 (tpt90) cc_final: 0.8490 (tpt90) REVERT: b 43 VAL cc_start: 0.8487 (t) cc_final: 0.8257 (m) REVERT: c 44 VAL cc_start: 0.8814 (t) cc_final: 0.8428 (p) REVERT: c 62 GLU cc_start: 0.8284 (tp30) cc_final: 0.7826 (tp30) REVERT: c 78 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.6881 (mtm110) REVERT: c 79 ILE cc_start: 0.8284 (mt) cc_final: 0.8023 (mm) REVERT: d 41 VAL cc_start: 0.7904 (t) cc_final: 0.7690 (t) REVERT: d 71 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7679 (tm-30) REVERT: d 76 GLU cc_start: 0.7236 (tp30) cc_final: 0.6993 (tp30) REVERT: d 85 LYS cc_start: 0.8279 (mttp) cc_final: 0.7888 (mtpt) REVERT: d 86 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7598 (mmm-85) REVERT: d 113 GLU cc_start: 0.8560 (tp30) cc_final: 0.8166 (tm-30) REVERT: d 120 LYS cc_start: 0.8589 (mttt) cc_final: 0.7879 (tptp) REVERT: e 74 GLU cc_start: 0.7367 (tt0) cc_final: 0.7062 (tt0) REVERT: f 25 ASN cc_start: 0.8357 (m-40) cc_final: 0.7915 (m-40) REVERT: f 43 VAL cc_start: 0.9081 (t) cc_final: 0.8866 (p) REVERT: f 74 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8736 (tt0) REVERT: g 85 GLN cc_start: 0.7337 (tp40) cc_final: 0.6959 (tp40) REVERT: g 96 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8258 (tptt) REVERT: g 105 GLN cc_start: 0.7821 (mm-40) cc_final: 0.6720 (mm-40) REVERT: h 54 ILE cc_start: 0.8383 (tt) cc_final: 0.8118 (tt) REVERT: h 85 LYS cc_start: 0.8538 (mtmm) cc_final: 0.8181 (mptt) REVERT: h 105 GLU cc_start: 0.7480 (tp30) cc_final: 0.7264 (tp30) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2927 time to fit residues: 131.4125 Evaluate side-chains 260 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 25 ASN e 94 GLN g 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.088477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.060806 restraints weight = 80229.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.063570 restraints weight = 36046.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065366 restraints weight = 22753.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066372 restraints weight = 17672.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.067073 restraints weight = 15441.161| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13856 Z= 0.193 Angle : 0.756 27.298 19760 Z= 0.453 Chirality : 0.064 2.100 2213 Planarity : 0.006 0.110 1657 Dihedral : 28.422 173.093 3850 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 983 helix: 1.21 (0.21), residues: 595 sheet: -0.68 (1.29), residues: 18 loop : -1.10 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG d 79 TYR 0.032 0.002 TYR d 83 PHE 0.026 0.001 PHE O1544 TRP 0.003 0.001 TRP O1562 HIS 0.004 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.19 (13856) covalent geometry : angle 0.75632 / 0.45 (19760) hydrogen bonds : bond 0.05667 / 6.25 ( 776) hydrogen bonds : angle 3.97369 / 5.10 ( 1961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.579 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: 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: O 1482 LEU cc_start: 0.8450 (mp) cc_final: 0.7216 (tt) REVERT: O 1587 LYS cc_start: 0.7628 (tttt) cc_final: 0.7214 (mttt) REVERT: O 1595 GLU cc_start: 0.8509 (tt0) cc_final: 0.8174 (tm-30) REVERT: O 1665 ASP cc_start: 0.8855 (t0) cc_final: 0.8569 (t0) REVERT: a 100 TYR cc_start: 0.8035 (t80) cc_final: 0.7798 (t80) REVERT: a 108 THR cc_start: 0.8668 (m) cc_final: 0.8402 (m) REVERT: a 130 ARG cc_start: 0.8753 (tpt90) cc_final: 0.8512 (tpt90) REVERT: b 26 ILE cc_start: 0.8467 (tp) cc_final: 0.8168 (mp) REVERT: c 44 VAL cc_start: 0.8800 (t) cc_final: 0.8415 (p) REVERT: c 62 GLU cc_start: 0.8291 (tp30) cc_final: 0.7814 (tp30) REVERT: c 79 ILE cc_start: 0.8169 (mt) cc_final: 0.7941 (mm) REVERT: c 109 LEU cc_start: 0.8520 (mp) cc_final: 0.8267 (mt) REVERT: d 71 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7754 (tm-30) REVERT: d 85 LYS cc_start: 0.8263 (mttp) cc_final: 0.7834 (mtpt) REVERT: d 86 ARG cc_start: 0.7947 (mmt-90) cc_final: 0.7606 (mmm-85) REVERT: d 113 GLU cc_start: 0.8652 (tp30) cc_final: 0.8147 (tm-30) REVERT: d 120 LYS cc_start: 0.8509 (mttt) cc_final: 0.7814 (tptp) REVERT: e 74 GLU cc_start: 0.7361 (tt0) cc_final: 0.6599 (tt0) REVERT: f 25 ASN cc_start: 0.8322 (m-40) cc_final: 0.7781 (m-40) REVERT: f 51 TYR cc_start: 0.8716 (m-80) cc_final: 0.8270 (m-80) REVERT: f 74 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8737 (tt0) REVERT: g 85 GLN cc_start: 0.7321 (tp40) cc_final: 0.7045 (tp40) REVERT: g 96 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8188 (tptt) REVERT: g 105 GLN cc_start: 0.7691 (mm-40) cc_final: 0.6558 (mm-40) REVERT: h 85 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8152 (mptt) REVERT: h 89 ILE cc_start: 0.7466 (mm) cc_final: 0.7160 (mm) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2827 time to fit residues: 124.4097 Evaluate side-chains 257 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 82 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1498 GLN a 86 GLN a 94 GLN g 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.087928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.060149 restraints weight = 80658.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.062909 restraints weight = 36058.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.064716 restraints weight = 22762.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.065799 restraints weight = 17628.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.066460 restraints weight = 15305.779| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13856 Z= 0.208 Angle : 0.720 27.625 19760 Z= 0.429 Chirality : 0.062 2.098 2213 Planarity : 0.005 0.058 1657 Dihedral : 28.540 172.843 3850 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.26), residues: 983 helix: 1.28 (0.21), residues: 597 sheet: -0.59 (1.28), residues: 18 loop : -0.98 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O1496 TYR 0.022 0.002 TYR a 55 PHE 0.018 0.001 PHE O1668 TRP 0.002 0.001 TRP O1460 HIS 0.006 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.21 (13856) covalent geometry : angle 0.71999 / 0.43 (19760) hydrogen bonds : bond 0.05119 / 5.61 ( 776) hydrogen bonds : angle 3.88297 / 5.00 ( 1961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.518 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: 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: O 1482 LEU cc_start: 0.8409 (mp) cc_final: 0.7221 (tt) REVERT: O 1587 LYS cc_start: 0.7763 (tttt) cc_final: 0.7310 (mttt) REVERT: O 1595 GLU cc_start: 0.8478 (tt0) cc_final: 0.8238 (tm-30) REVERT: a 108 THR cc_start: 0.8708 (m) cc_final: 0.8467 (m) REVERT: a 130 ARG cc_start: 0.8787 (tpt90) cc_final: 0.8525 (tpt90) REVERT: c 44 VAL cc_start: 0.8816 (t) cc_final: 0.8357 (p) REVERT: c 62 GLU cc_start: 0.8236 (tp30) cc_final: 0.7772 (tp30) REVERT: c 86 LEU cc_start: 0.8419 (mt) cc_final: 0.8205 (mt) REVERT: d 71 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7729 (tm-30) REVERT: d 85 LYS cc_start: 0.8267 (mttp) cc_final: 0.7831 (mtpt) REVERT: d 86 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7568 (mmm-85) REVERT: d 113 GLU cc_start: 0.8751 (tp30) cc_final: 0.8236 (tm-30) REVERT: d 120 LYS cc_start: 0.8475 (mttt) cc_final: 0.7819 (tptp) REVERT: e 94 GLN cc_start: 0.8645 (tt0) cc_final: 0.8324 (tt0) REVERT: f 74 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8759 (tt0) REVERT: g 85 GLN cc_start: 0.7241 (tp40) cc_final: 0.7011 (tp40) REVERT: g 96 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8214 (tptt) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2395 time to fit residues: 100.2807 Evaluate side-chains 250 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 23 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 69 GLN a 86 GLN a 109 ASN b 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.058200 restraints weight = 82878.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.060809 restraints weight = 37423.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.062478 restraints weight = 23792.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.063578 restraints weight = 18591.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.064110 restraints weight = 16210.708| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 13856 Z= 0.311 Angle : 0.777 28.012 19760 Z= 0.459 Chirality : 0.062 2.032 2213 Planarity : 0.005 0.054 1657 Dihedral : 28.579 172.062 3850 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 983 helix: 0.87 (0.20), residues: 601 sheet: -0.75 (1.29), residues: 18 loop : -1.05 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 92 TYR 0.026 0.003 TYR g 58 PHE 0.026 0.002 PHE a 68 TRP 0.006 0.001 TRP O1640 HIS 0.011 0.002 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.31 (13856) covalent geometry : angle 0.77654 / 0.46 (19760) hydrogen bonds : bond 0.05699 / 6.26 ( 776) hydrogen bonds : angle 4.29686 / 5.66 ( 1961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.562 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8372 (mp) cc_final: 0.7307 (tt) REVERT: O 1483 THR cc_start: 0.7295 (t) cc_final: 0.7079 (t) REVERT: O 1579 TYR cc_start: 0.7317 (t80) cc_final: 0.6662 (t80) REVERT: O 1587 LYS cc_start: 0.7786 (tttt) cc_final: 0.7351 (mttt) REVERT: O 1595 GLU cc_start: 0.8499 (tt0) cc_final: 0.8232 (tt0) REVERT: O 1612 ASP cc_start: 0.7918 (t0) cc_final: 0.6684 (t70) REVERT: a 59 THR cc_start: 0.8795 (p) cc_final: 0.8373 (t) REVERT: a 100 TYR cc_start: 0.7972 (t80) cc_final: 0.7703 (t80) REVERT: a 108 THR cc_start: 0.8676 (m) cc_final: 0.8415 (m) REVERT: a 119 THR cc_start: 0.8746 (m) cc_final: 0.8462 (m) REVERT: a 130 ARG cc_start: 0.8843 (tpt90) cc_final: 0.8373 (tpt90) REVERT: b 26 ILE cc_start: 0.8570 (tp) cc_final: 0.8214 (mp) REVERT: c 44 VAL cc_start: 0.8768 (t) cc_final: 0.8397 (p) REVERT: c 62 GLU cc_start: 0.8177 (tp30) cc_final: 0.7649 (tp30) REVERT: c 86 LEU cc_start: 0.8448 (mt) cc_final: 0.8209 (mt) REVERT: d 71 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7770 (tm-30) REVERT: d 85 LYS cc_start: 0.8391 (mttp) cc_final: 0.7987 (mtpt) REVERT: d 86 ARG cc_start: 0.8046 (mmt-90) cc_final: 0.7577 (mmm-85) REVERT: d 113 GLU cc_start: 0.8839 (tp30) cc_final: 0.8389 (tm-30) REVERT: d 120 LYS cc_start: 0.8470 (mttt) cc_final: 0.7914 (tptp) REVERT: e 57 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8437 (ttmm) REVERT: e 94 GLN cc_start: 0.8569 (tt0) cc_final: 0.7717 (tt0) REVERT: f 74 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8816 (tt0) REVERT: g 65 GLU cc_start: 0.8676 (tp30) cc_final: 0.8226 (tm-30) REVERT: g 85 GLN cc_start: 0.7355 (tp40) cc_final: 0.7111 (tp40) REVERT: g 96 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8320 (tptt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2644 time to fit residues: 101.3383 Evaluate side-chains 235 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 81 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 69 GLN g 25 GLN h 63 ASN j 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.088114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.060436 restraints weight = 80640.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.063165 restraints weight = 36793.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.064917 restraints weight = 23376.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.065994 restraints weight = 18221.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.066509 restraints weight = 15876.672| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13856 Z= 0.164 Angle : 0.679 27.233 19760 Z= 0.408 Chirality : 0.061 2.098 2213 Planarity : 0.005 0.075 1657 Dihedral : 28.546 171.936 3850 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.12 % Allowed : 1.18 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 983 helix: 1.32 (0.21), residues: 597 sheet: -0.50 (1.26), residues: 18 loop : -0.89 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O1543 TYR 0.019 0.002 TYR g 58 PHE 0.015 0.001 PHE O1668 TRP 0.001 0.000 TRP O1460 HIS 0.009 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (13856) covalent geometry : angle 0.67940 / 0.41 (19760) hydrogen bonds : bond 0.04865 / 5.31 ( 776) hydrogen bonds : angle 3.74641 / 4.86 ( 1961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.567 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8422 (mp) cc_final: 0.7299 (tt) REVERT: O 1579 TYR cc_start: 0.7292 (t80) cc_final: 0.6657 (t80) REVERT: O 1587 LYS cc_start: 0.7777 (tttt) cc_final: 0.7316 (mttt) REVERT: O 1595 GLU cc_start: 0.8489 (tt0) cc_final: 0.8283 (tp30) REVERT: O 1612 ASP cc_start: 0.6988 (t0) cc_final: 0.6705 (t0) REVERT: O 1665 ASP cc_start: 0.8688 (t0) cc_final: 0.8402 (t0) REVERT: a 59 THR cc_start: 0.8755 (p) cc_final: 0.8360 (t) REVERT: a 100 TYR cc_start: 0.7929 (t80) cc_final: 0.7575 (t80) REVERT: a 119 THR cc_start: 0.8643 (m) cc_final: 0.8311 (m) REVERT: a 130 ARG cc_start: 0.8849 (tpt90) cc_final: 0.8414 (tpt90) REVERT: b 26 ILE cc_start: 0.8440 (tp) cc_final: 0.8120 (mp) REVERT: c 44 VAL cc_start: 0.8650 (t) cc_final: 0.8282 (p) REVERT: c 62 GLU cc_start: 0.8042 (tp30) cc_final: 0.7694 (tp30) REVERT: c 79 ILE cc_start: 0.8001 (mt) cc_final: 0.7434 (tp) REVERT: d 79 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7256 (ttm-80) REVERT: d 85 LYS cc_start: 0.8340 (mttp) cc_final: 0.7849 (mtpt) REVERT: d 86 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7527 (mmm-85) REVERT: d 113 GLU cc_start: 0.8816 (tp30) cc_final: 0.8281 (tm-30) REVERT: d 120 LYS cc_start: 0.8455 (mttt) cc_final: 0.7843 (tptp) REVERT: e 94 GLN cc_start: 0.8526 (tt0) cc_final: 0.7714 (tt0) REVERT: f 51 TYR cc_start: 0.8817 (m-80) cc_final: 0.8227 (m-80) REVERT: f 74 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8786 (tt0) REVERT: f 98 TYR cc_start: 0.7612 (m-10) cc_final: 0.7346 (m-10) REVERT: g 57 GLU cc_start: 0.8390 (tt0) cc_final: 0.8187 (tt0) REVERT: g 65 GLU cc_start: 0.8594 (tp30) cc_final: 0.8315 (tm-30) REVERT: g 85 GLN cc_start: 0.7334 (tp40) cc_final: 0.7047 (tp40) REVERT: g 96 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8254 (tptt) REVERT: h 36 SER cc_start: 0.8540 (t) cc_final: 0.8282 (t) REVERT: h 100 LEU cc_start: 0.7969 (tp) cc_final: 0.7436 (tp) REVERT: h 105 GLU cc_start: 0.7160 (tp30) cc_final: 0.6709 (tp30) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.2387 time to fit residues: 97.3518 Evaluate side-chains 253 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 69 GLN a 109 ASN b 25 ASN f 25 ASN g 25 GLN h 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.059216 restraints weight = 81550.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.061876 restraints weight = 37483.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.063571 restraints weight = 23994.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.064701 restraints weight = 18802.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.065170 restraints weight = 16348.891| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13856 Z= 0.223 Angle : 0.703 27.540 19760 Z= 0.419 Chirality : 0.061 2.065 2213 Planarity : 0.005 0.083 1657 Dihedral : 28.502 171.948 3850 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.27), residues: 983 helix: 1.29 (0.21), residues: 597 sheet: -0.63 (1.24), residues: 18 loop : -0.80 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG g 72 TYR 0.018 0.002 TYR g 58 PHE 0.014 0.001 PHE O1668 TRP 0.004 0.001 TRP O1640 HIS 0.012 0.002 HIS h 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.22 (13856) covalent geometry : angle 0.70311 / 0.42 (19760) hydrogen bonds : bond 0.04941 / 5.39 ( 776) hydrogen bonds : angle 3.89037 / 5.10 ( 1961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.596 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: 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: O 1482 LEU cc_start: 0.8327 (mp) cc_final: 0.7203 (tt) REVERT: O 1579 TYR cc_start: 0.7269 (t80) cc_final: 0.6663 (t80) REVERT: O 1587 LYS cc_start: 0.7780 (tttt) cc_final: 0.7320 (mttt) REVERT: O 1595 GLU cc_start: 0.8489 (tt0) cc_final: 0.8279 (tp30) REVERT: a 59 THR cc_start: 0.8842 (p) cc_final: 0.8503 (t) REVERT: a 104 LEU cc_start: 0.7471 (tt) cc_final: 0.7144 (tt) REVERT: a 108 THR cc_start: 0.8526 (m) cc_final: 0.8303 (m) REVERT: a 121 MET cc_start: 0.6282 (mtt) cc_final: 0.5955 (mtt) REVERT: a 130 ARG cc_start: 0.8877 (tpt90) cc_final: 0.8401 (tpt90) REVERT: b 26 ILE cc_start: 0.8498 (tp) cc_final: 0.8172 (mp) REVERT: c 44 VAL cc_start: 0.8710 (t) cc_final: 0.8284 (p) REVERT: c 62 GLU cc_start: 0.8119 (tp30) cc_final: 0.7599 (tp30) REVERT: c 79 ILE cc_start: 0.7952 (mt) cc_final: 0.7365 (tp) REVERT: c 86 LEU cc_start: 0.8439 (mt) cc_final: 0.8150 (mt) REVERT: d 68 ASP cc_start: 0.8435 (t70) cc_final: 0.8200 (t0) REVERT: d 71 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7803 (tm-30) REVERT: d 85 LYS cc_start: 0.8341 (mttp) cc_final: 0.7927 (mtpt) REVERT: d 86 ARG cc_start: 0.8049 (mmt-90) cc_final: 0.7551 (mmm-85) REVERT: d 113 GLU cc_start: 0.8787 (tp30) cc_final: 0.8301 (tm-30) REVERT: d 120 LYS cc_start: 0.8487 (mttt) cc_final: 0.7932 (tptp) REVERT: e 57 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8546 (ttmm) REVERT: e 94 GLN cc_start: 0.8418 (tt0) cc_final: 0.7342 (tt0) REVERT: f 68 ASP cc_start: 0.8183 (m-30) cc_final: 0.7731 (m-30) REVERT: f 74 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8790 (tt0) REVERT: f 92 ARG cc_start: 0.6996 (tmm-80) cc_final: 0.6749 (tmm-80) REVERT: g 85 GLN cc_start: 0.7396 (tp40) cc_final: 0.7055 (tp40) REVERT: g 96 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8282 (tptt) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2571 time to fit residues: 98.4490 Evaluate side-chains 239 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 69 GLN b 25 ASN h 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.087586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.060209 restraints weight = 81056.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.062915 restraints weight = 36922.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.064700 restraints weight = 23485.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.065728 restraints weight = 18215.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.066385 restraints weight = 15867.739| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13856 Z= 0.184 Angle : 0.683 27.269 19760 Z= 0.408 Chirality : 0.060 2.072 2213 Planarity : 0.006 0.116 1657 Dihedral : 28.492 171.704 3850 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.12 % Allowed : 0.94 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.27), residues: 983 helix: 1.36 (0.21), residues: 597 sheet: -0.62 (1.21), residues: 18 loop : -0.78 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1543 TYR 0.020 0.002 TYR a 100 PHE 0.013 0.001 PHE O1668 TRP 0.002 0.001 TRP O1640 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.18 (13856) covalent geometry : angle 0.68287 / 0.41 (19760) hydrogen bonds : bond 0.04700 / 5.14 ( 776) hydrogen bonds : angle 3.73463 / 4.86 ( 1961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.485 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8295 (mp) cc_final: 0.7156 (tt) REVERT: O 1579 TYR cc_start: 0.7262 (t80) cc_final: 0.6686 (t80) REVERT: O 1587 LYS cc_start: 0.7731 (tttt) cc_final: 0.7288 (mttt) REVERT: O 1595 GLU cc_start: 0.8462 (tt0) cc_final: 0.8226 (tp30) REVERT: O 1612 ASP cc_start: 0.7362 (t70) cc_final: 0.7153 (t70) REVERT: a 59 THR cc_start: 0.8953 (p) cc_final: 0.8439 (t) REVERT: a 61 LEU cc_start: 0.8536 (mm) cc_final: 0.7743 (mm) REVERT: a 65 LYS cc_start: 0.8096 (mttt) cc_final: 0.7859 (ttmt) REVERT: a 94 GLN cc_start: 0.8371 (tt0) cc_final: 0.8022 (tt0) REVERT: a 108 THR cc_start: 0.8694 (m) cc_final: 0.8452 (m) REVERT: a 130 ARG cc_start: 0.8881 (tpt90) cc_final: 0.8407 (tpt90) REVERT: b 26 ILE cc_start: 0.8464 (tp) cc_final: 0.8129 (mp) REVERT: c 44 VAL cc_start: 0.8655 (t) cc_final: 0.8279 (p) REVERT: c 62 GLU cc_start: 0.8082 (tp30) cc_final: 0.7626 (tp30) REVERT: c 79 ILE cc_start: 0.7921 (mt) cc_final: 0.7357 (tp) REVERT: c 86 LEU cc_start: 0.8513 (mt) cc_final: 0.8266 (mt) REVERT: d 85 LYS cc_start: 0.8339 (mttp) cc_final: 0.7918 (mtpt) REVERT: d 86 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7543 (mmm-85) REVERT: d 113 GLU cc_start: 0.8808 (tp30) cc_final: 0.8285 (tm-30) REVERT: d 120 LYS cc_start: 0.8472 (mttt) cc_final: 0.7903 (tptp) REVERT: e 94 GLN cc_start: 0.8458 (tt0) cc_final: 0.7389 (tt0) REVERT: f 51 TYR cc_start: 0.8802 (m-80) cc_final: 0.8178 (m-80) REVERT: f 74 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8811 (tt0) REVERT: g 85 GLN cc_start: 0.7377 (tp40) cc_final: 0.7036 (tp40) REVERT: g 96 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8220 (tptt) REVERT: h 36 SER cc_start: 0.8504 (t) cc_final: 0.8293 (t) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2436 time to fit residues: 94.6318 Evaluate side-chains 245 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 69 GLN ** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN f 75 HIS g 25 GLN h 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.085780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.058769 restraints weight = 82804.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.061289 restraints weight = 38862.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.062940 restraints weight = 25155.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.063962 restraints weight = 19768.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.064477 restraints weight = 17265.120| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 13856 Z= 0.296 Angle : 0.757 27.713 19760 Z= 0.444 Chirality : 0.061 2.029 2213 Planarity : 0.006 0.094 1657 Dihedral : 28.509 171.808 3850 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.12 % Allowed : 0.83 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 983 helix: 0.96 (0.21), residues: 601 sheet: -0.71 (1.20), residues: 18 loop : -0.99 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O1543 TYR 0.013 0.002 TYR a 100 PHE 0.013 0.002 PHE O1668 TRP 0.008 0.001 TRP O1640 HIS 0.011 0.002 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.30 (13856) covalent geometry : angle 0.75672 / 0.44 (19760) hydrogen bonds : bond 0.05235 / 5.73 ( 776) hydrogen bonds : angle 4.15521 / 5.49 ( 1961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.470 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8183 (mp) cc_final: 0.7193 (tt) REVERT: O 1579 TYR cc_start: 0.7269 (t80) cc_final: 0.6726 (t80) REVERT: O 1587 LYS cc_start: 0.7759 (tttt) cc_final: 0.7343 (mttt) REVERT: O 1595 GLU cc_start: 0.8457 (tt0) cc_final: 0.8203 (tp30) REVERT: O 1612 ASP cc_start: 0.7154 (t70) cc_final: 0.6915 (t0) REVERT: a 59 THR cc_start: 0.8919 (p) cc_final: 0.8450 (t) REVERT: a 121 MET cc_start: 0.6357 (mtt) cc_final: 0.6119 (mtt) REVERT: a 130 ARG cc_start: 0.8942 (tpt90) cc_final: 0.8637 (tpt90) REVERT: b 26 ILE cc_start: 0.8545 (tp) cc_final: 0.8216 (mp) REVERT: c 44 VAL cc_start: 0.8665 (t) cc_final: 0.8268 (p) REVERT: c 62 GLU cc_start: 0.8044 (tp30) cc_final: 0.7582 (tp30) REVERT: c 79 ILE cc_start: 0.7944 (mt) cc_final: 0.7301 (tp) REVERT: c 86 LEU cc_start: 0.8443 (mt) cc_final: 0.8154 (mt) REVERT: d 68 ASP cc_start: 0.8485 (t70) cc_final: 0.7797 (t0) REVERT: d 71 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7173 (tm-30) REVERT: d 85 LYS cc_start: 0.8383 (mttp) cc_final: 0.8003 (mtpt) REVERT: d 86 ARG cc_start: 0.8153 (mmt-90) cc_final: 0.7629 (mmm-85) REVERT: d 113 GLU cc_start: 0.8805 (tp30) cc_final: 0.8354 (tm-30) REVERT: d 120 LYS cc_start: 0.8512 (mttt) cc_final: 0.7954 (tptp) REVERT: e 57 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8607 (ttmm) REVERT: e 94 GLN cc_start: 0.8513 (tt0) cc_final: 0.7592 (tt0) REVERT: f 43 VAL cc_start: 0.9194 (t) cc_final: 0.8969 (p) REVERT: f 74 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8885 (tt0) REVERT: g 85 GLN cc_start: 0.7382 (tp40) cc_final: 0.7164 (tp40) REVERT: g 91 ASP cc_start: 0.7746 (t70) cc_final: 0.7463 (t0) REVERT: g 96 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8311 (tptt) outliers start: 1 outliers final: 1 residues processed: 261 average time/residue: 0.2113 time to fit residues: 80.1159 Evaluate side-chains 230 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 109 ASN b 25 ASN g 25 GLN j 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.087834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.060077 restraints weight = 80736.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.062775 restraints weight = 36986.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.064573 restraints weight = 23562.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.065528 restraints weight = 18296.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.066220 restraints weight = 16057.317| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13856 Z= 0.161 Angle : 0.677 27.079 19760 Z= 0.403 Chirality : 0.060 2.076 2213 Planarity : 0.005 0.074 1657 Dihedral : 28.497 171.437 3850 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.27), residues: 983 helix: 1.31 (0.21), residues: 597 sheet: -0.61 (1.20), residues: 18 loop : -0.84 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG b 92 TYR 0.016 0.001 TYR g 58 PHE 0.013 0.001 PHE O1668 TRP 0.002 0.000 TRP O1460 HIS 0.008 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (13856) covalent geometry : angle 0.67740 / 0.40 (19760) hydrogen bonds : bond 0.04608 / 4.98 ( 776) hydrogen bonds : angle 3.69022 / 4.82 ( 1961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.463 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1482 LEU cc_start: 0.8249 (mp) cc_final: 0.7130 (tt) REVERT: O 1549 HIS cc_start: 0.7794 (p-80) cc_final: 0.7291 (p-80) REVERT: O 1579 TYR cc_start: 0.7278 (t80) cc_final: 0.6719 (t80) REVERT: O 1587 LYS cc_start: 0.7744 (tttt) cc_final: 0.7314 (mttt) REVERT: O 1595 GLU cc_start: 0.8412 (tt0) cc_final: 0.8179 (tp30) REVERT: a 59 THR cc_start: 0.8866 (p) cc_final: 0.8401 (t) REVERT: a 61 LEU cc_start: 0.8674 (mm) cc_final: 0.8465 (mm) REVERT: a 121 MET cc_start: 0.6204 (mtt) cc_final: 0.5986 (mtt) REVERT: a 130 ARG cc_start: 0.8927 (tpt90) cc_final: 0.8671 (tpt90) REVERT: b 26 ILE cc_start: 0.8478 (tp) cc_final: 0.8165 (mp) REVERT: c 44 VAL cc_start: 0.8611 (t) cc_final: 0.8213 (p) REVERT: c 62 GLU cc_start: 0.8089 (tp30) cc_final: 0.7669 (tp30) REVERT: c 86 LEU cc_start: 0.8413 (mt) cc_final: 0.8127 (mt) REVERT: d 71 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7144 (tm-30) REVERT: d 85 LYS cc_start: 0.8368 (mttp) cc_final: 0.7912 (mtpt) REVERT: d 86 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.7481 (mmm-85) REVERT: d 93 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7874 (mm-30) REVERT: d 113 GLU cc_start: 0.8780 (tp30) cc_final: 0.8282 (tm-30) REVERT: d 120 LYS cc_start: 0.8453 (mttt) cc_final: 0.7889 (tptp) REVERT: e 94 GLN cc_start: 0.8431 (tt0) cc_final: 0.7412 (tt0) REVERT: e 108 THR cc_start: 0.8935 (m) cc_final: 0.8724 (m) REVERT: f 51 TYR cc_start: 0.8784 (m-80) cc_final: 0.8117 (m-80) REVERT: f 74 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8806 (tt0) REVERT: g 85 GLN cc_start: 0.7457 (tp40) cc_final: 0.7212 (tp40) REVERT: g 91 ASP cc_start: 0.7693 (t70) cc_final: 0.7466 (t0) REVERT: g 96 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8195 (tptt) REVERT: h 90 THR cc_start: 0.8419 (p) cc_final: 0.8067 (p) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2232 time to fit residues: 88.1111 Evaluate side-chains 243 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 25 ASN d 109 HIS h 63 ASN j 949 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.087507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.060257 restraints weight = 80796.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.063004 restraints weight = 36267.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.064746 restraints weight = 22827.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.065807 restraints weight = 17715.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.066433 restraints weight = 15376.581| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13856 Z= 0.186 Angle : 0.688 27.214 19760 Z= 0.407 Chirality : 0.060 2.056 2213 Planarity : 0.005 0.074 1657 Dihedral : 28.467 171.502 3850 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.27), residues: 983 helix: 1.36 (0.21), residues: 595 sheet: -0.67 (1.18), residues: 18 loop : -0.77 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG b 92 TYR 0.015 0.002 TYR a 100 PHE 0.021 0.001 PHE O1650 TRP 0.003 0.001 TRP O1640 HIS 0.012 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 (13856) covalent geometry : angle 0.68787 / 0.41 (19760) hydrogen bonds : bond 0.04595 / 5.00 ( 776) hydrogen bonds : angle 3.70604 / 4.88 ( 1961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4081.97 seconds wall clock time: 70 minutes 25.17 seconds (4225.17 seconds total)